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<h1 class="epydoc">Source Code for <a href="Bio.Blast.NCBIWWW-module.html">Module Bio.Blast.NCBIWWW</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright 1999 by Jeffrey Chang. All rights reserved.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-comment"># Patched by Brad Chapman.</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Chris Wroe added modifications for work in myGrid</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring">This module provides code to work with the WWW version of BLAST</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring">provided by the NCBI.</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring">http://www.ncbi.nlm.nih.gov/BLAST/</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring">Classes:</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring">BlastParser Parses output from WWW blast.</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring">_Scanner Scans output from NCBI's BLAST WWW server.</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring">Functions:</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-docstring">qblast Do a BLAST search using the QBLAST API.</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">re</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">cStringIO</tt> <tt class="py-keyword">as</tt> <tt class="py-name">StringIO</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-keyword">except</tt> <tt class="py-name">ImportError</tt><tt class="py-op">:</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">StringIO</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Module Bio.ParserSupport=Bio.ParserSupport-module.html"><a title="Bio.ParserSupport" class="py-name" href="#" onclick="return doclink('link-1', 'ParserSupport', 'link-1');">ParserSupport</a></tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"> </tt>
<a name="BlastParser"></a><div id="BlastParser-def"><a name="L31"></a><tt class="py-lineno"> 31</tt> <a class="py-toggle" href="#" id="BlastParser-toggle" onclick="return toggle('BlastParser');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Blast.NCBIWWW.BlastParser-class.html">BlastParser</a><tt class="py-op">(</tt><tt class="py-base-class">AbstractParser</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BlastParser-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="BlastParser-expanded"><a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> <tt class="py-docstring">"""Parses WWW BLAST data into a Record.Blast object.</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="BlastParser.__init__"></a><div id="BlastParser.__init__-def"><a name="L35"></a><tt class="py-lineno"> 35</tt> <a class="py-toggle" href="#" id="BlastParser.__init__-toggle" onclick="return toggle('BlastParser.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIWWW.BlastParser-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BlastParser.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser.__init__-expanded"><a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-docstring">"""__init__(self)"""</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name" targets="Module Bio.Blast.NCBIStandalone=Bio.Blast.NCBIStandalone-module.html"><a title="Bio.Blast.NCBIStandalone" class="py-name" href="#" onclick="return doclink('link-2', 'NCBIStandalone', 'link-2');">NCBIStandalone</a></tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_scanner</tt> <tt class="py-op">=</tt> <tt id="link-3" class="py-name" targets="Class Bio.Blast.NCBIStandalone._Scanner=Bio.Blast.NCBIStandalone._Scanner-class.html,Class Bio.Blast.NCBIWWW._Scanner=Bio.Blast.NCBIWWW._Scanner-class.html,Class Bio.CDD._Scanner=Bio.CDD._Scanner-class.html,Class Bio.Compass._Scanner=Bio.Compass._Scanner-class.html,Class Bio.ECell._Scanner=Bio.ECell._Scanner-class.html,Class Bio.Enzyme._Scanner=Bio.Enzyme._Scanner-class.html,Class Bio.Gobase._Scanner=Bio.Gobase._Scanner-class.html,Class Bio.IntelliGenetics._Scanner=Bio.IntelliGenetics._Scanner-class.html,Class Bio.LocusLink._Scanner=Bio.LocusLink._Scanner-class.html,Class Bio.Medline._Scanner=Bio.Medline._Scanner-class.html,Class Bio.MetaTool._Scanner=Bio.MetaTool._Scanner-class.html,Class Bio.NBRF._Scanner=Bio.NBRF._Scanner-class.html,Class Bio.PopGen.FDist._Scanner=Bio.PopGen.FDist._Scanner-class.html,Class Bio.PopGen.GenePop._Scanner=Bio.PopGen.GenePop._Scanner-class.html,Class Bio.Prosite.Prodoc._Scanner=Bio.Prosite.Prodoc._Scanner-class.html,Class Bio.Prosite._Scanner=Bio.Prosite._Scanner-class.html,Class Bio.Rebase._Scanner=Bio.Rebase._Scanner-class.html,Class Bio.Saf._Scanner=Bio.Saf._Scanner-class.html,Class Bio.Sequencing.Ace._Scanner=Bio.Sequencing.Ace._Scanner-class.html,Class Bio.Sequencing.Phd._Scanner=Bio.Sequencing.Phd._Scanner-class.html,Class Bio.SwissProt.KeyWList._Scanner=Bio.SwissProt.KeyWList._Scanner-class.html,Class Bio.SwissProt.SProt._Scanner=Bio.SwissProt.SProt._Scanner-class.html,Class Bio.UniGene._Scanner=Bio.UniGene._Scanner-class.html"><a title="Bio.Blast.NCBIStandalone._Scanner
Bio.Blast.NCBIWWW._Scanner
Bio.CDD._Scanner
Bio.Compass._Scanner
Bio.ECell._Scanner
Bio.Enzyme._Scanner
Bio.Gobase._Scanner
Bio.IntelliGenetics._Scanner
Bio.LocusLink._Scanner
Bio.Medline._Scanner
Bio.MetaTool._Scanner
Bio.NBRF._Scanner
Bio.PopGen.FDist._Scanner
Bio.PopGen.GenePop._Scanner
Bio.Prosite.Prodoc._Scanner
Bio.Prosite._Scanner
Bio.Rebase._Scanner
Bio.Saf._Scanner
Bio.Sequencing.Ace._Scanner
Bio.Sequencing.Phd._Scanner
Bio.SwissProt.KeyWList._Scanner
Bio.SwissProt.SProt._Scanner
Bio.UniGene._Scanner" class="py-name" href="#" onclick="return doclink('link-3', '_Scanner', 'link-3');">_Scanner</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_consumer</tt> <tt class="py-op">=</tt> <tt id="link-4" class="py-name" targets="Class Bio.ParserSupport.SGMLStrippingConsumer=Bio.ParserSupport.SGMLStrippingConsumer-class.html"><a title="Bio.ParserSupport.SGMLStrippingConsumer" class="py-name" href="#" onclick="return doclink('link-4', 'SGMLStrippingConsumer', 'link-4');">SGMLStrippingConsumer</a></tt><tt class="py-op">(</tt><tt id="link-5" class="py-name"><a title="Bio.Blast.NCBIStandalone" class="py-name" href="#" onclick="return doclink('link-5', 'NCBIStandalone', 'link-2');">NCBIStandalone</a></tt><tt class="py-op">.</tt><tt id="link-6" class="py-name" targets="Class Bio.Blast.NCBIStandalone._BlastConsumer=Bio.Blast.NCBIStandalone._BlastConsumer-class.html"><a title="Bio.Blast.NCBIStandalone._BlastConsumer" class="py-name" href="#" onclick="return doclink('link-6', '_BlastConsumer', 'link-6');">_BlastConsumer</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> </tt>
<a name="BlastParser.parse"></a><div id="BlastParser.parse-def"><a name="L41"></a><tt class="py-lineno"> 41</tt> <a class="py-toggle" href="#" id="BlastParser.parse-toggle" onclick="return toggle('BlastParser.parse');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIWWW.BlastParser-class.html#parse">parse</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">handle</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BlastParser.parse-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser.parse-expanded"><a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt class="py-docstring">"""parse(self, handle)"""</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_scanner</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name" targets="Method Bio.Affy.CelFile.CelScanner.feed()=Bio.Affy.CelFile.CelScanner-class.html#feed,Method Bio.AlignAce.Scanner.AlignAceScanner.feed()=Bio.AlignAce.Scanner.AlignAceScanner-class.html#feed,Method Bio.AlignAce.Scanner.CompareAceScanner.feed()=Bio.AlignAce.Scanner.CompareAceScanner-class.html#feed,Method Bio.Blast.NCBIStandalone._Scanner.feed()=Bio.Blast.NCBIStandalone._Scanner-class.html#feed,Method Bio.Blast.NCBIWWW._Scanner.feed()=Bio.Blast.NCBIWWW._Scanner-class.html#feed,Method Bio.CDD._Scanner.feed()=Bio.CDD._Scanner-class.html#feed,Method Bio.Compass._Scanner.feed()=Bio.Compass._Scanner-class.html#feed,Method Bio.ECell._Scanner.feed()=Bio.ECell._Scanner-class.html#feed,Method Bio.Emboss.Primer._Primer3Scanner.feed()=Bio.Emboss.Primer._Primer3Scanner-class.html#feed,Method Bio.Emboss.Primer._PrimerSearchScanner.feed()=Bio.Emboss.Primer._PrimerSearchScanner-class.html#feed,Method Bio.Enzyme._Scanner.feed()=Bio.Enzyme._Scanner-class.html#feed,Method Bio.GenBank.Scanner.InsdcScanner.feed()=Bio.GenBank.Scanner.InsdcScanner-class.html#feed,Method Bio.Gobase._Scanner.feed()=Bio.Gobase._Scanner-class.html#feed,Method Bio.IntelliGenetics._Scanner.feed()=Bio.IntelliGenetics._Scanner-class.html#feed,Method Bio.InterPro.InterProParser.feed()=Bio.InterPro.InterProParser-class.html#feed,Method Bio.LocusLink._Scanner.feed()=Bio.LocusLink._Scanner-class.html#feed,Method Bio.LocusLink.web_parse.LocusLinkParser.feed()=Bio.LocusLink.web_parse.LocusLinkParser-class.html#feed,Method Bio.MEME.Parser._MASTScanner.feed()=Bio.MEME.Parser._MASTScanner-class.html#feed,Method Bio.MEME.Parser._MEMEScanner.feed()=Bio.MEME.Parser._MEMEScanner-class.html#feed,Method Bio.Medline._Scanner.feed()=Bio.Medline._Scanner-class.html#feed,Method Bio.MetaTool._Scanner.feed()=Bio.MetaTool._Scanner-class.html#feed,Method Bio.NBRF._Scanner.feed()=Bio.NBRF._Scanner-class.html#feed,Method Bio.Ndb.NdbParser.feed()=Bio.Ndb.NdbParser-class.html#feed,Method Bio.NetCatch.ExtractUrls.feed()=Bio.NetCatch.ExtractUrls-class.html#feed,Method Bio.PopGen.FDist._Scanner.feed()=Bio.PopGen.FDist._Scanner-class.html#feed,Method Bio.PopGen.GenePop._Scanner.feed()=Bio.PopGen.GenePop._Scanner-class.html#feed,Method Bio.Prosite.Prodoc._Scanner.feed()=Bio.Prosite.Prodoc._Scanner-class.html#feed,Method Bio.Prosite._Scanner.feed()=Bio.Prosite._Scanner-class.html#feed,Method Bio.Rebase._Scanner.feed()=Bio.Rebase._Scanner-class.html#feed,Method Bio.Saf._Scanner.feed()=Bio.Saf._Scanner-class.html#feed,Method Bio.Sequencing.Ace._Scanner.feed()=Bio.Sequencing.Ace._Scanner-class.html#feed,Method Bio.Sequencing.Phd._Scanner.feed()=Bio.Sequencing.Phd._Scanner-class.html#feed,Method Bio.SwissProt.KeyWList._Scanner.feed()=Bio.SwissProt.KeyWList._Scanner-class.html#feed,Method Bio.SwissProt.SProt._Scanner.feed()=Bio.SwissProt.SProt._Scanner-class.html#feed,Method Bio.UniGene._Scanner.feed()=Bio.UniGene._Scanner-class.html#feed"><a title="Bio.Affy.CelFile.CelScanner.feed
Bio.AlignAce.Scanner.AlignAceScanner.feed
Bio.AlignAce.Scanner.CompareAceScanner.feed
Bio.Blast.NCBIStandalone._Scanner.feed
Bio.Blast.NCBIWWW._Scanner.feed
Bio.CDD._Scanner.feed
Bio.Compass._Scanner.feed
Bio.ECell._Scanner.feed
Bio.Emboss.Primer._Primer3Scanner.feed
Bio.Emboss.Primer._PrimerSearchScanner.feed
Bio.Enzyme._Scanner.feed
Bio.GenBank.Scanner.InsdcScanner.feed
Bio.Gobase._Scanner.feed
Bio.IntelliGenetics._Scanner.feed
Bio.InterPro.InterProParser.feed
Bio.LocusLink._Scanner.feed
Bio.LocusLink.web_parse.LocusLinkParser.feed
Bio.MEME.Parser._MASTScanner.feed
Bio.MEME.Parser._MEMEScanner.feed
Bio.Medline._Scanner.feed
Bio.MetaTool._Scanner.feed
Bio.NBRF._Scanner.feed
Bio.Ndb.NdbParser.feed
Bio.NetCatch.ExtractUrls.feed
Bio.PopGen.FDist._Scanner.feed
Bio.PopGen.GenePop._Scanner.feed
Bio.Prosite.Prodoc._Scanner.feed
Bio.Prosite._Scanner.feed
Bio.Rebase._Scanner.feed
Bio.Saf._Scanner.feed
Bio.Sequencing.Ace._Scanner.feed
Bio.Sequencing.Phd._Scanner.feed
Bio.SwissProt.KeyWList._Scanner.feed
Bio.SwissProt.SProt._Scanner.feed
Bio.UniGene._Scanner.feed" class="py-name" href="#" onclick="return doclink('link-7', 'feed', 'link-7');">feed</a></tt><tt class="py-op">(</tt><tt id="link-8" class="py-name" targets="Variable Bio.LocusLink.web_parse.handle=Bio.LocusLink.web_parse-module.html#handle,Variable Bio.Ndb.handle=Bio.Ndb-module.html#handle"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-8', 'handle', 'link-8');">handle</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_consumer</tt><tt class="py-op">)</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_consumer</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Variable BioSQL.BioSeq.DBSeq.data=BioSQL.BioSeq.DBSeq-class.html#data"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-9', 'data', 'link-9');">data</a></tt> </tt>
</div></div><a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> </tt>
<a name="_Scanner"></a><div id="_Scanner-def"><a name="L46"></a><tt class="py-lineno"> 46</tt> <a class="py-toggle" href="#" id="_Scanner-toggle" onclick="return toggle('_Scanner');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Blast.NCBIWWW._Scanner-class.html">_Scanner</a><tt class="py-op">:</tt> </tt>
</div><div id="_Scanner-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_Scanner-expanded"><a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-docstring">"""Scan BLAST output from NCBI's web server at:</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"><tt class="py-docstring"> http://www.ncbi.nlm.nih.gov/BLAST/</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-docstring"> Tested with BLAST v2.0.10</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"><tt class="py-docstring"> Methods:</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"><tt class="py-docstring"> feed Feed data into the scanner.</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="_Scanner.feed"></a><div id="_Scanner.feed-def"><a name="L56"></a><tt class="py-lineno"> 56</tt> <a class="py-toggle" href="#" id="_Scanner.feed-toggle" onclick="return toggle('_Scanner.feed');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIWWW._Scanner-class.html#feed">feed</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">handle</tt><tt class="py-op">,</tt> <tt class="py-param">consumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Scanner.feed-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Scanner.feed-expanded"><a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-docstring">"""S.feed(handle, consumer)</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"><tt class="py-docstring"> Feed in a BLAST report for scanning. handle is a file-like</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"><tt class="py-docstring"> object that contains the BLAST report. consumer is a Consumer</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"><tt class="py-docstring"> object that will receive events as the report is scanned.</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt id="link-10" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-10', 'Bio', 'link-0');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-11" class="py-name" targets="Module Bio.File=Bio.File-module.html"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-11', 'File', 'link-11');">File</a></tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-comment"># This stuff appears in 2.0.12.</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <p><!--</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># QBlastInfoBegin</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Status=READY</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># QBlastInfoEnd</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># --><p></tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-comment"># <HTML></tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <HEAD></tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <TITLE>BLAST Search Results </TITLE></tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># </HEAD></tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <A HREF="http://www.ncbi.nlm.nih.gov/BLAST/blast_form.map"> <IMG SRC=</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <BR><BR><PRE></tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-comment"># BLAST Formatted information</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-comment"># </tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># </BODY></tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># </HTML></tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># </BODY></tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># </HTML></tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-12" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-12', 'handle', 'link-8');">handle</a></tt><tt class="py-op">,</tt> <tt id="link-13" class="py-name"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-13', 'File', 'link-11');">File</a></tt><tt class="py-op">.</tt><tt id="link-14" class="py-name" targets="Class Bio.File.UndoHandle=Bio.File.UndoHandle-class.html"><a title="Bio.File.UndoHandle" class="py-name" href="#" onclick="return doclink('link-14', 'UndoHandle', 'link-14');">UndoHandle</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-name">uhandle</tt> <tt class="py-op">=</tt> <tt id="link-15" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-15', 'handle', 'link-8');">handle</a></tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-name">uhandle</tt> <tt class="py-op">=</tt> <tt id="link-16" class="py-name"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-16', 'File', 'link-11');">File</a></tt><tt class="py-op">.</tt><tt id="link-17" class="py-name"><a title="Bio.File.UndoHandle" class="py-name" href="#" onclick="return doclink('link-17', 'UndoHandle', 'link-14');">UndoHandle</a></tt><tt class="py-op">(</tt><tt id="link-18" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-18', 'handle', 'link-8');">handle</a></tt><tt class="py-op">)</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-comment"># Read HTML formatting up to the "BLAST" version line.</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-19" class="py-name" targets="Function Bio.ParserSupport.read_and_call_until()=Bio.ParserSupport-module.html#read_and_call_until"><a title="Bio.ParserSupport.read_and_call_until" class="py-name" href="#" onclick="return doclink('link-19', 'read_and_call_until', 'link-19');">read_and_call_until</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name" targets="Method Bio.AlignAce.Parser.AlignAceConsumer.noevent()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#noevent,Method Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent()=Bio.Blast.NCBIStandalone._BlastErrorConsumer-class.html#noevent,Method Bio.MEME.Parser._MASTConsumer.noevent()=Bio.MEME.Parser._MASTConsumer-class.html#noevent,Method Bio.MEME.Parser._MEMEConsumer.noevent()=Bio.MEME.Parser._MEMEConsumer-class.html#noevent"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-20', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-name">has_re</tt><tt class="py-op">=</tt><tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-21" class="py-name" targets="Function Bio.Prosite.Pattern.compile()=Bio.Prosite.Pattern-module.html#compile"><a title="Bio.Prosite.Pattern.compile" class="py-name" href="#" onclick="return doclink('link-21', 'compile', 'link-21');">compile</a></tt><tt class="py-op">(</tt><tt class="py-string">r'<b>.?BLAST'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name" targets="Method Bio.Blast.NCBIStandalone._Scanner._scan_header()=Bio.Blast.NCBIStandalone._Scanner-class.html#_scan_header,Method Bio.Blast.NCBIWWW._Scanner._scan_header()=Bio.Blast.NCBIWWW._Scanner-class.html#_scan_header,Method Bio.MEME.Parser._MASTScanner._scan_header()=Bio.MEME.Parser._MASTScanner-class.html#_scan_header,Method Bio.MEME.Parser._MEMEScanner._scan_header()=Bio.MEME.Parser._MEMEScanner-class.html#_scan_header,Method Bio.SwissProt.KeyWList._Scanner._scan_header()=Bio.SwissProt.KeyWList._Scanner-class.html#_scan_header"><a title="Bio.Blast.NCBIStandalone._Scanner._scan_header
Bio.Blast.NCBIWWW._Scanner._scan_header
Bio.MEME.Parser._MASTScanner._scan_header
Bio.MEME.Parser._MEMEScanner._scan_header
Bio.SwissProt.KeyWList._Scanner._scan_header" class="py-name" href="#" onclick="return doclink('link-22', '_scan_header', 'link-22');">_scan_header</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">)</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name" targets="Method Bio.Blast.NCBIStandalone._Scanner._scan_rounds()=Bio.Blast.NCBIStandalone._Scanner-class.html#_scan_rounds,Method Bio.Blast.NCBIWWW._Scanner._scan_rounds()=Bio.Blast.NCBIWWW._Scanner-class.html#_scan_rounds"><a title="Bio.Blast.NCBIStandalone._Scanner._scan_rounds
Bio.Blast.NCBIWWW._Scanner._scan_rounds" class="py-name" href="#" onclick="return doclink('link-23', '_scan_rounds', 'link-23');">_scan_rounds</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">)</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-24" class="py-name" targets="Method Bio.Blast.NCBIStandalone._Scanner._scan_database_report()=Bio.Blast.NCBIStandalone._Scanner-class.html#_scan_database_report,Method Bio.Blast.NCBIWWW._Scanner._scan_database_report()=Bio.Blast.NCBIWWW._Scanner-class.html#_scan_database_report"><a title="Bio.Blast.NCBIStandalone._Scanner._scan_database_report
Bio.Blast.NCBIWWW._Scanner._scan_database_report" class="py-name" href="#" onclick="return doclink('link-24', '_scan_database_report', 'link-24');">_scan_database_report</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">)</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-25" class="py-name" targets="Method Bio.Blast.NCBIStandalone._Scanner._scan_parameters()=Bio.Blast.NCBIStandalone._Scanner-class.html#_scan_parameters,Method Bio.Blast.NCBIWWW._Scanner._scan_parameters()=Bio.Blast.NCBIWWW._Scanner-class.html#_scan_parameters"><a title="Bio.Blast.NCBIStandalone._Scanner._scan_parameters
Bio.Blast.NCBIWWW._Scanner._scan_parameters" class="py-name" href="#" onclick="return doclink('link-25', '_scan_parameters', 'link-25');">_scan_parameters</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">)</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-comment"># Read HTML footer information.</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">while</tt> <tt class="py-name">uhandle</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name" targets="Method Bio.File.UndoHandle.peekline()=Bio.File.UndoHandle-class.html#peekline"><a title="Bio.File.UndoHandle.peekline" class="py-name" href="#" onclick="return doclink('link-26', 'peekline', 'link-26');">peekline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt id="link-27" class="py-name" targets="Function Bio.ParserSupport.read_and_call()=Bio.ParserSupport-module.html#read_and_call"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-27', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-28" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-28', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> </tt>
<a name="_Scanner._scan_header"></a><div id="_Scanner._scan_header-def"><a name="L105"></a><tt class="py-lineno">105</tt> <a class="py-toggle" href="#" id="_Scanner._scan_header-toggle" onclick="return toggle('_Scanner._scan_header');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIWWW._Scanner-class.html#_scan_header">_scan_header</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">uhandle</tt><tt class="py-op">,</tt> <tt class="py-param">consumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Scanner._scan_header-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Scanner._scan_header-expanded"><a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-comment"># <b>BLASTP 2.0.10 [Aug-26-1999]</b></tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># </tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># </tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <b><a href="http://www.ncbi.nlm.nih.gov/htbin-</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># post/Entrez/query?uid=9254694&form=6&db=m&Dopt=r">Reference</a>:</b></tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Altschul, Stephen F., Thomas L. Madden, Alejandro A. Sch&auml;ffer, </tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), </tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># "Gapped BLAST and PSI-BLAST: a new generation of protein database sea</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># programs", Nucleic Acids Res. 25:3389-3402.</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <p></tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <b>Query=</b> gi|120291|sp|P21297|FLBT_CAUCR FLBT PROTEIN.</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># (141 letters)</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># </tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <b>Database:</b> Non-redundant SwissProt sequences</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># 82,258 sequences; 29,652,561 total letters</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># </tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <p> <p>If you have any problems or questions with the results of this</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-comment"># If there are hits, and Graphical Overview was selected:</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <FORM NAME="BLASTFORM"></tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># </PRE></tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <CENTER></tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <H3><a href="/BLAST/newoptions.html#graphical-overview"> Distribution</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <input name=defline size=80 value="Mouse-over to show defline and sco</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># </CENTER></tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <map name=img_map></tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <area shape=rect coords=69,101,476,106 href="#120291" ONMOUSEOVER='do</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <area shape=rect coords=156,108,305,113 href="#3024946" ONMOUSEOVER='</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># </map></tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <CENTER></tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <IMG WIDTH=529 HEIGHT=115 USEMAP=#img_map BORDER=1 SRC="nph-getgif.cg</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <HR></tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <PRE> XXX</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-29" class="py-name" targets="Method Bio.Blast.NCBIStandalone._BlastConsumer.start_header()=Bio.Blast.NCBIStandalone._BlastConsumer-class.html#start_header,Method Bio.Blast.NCBIStandalone._HeaderConsumer.start_header()=Bio.Blast.NCBIStandalone._HeaderConsumer-class.html#start_header,Method Bio.Blast.NCBIStandalone._PSIBlastConsumer.start_header()=Bio.Blast.NCBIStandalone._PSIBlastConsumer-class.html#start_header"><a title="Bio.Blast.NCBIStandalone._BlastConsumer.start_header
Bio.Blast.NCBIStandalone._HeaderConsumer.start_header
Bio.Blast.NCBIStandalone._PSIBlastConsumer.start_header" class="py-name" href="#" onclick="return doclink('link-29', 'start_header', 'link-29');">start_header</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-comment"># Read the "BLAST" version line and the following blanks.</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-30" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-30', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-31" class="py-name" targets="Method Bio.AlignAce.Parser.AlignAceConsumer.version()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#version,Method Bio.Blast.NCBIStandalone._HeaderConsumer.version()=Bio.Blast.NCBIStandalone._HeaderConsumer-class.html#version,Method Bio.GenBank._FeatureConsumer.version()=Bio.GenBank._FeatureConsumer-class.html#version,Method Bio.GenBank._RecordConsumer.version()=Bio.GenBank._RecordConsumer-class.html#version,Variable Bio.MetaTool.metatool_format.version=Bio.MetaTool.metatool_format-module.html#version,Variable Bio.expressions.genbank.version=Bio.expressions.genbank-module.html#version"><a title="Bio.AlignAce.Parser.AlignAceConsumer.version
Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version
Bio.MetaTool.metatool_format.version
Bio.expressions.genbank.version" class="py-name" href="#" onclick="return doclink('link-31', 'version', 'link-31');">version</a></tt><tt class="py-op">,</tt> <tt id="link-32" class="py-name" targets="Method Bio.Alphabet.Alphabet.contains()=Bio.Alphabet.Alphabet-class.html#contains,Method Bio.Alphabet.AlphabetEncoder.contains()=Bio.Alphabet.AlphabetEncoder-class.html#contains,Method Bio.Alphabet.Gapped.contains()=Bio.Alphabet.Gapped-class.html#contains,Method Bio.Alphabet.HasStopCodon.contains()=Bio.Alphabet.HasStopCodon-class.html#contains,Method Bio.Pathway.Rep.HashSet.HashSet.contains()=Bio.Pathway.Rep.HashSet.HashSet-class.html#contains,Method Bio.biblio.Biblio.contains()=Bio.biblio.Biblio-class.html#contains"><a title="Bio.Alphabet.Alphabet.contains
Bio.Alphabet.AlphabetEncoder.contains
Bio.Alphabet.Gapped.contains
Bio.Alphabet.HasStopCodon.contains
Bio.Pathway.Rep.HashSet.HashSet.contains
Bio.biblio.Biblio.contains" class="py-name" href="#" onclick="return doclink('link-32', 'contains', 'link-32');">contains</a></tt><tt class="py-op">=</tt><tt class="py-string">'BLAST'</tt><tt class="py-op">)</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt id="link-33" class="py-name" targets="Function Bio.ParserSupport.read_and_call_while()=Bio.ParserSupport-module.html#read_and_call_while"><a title="Bio.ParserSupport.read_and_call_while" class="py-name" href="#" onclick="return doclink('link-33', 'read_and_call_while', 'link-33');">read_and_call_while</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-34" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-34', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-35" class="py-name" targets="Variable Bio.MetaTool.metatool_format.blank=Bio.MetaTool.metatool_format-module.html#blank"><a title="Bio.MetaTool.metatool_format.blank" class="py-name" href="#" onclick="return doclink('link-35', 'blank', 'link-35');">blank</a></tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-comment"># Read the reference lines and the '<p>' line.</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># TBLASTN 2.2.6 has a blank line instead of a "<p>".</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">uhandle</tt><tt class="py-op">.</tt><tt id="link-36" class="py-name" targets="Method Bio.EUtils.ReseekFile.ReseekFile.readline()=Bio.EUtils.ReseekFile.ReseekFile-class.html#readline,Method Bio.File.SGMLHandle.readline()=Bio.File.SGMLHandle-class.html#readline,Method Bio.File.UndoHandle.readline()=Bio.File.UndoHandle-class.html#readline,Method Bio.SGMLExtractor.SGMLExtractorHandle.readline()=Bio.SGMLExtractor.SGMLExtractorHandle-class.html#readline"><a title="Bio.EUtils.ReseekFile.ReseekFile.readline
Bio.File.SGMLHandle.readline
Bio.File.UndoHandle.readline
Bio.SGMLExtractor.SGMLExtractorHandle.readline" class="py-name" href="#" onclick="return doclink('link-36', 'readline', 'link-36');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">3</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'<p>'</tt> <tt class="py-keyword">or</tt> <tt class="py-keyword">not</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name" targets="Class Bio.EUtils.DTDs.LinkOut.strip=Bio.EUtils.DTDs.LinkOut.strip-class.html,Method Bio.File.SGMLStripper.strip()=Bio.File.SGMLStripper-class.html#strip,Method Bio.SGMLExtractor.SGMLExtractor.strip()=Bio.SGMLExtractor.SGMLExtractor-class.html#strip"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-37', 'strip', 'link-37');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-38" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-38', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-39" class="py-name" targets="Method Bio.Blast.NCBIStandalone._HeaderConsumer.reference()=Bio.Blast.NCBIStandalone._HeaderConsumer-class.html#reference,Method Bio.Prosite.Prodoc._RecordConsumer.reference()=Bio.Prosite.Prodoc._RecordConsumer-class.html#reference,Variable Bio.expressions.embl.embl65.reference=Bio.expressions.embl.embl65-module.html#reference,Variable Bio.expressions.genbank.reference=Bio.expressions.genbank-module.html#reference,Variable Bio.expressions.swissprot.sprot38.reference=Bio.expressions.swissprot.sprot38-module.html#reference,Variable Martel.test.test_swissprot38.reference=Martel.test.test_swissprot38-module.html#reference,Variable Martel.test.testformats.swissprot38.reference=Martel.test.testformats.swissprot38-module.html#reference"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.reference
Bio.Prosite.Prodoc._RecordConsumer.reference
Bio.expressions.embl.embl65.reference
Bio.expressions.genbank.reference
Bio.expressions.swissprot.sprot38.reference
Martel.test.test_swissprot38.reference
Martel.test.testformats.swissprot38.reference" class="py-name" href="#" onclick="return doclink('link-39', 'reference', 'link-39');">reference</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-comment"># Read the RID line, for version 2.0.12 (2.0.11?) and above.</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-40" class="py-name" targets="Function Bio.ParserSupport.attempt_read_and_call()=Bio.ParserSupport-module.html#attempt_read_and_call"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-40', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-41" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-41', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-42" class="py-name" targets="Method Bio.GFF.easy.Location.start()=Bio.GFF.easy.Location-class.html#start,Method Bio.Prosite.Pattern.PrositeMatch.start()=Bio.Prosite.Pattern.PrositeMatch-class.html#start,Variable Bio.Restriction._Update.RestrictionCompiler.start=Bio.Restriction._Update.RestrictionCompiler-module.html#start,Method Martel.LAX.LAX.start()=Martel.LAX.LAX-class.html#start"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-42', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'RID'</tt><tt class="py-op">)</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-comment"># Brad Chapman noticed a '<p>' line in BLASTN 2.1.1; this line</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># seems to have disappeared again.</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># attempt_read_and_call(uhandle, consumer.noevent, start='<p>')</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-43" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-43', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-44" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-44', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">)</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-comment"># Apparently, there's some discrepancy between whether the</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Query or database comes first. Usually the Query does, but</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Brad noticed a case where the database came first.</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">uhandle</tt><tt class="py-op">.</tt><tt id="link-45" class="py-name"><a title="Bio.File.UndoHandle.peekline" class="py-name" href="#" onclick="return doclink('link-45', 'peekline', 'link-26');">peekline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-46" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.find()=Bio.EUtils.POM.ElementNode-class.html#find,Method Bio.NeuralNetwork.Gene.Motif.MotifFinder.find()=Bio.NeuralNetwork.Gene.Motif.MotifFinder-class.html#find,Method Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find()=Bio.NeuralNetwork.Gene.Schema.SchemaFinder-class.html#find,Method Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find()=Bio.NeuralNetwork.Gene.Signature.SignatureFinder-class.html#find,Method Bio.biblio.Biblio.find()=Bio.biblio.Biblio-class.html#find,Function Bio.triefind.find()=Bio.triefind-module.html#find"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-46', 'find', 'link-46');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">"Query="</tt><tt class="py-op">)</tt> <tt class="py-op">>=</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-47" class="py-name" targets="Method Bio.Blast.NCBIWWW._Scanner._scan_query_info()=Bio.Blast.NCBIWWW._Scanner-class.html#_scan_query_info"><a title="Bio.Blast.NCBIWWW._Scanner._scan_query_info" class="py-name" href="#" onclick="return doclink('link-47', '_scan_query_info', 'link-47');">_scan_query_info</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">)</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-48" class="py-name" targets="Method Bio.Blast.NCBIWWW._Scanner._scan_database_info()=Bio.Blast.NCBIWWW._Scanner-class.html#_scan_database_info"><a title="Bio.Blast.NCBIWWW._Scanner._scan_database_info" class="py-name" href="#" onclick="return doclink('link-48', '_scan_database_info', 'link-48');">_scan_database_info</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">)</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-49" class="py-name"><a title="Bio.Blast.NCBIWWW._Scanner._scan_database_info" class="py-name" href="#" onclick="return doclink('link-49', '_scan_database_info', 'link-48');">_scan_database_info</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">)</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-50" class="py-name"><a title="Bio.Blast.NCBIWWW._Scanner._scan_query_info" class="py-name" href="#" onclick="return doclink('link-50', '_scan_query_info', 'link-47');">_scan_query_info</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">)</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt id="link-51" class="py-name"><a title="Bio.ParserSupport.read_and_call_while" class="py-name" href="#" onclick="return doclink('link-51', 'read_and_call_while', 'link-33');">read_and_call_while</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-52" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-52', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-53" class="py-name"><a title="Bio.MetaTool.metatool_format.blank" class="py-name" href="#" onclick="return doclink('link-53', 'blank', 'link-35');">blank</a></tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-54" class="py-name" targets="Method Bio.Blast.NCBIStandalone._BlastConsumer.end_header()=Bio.Blast.NCBIStandalone._BlastConsumer-class.html#end_header,Method Bio.Blast.NCBIStandalone._HeaderConsumer.end_header()=Bio.Blast.NCBIStandalone._HeaderConsumer-class.html#end_header,Method Bio.Blast.NCBIStandalone._PSIBlastConsumer.end_header()=Bio.Blast.NCBIStandalone._PSIBlastConsumer-class.html#end_header"><a title="Bio.Blast.NCBIStandalone._BlastConsumer.end_header
Bio.Blast.NCBIStandalone._HeaderConsumer.end_header
Bio.Blast.NCBIStandalone._PSIBlastConsumer.end_header" class="py-name" href="#" onclick="return doclink('link-54', 'end_header', 'link-54');">end_header</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> </tt>
<a name="_Scanner._scan_blastform"></a><div id="_Scanner._scan_blastform-def"><a name="L173"></a><tt class="py-lineno">173</tt> <a class="py-toggle" href="#" id="_Scanner._scan_blastform-toggle" onclick="return toggle('_Scanner._scan_blastform');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIWWW._Scanner-class.html#_scan_blastform">_scan_blastform</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">uhandle</tt><tt class="py-op">,</tt> <tt class="py-param">consumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Scanner._scan_blastform-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Scanner._scan_blastform-expanded"><a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-55" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-55', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-56" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-56', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt id="link-57" class="py-name"><a title="Bio.Alphabet.Alphabet.contains
Bio.Alphabet.AlphabetEncoder.contains
Bio.Alphabet.Gapped.contains
Bio.Alphabet.HasStopCodon.contains
Bio.Pathway.Rep.HashSet.HashSet.contains
Bio.biblio.Biblio.contains" class="py-name" href="#" onclick="return doclink('link-57', 'contains', 'link-32');">contains</a></tt><tt class="py-op">=</tt><tt class="py-string">"BLASTFORM"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">uhandle</tt><tt class="py-op">.</tt><tt id="link-58" class="py-name"><a title="Bio.File.UndoHandle.peekline" class="py-name" href="#" onclick="return doclink('link-58', 'peekline', 'link-26');">peekline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-59" class="py-name" targets="Function Bio.ParserSupport.is_blank_line()=Bio.ParserSupport-module.html#is_blank_line"><a title="Bio.ParserSupport.is_blank_line" class="py-name" href="#" onclick="return doclink('link-59', 'is_blank_line', 'link-59');">is_blank_line</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-string">"Query="</tt> <tt class="py-keyword">in</tt> <tt class="py-name">line</tt><tt class="py-op">:</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-60" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-60', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">.</tt><tt id="link-61" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.readline
Bio.File.SGMLHandle.readline
Bio.File.UndoHandle.readline
Bio.SGMLExtractor.SGMLExtractorHandle.readline" class="py-name" href="#" onclick="return doclink('link-61', 'readline', 'link-36');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> </tt>
<a name="_Scanner._scan_database_info"></a><div id="_Scanner._scan_database_info-def"><a name="L184"></a><tt class="py-lineno">184</tt> <a class="py-toggle" href="#" id="_Scanner._scan_database_info-toggle" onclick="return toggle('_Scanner._scan_database_info');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIWWW._Scanner-class.html#_scan_database_info">_scan_database_info</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">uhandle</tt><tt class="py-op">,</tt> <tt class="py-param">consumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Scanner._scan_database_info-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Scanner._scan_database_info-expanded"><a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt id="link-62" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-62', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-63" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-63', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-64" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-64', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'<p>'</tt><tt class="py-op">)</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> <tt id="link-65" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-65', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-66" class="py-name" targets="Method Bio.Blast.NCBIStandalone._HeaderConsumer.database_info()=Bio.Blast.NCBIStandalone._HeaderConsumer-class.html#database_info"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.database_info" class="py-name" href="#" onclick="return doclink('link-66', 'database_info', 'link-66');">database_info</a></tt><tt class="py-op">,</tt> <tt id="link-67" class="py-name"><a title="Bio.Alphabet.Alphabet.contains
Bio.Alphabet.AlphabetEncoder.contains
Bio.Alphabet.Gapped.contains
Bio.Alphabet.HasStopCodon.contains
Bio.Pathway.Rep.HashSet.HashSet.contains
Bio.biblio.Biblio.contains" class="py-name" href="#" onclick="return doclink('link-67', 'contains', 'link-32');">contains</a></tt><tt class="py-op">=</tt><tt class="py-string">'Database'</tt><tt class="py-op">)</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt class="py-comment"># Sagar Damle reported that databases can consist of multiple lines.</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># But, trickily enough, sometimes the second line can also have the</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># word sequences in it. Try to use 'sequences;' (with a semicolon)</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-68" class="py-name"><a title="Bio.ParserSupport.read_and_call_until" class="py-name" href="#" onclick="return doclink('link-68', 'read_and_call_until', 'link-19');">read_and_call_until</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-69" class="py-name"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.database_info" class="py-name" href="#" onclick="return doclink('link-69', 'database_info', 'link-66');">database_info</a></tt><tt class="py-op">,</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> <tt id="link-70" class="py-name"><a title="Bio.Alphabet.Alphabet.contains
Bio.Alphabet.AlphabetEncoder.contains
Bio.Alphabet.Gapped.contains
Bio.Alphabet.HasStopCodon.contains
Bio.Pathway.Rep.HashSet.HashSet.contains
Bio.biblio.Biblio.contains" class="py-name" href="#" onclick="return doclink('link-70', 'contains', 'link-32');">contains</a></tt><tt class="py-op">=</tt><tt class="py-string">'sequences;'</tt><tt class="py-op">)</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt id="link-71" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-71', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-72" class="py-name"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.database_info" class="py-name" href="#" onclick="return doclink('link-72', 'database_info', 'link-66');">database_info</a></tt><tt class="py-op">,</tt> <tt id="link-73" class="py-name"><a title="Bio.Alphabet.Alphabet.contains
Bio.Alphabet.AlphabetEncoder.contains
Bio.Alphabet.Gapped.contains
Bio.Alphabet.HasStopCodon.contains
Bio.Pathway.Rep.HashSet.HashSet.contains
Bio.biblio.Biblio.contains" class="py-name" href="#" onclick="return doclink('link-73', 'contains', 'link-32');">contains</a></tt><tt class="py-op">=</tt><tt class="py-string">'sequences;'</tt><tt class="py-op">)</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt id="link-74" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-74', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-75" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-75', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-76" class="py-name"><a title="Bio.MetaTool.metatool_format.blank" class="py-name" href="#" onclick="return doclink('link-76', 'blank', 'link-35');">blank</a></tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt id="link-77" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-77', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-78" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-78', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt id="link-79" class="py-name"><a title="Bio.Alphabet.Alphabet.contains
Bio.Alphabet.AlphabetEncoder.contains
Bio.Alphabet.Gapped.contains
Bio.Alphabet.HasStopCodon.contains
Bio.Pathway.Rep.HashSet.HashSet.contains
Bio.biblio.Biblio.contains" class="py-name" href="#" onclick="return doclink('link-79', 'contains', 'link-32');">contains</a></tt><tt class="py-op">=</tt><tt class="py-string">'problems or questions'</tt><tt class="py-op">)</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-80" class="py-name" targets="Method Bio.Blast.NCBIWWW._Scanner._scan_blastform()=Bio.Blast.NCBIWWW._Scanner-class.html#_scan_blastform"><a title="Bio.Blast.NCBIWWW._Scanner._scan_blastform" class="py-name" href="#" onclick="return doclink('link-80', '_scan_blastform', 'link-80');">_scan_blastform</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">)</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt id="link-81" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-81', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-82" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-82', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-83" class="py-name"><a title="Bio.MetaTool.metatool_format.blank" class="py-name" href="#" onclick="return doclink('link-83', 'blank', 'link-35');">blank</a></tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-84" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-84', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-85" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-85', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt id="link-86" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-86', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">"<table border=0 width=600"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt id="link-87" class="py-name"><a title="Bio.ParserSupport.read_and_call_until" class="py-name" href="#" onclick="return doclink('link-87', 'read_and_call_until', 'link-19');">read_and_call_until</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-88" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-88', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt id="link-89" class="py-name"><a title="Bio.Alphabet.Alphabet.contains
Bio.Alphabet.AlphabetEncoder.contains
Bio.Alphabet.Gapped.contains
Bio.Alphabet.HasStopCodon.contains
Bio.Pathway.Rep.HashSet.HashSet.contains
Bio.biblio.Biblio.contains" class="py-name" href="#" onclick="return doclink('link-89', 'contains', 'link-32');">contains</a></tt><tt class="py-op">=</tt><tt class="py-string">"</table>"</tt><tt class="py-op">)</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-90" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-90', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">.</tt><tt id="link-91" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.readline
Bio.File.SGMLHandle.readline
Bio.File.UndoHandle.readline
Bio.SGMLExtractor.SGMLExtractorHandle.readline" class="py-name" href="#" onclick="return doclink('link-91', 'readline', 'link-36');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt id="link-92" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-92', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-93" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-93', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-94" class="py-name"><a title="Bio.MetaTool.metatool_format.blank" class="py-name" href="#" onclick="return doclink('link-94', 'blank', 'link-35');">blank</a></tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> <tt id="link-95" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-95', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-96" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-96', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-97" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-97', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">"<p>"</tt><tt class="py-op">)</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-98" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-98', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-99" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-99', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> <tt id="link-100" class="py-name"><a title="Bio.Alphabet.Alphabet.contains
Bio.Alphabet.AlphabetEncoder.contains
Bio.Alphabet.Gapped.contains
Bio.Alphabet.HasStopCodon.contains
Bio.Pathway.Rep.HashSet.HashSet.contains
Bio.biblio.Biblio.contains" class="py-name" href="#" onclick="return doclink('link-100', 'contains', 'link-32');">contains</a></tt><tt class="py-op">=</tt><tt class="py-string">"Taxonomy reports"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> <tt id="link-101" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-101', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-102" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-102', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-103" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-103', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">"<BR>"</tt><tt class="py-op">)</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt id="link-104" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-104', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-105" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-105', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-106" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-106', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">"<PRE>"</tt><tt class="py-op">)</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-comment"># </PRE></tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <!-- Progress msg from the server 500 7--></tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <!-- Progress msg from the server 1000 15--></tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <!-- Progress msg from the server 1500 21--></tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># ...</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <PRE><HR><BR><b>Query=</b> test</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># (60 letters)</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt id="link-107" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-107', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-108" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-108', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-109" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-109', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">"</PRE>"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt id="link-110" class="py-name"><a title="Bio.ParserSupport.read_and_call_until" class="py-name" href="#" onclick="return doclink('link-110', 'read_and_call_until', 'link-19');">read_and_call_until</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-111" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-111', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-112" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-112', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">"<PRE>"</tt><tt class="py-op">)</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">uhandle</tt><tt class="py-op">.</tt><tt id="link-113" class="py-name"><a title="Bio.File.UndoHandle.peekline" class="py-name" href="#" onclick="return doclink('link-113', 'peekline', 'link-26');">peekline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">5</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"<PRE>"</tt> <tt class="py-keyword">or</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-114" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-114', 'find', 'link-46');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">"Query="</tt><tt class="py-op">)</tt> <tt class="py-op">>=</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> <tt id="link-115" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-115', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-116" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-116', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-117" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-117', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">"<PRE>"</tt><tt class="py-op">)</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt id="link-118" class="py-name"><a title="Bio.ParserSupport.read_and_call_while" class="py-name" href="#" onclick="return doclink('link-118', 'read_and_call_while', 'link-33');">read_and_call_while</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-119" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-119', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-120" class="py-name"><a title="Bio.MetaTool.metatool_format.blank" class="py-name" href="#" onclick="return doclink('link-120', 'blank', 'link-35');">blank</a></tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
</div><a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> </tt>
<a name="_Scanner._scan_query_info"></a><div id="_Scanner._scan_query_info-def"><a name="L230"></a><tt class="py-lineno">230</tt> <a class="py-toggle" href="#" id="_Scanner._scan_query_info-toggle" onclick="return toggle('_Scanner._scan_query_info');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIWWW._Scanner-class.html#_scan_query_info">_scan_query_info</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">uhandle</tt><tt class="py-op">,</tt> <tt class="py-param">consumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Scanner._scan_query_info-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Scanner._scan_query_info-expanded"><a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> <tt class="py-comment"># Read the Query lines and the following blank line.</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-121" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-121', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-122" class="py-name" targets="Method Bio.Blast.NCBIStandalone._HeaderConsumer.query_info()=Bio.Blast.NCBIStandalone._HeaderConsumer-class.html#query_info"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.query_info" class="py-name" href="#" onclick="return doclink('link-122', 'query_info', 'link-122');">query_info</a></tt><tt class="py-op">,</tt> <tt id="link-123" class="py-name"><a title="Bio.Alphabet.Alphabet.contains
Bio.Alphabet.AlphabetEncoder.contains
Bio.Alphabet.Gapped.contains
Bio.Alphabet.HasStopCodon.contains
Bio.Pathway.Rep.HashSet.HashSet.contains
Bio.biblio.Biblio.contains" class="py-name" href="#" onclick="return doclink('link-123', 'contains', 'link-32');">contains</a></tt><tt class="py-op">=</tt><tt class="py-string">'Query='</tt><tt class="py-op">)</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> <tt id="link-124" class="py-name"><a title="Bio.ParserSupport.read_and_call_until" class="py-name" href="#" onclick="return doclink('link-124', 'read_and_call_until', 'link-19');">read_and_call_until</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-125" class="py-name"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.query_info" class="py-name" href="#" onclick="return doclink('link-125', 'query_info', 'link-122');">query_info</a></tt><tt class="py-op">,</tt> <tt id="link-126" class="py-name"><a title="Bio.MetaTool.metatool_format.blank" class="py-name" href="#" onclick="return doclink('link-126', 'blank', 'link-35');">blank</a></tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"> <tt id="link-127" class="py-name"><a title="Bio.ParserSupport.read_and_call_while" class="py-name" href="#" onclick="return doclink('link-127', 'read_and_call_while', 'link-33');">read_and_call_while</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-128" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-128', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-129" class="py-name"><a title="Bio.MetaTool.metatool_format.blank" class="py-name" href="#" onclick="return doclink('link-129', 'blank', 'link-35');">blank</a></tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-130" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-130', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-131" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-131', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-132" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-132', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">"<PRE>"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> <tt id="link-133" class="py-name"><a title="Bio.ParserSupport.read_and_call_while" class="py-name" href="#" onclick="return doclink('link-133', 'read_and_call_while', 'link-33');">read_and_call_while</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-134" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-134', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-135" class="py-name"><a title="Bio.MetaTool.metatool_format.blank" class="py-name" href="#" onclick="return doclink('link-135', 'blank', 'link-35');">blank</a></tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-136" class="py-name"><a title="Bio.Blast.NCBIWWW._Scanner._scan_blastform" class="py-name" href="#" onclick="return doclink('link-136', '_scan_blastform', 'link-80');">_scan_blastform</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">)</tt> </tt>
</div><a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> </tt>
<a name="_Scanner._scan_rounds"></a><div id="_Scanner._scan_rounds-def"><a name="L239"></a><tt class="py-lineno">239</tt> <a class="py-toggle" href="#" id="_Scanner._scan_rounds-toggle" onclick="return toggle('_Scanner._scan_rounds');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIWWW._Scanner-class.html#_scan_rounds">_scan_rounds</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">uhandle</tt><tt class="py-op">,</tt> <tt class="py-param">consumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Scanner._scan_rounds-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Scanner._scan_rounds-expanded"><a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-137" class="py-name" targets="Method Bio.Blast.NCBIStandalone._Scanner._scan_descriptions()=Bio.Blast.NCBIStandalone._Scanner-class.html#_scan_descriptions,Method Bio.Blast.NCBIWWW._Scanner._scan_descriptions()=Bio.Blast.NCBIWWW._Scanner-class.html#_scan_descriptions"><a title="Bio.Blast.NCBIStandalone._Scanner._scan_descriptions
Bio.Blast.NCBIWWW._Scanner._scan_descriptions" class="py-name" href="#" onclick="return doclink('link-137', '_scan_descriptions', 'link-137');">_scan_descriptions</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">)</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-138" class="py-name" targets="Method Bio.Blast.NCBIStandalone._Scanner._scan_alignments()=Bio.Blast.NCBIStandalone._Scanner-class.html#_scan_alignments,Method Bio.Blast.NCBIWWW._Scanner._scan_alignments()=Bio.Blast.NCBIWWW._Scanner-class.html#_scan_alignments"><a title="Bio.Blast.NCBIStandalone._Scanner._scan_alignments
Bio.Blast.NCBIWWW._Scanner._scan_alignments" class="py-name" href="#" onclick="return doclink('link-138', '_scan_alignments', 'link-138');">_scan_alignments</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">)</tt> </tt>
</div><a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> </tt>
<a name="_Scanner._scan_descriptions"></a><div id="_Scanner._scan_descriptions-def"><a name="L243"></a><tt class="py-lineno">243</tt> <a class="py-toggle" href="#" id="_Scanner._scan_descriptions-toggle" onclick="return toggle('_Scanner._scan_descriptions');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIWWW._Scanner-class.html#_scan_descriptions">_scan_descriptions</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">uhandle</tt><tt class="py-op">,</tt> <tt class="py-param">consumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Scanner._scan_descriptions-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Scanner._scan_descriptions-expanded"><a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-139" class="py-name" targets="Method Bio.Blast.NCBIStandalone._DescriptionConsumer.start_descriptions()=Bio.Blast.NCBIStandalone._DescriptionConsumer-class.html#start_descriptions,Method Bio.Blast.NCBIStandalone._PSIBlastConsumer.start_descriptions()=Bio.Blast.NCBIStandalone._PSIBlastConsumer-class.html#start_descriptions"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.start_descriptions
Bio.Blast.NCBIStandalone._PSIBlastConsumer.start_descriptions" class="py-name" href="#" onclick="return doclink('link-139', 'start_descriptions', 'link-139');">start_descriptions</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> <tt class="py-comment"># Three things can happen here:</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># 1. line contains 'Score E'</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># 2. line contains "No significant similarity"</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># 3. no descriptions</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-140" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-140', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"> <tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-141" class="py-name" targets="Method Bio.Blast.NCBIStandalone._DescriptionConsumer.description_header()=Bio.Blast.NCBIStandalone._DescriptionConsumer-class.html#description_header"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description_header" class="py-name" href="#" onclick="return doclink('link-141', 'description_header', 'link-141');">description_header</a></tt><tt class="py-op">,</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> <tt class="py-name">has_re</tt><tt class="py-op">=</tt><tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-142" class="py-name"><a title="Bio.Prosite.Pattern.compile" class="py-name" href="#" onclick="return doclink('link-142', 'compile', 'link-21');">compile</a></tt><tt class="py-op">(</tt><tt class="py-string">r"Score {4,5}E"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> <tt class="py-comment"># Either case 2 or 3. Look for "No hits found".</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-143" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-143', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-144" class="py-name" targets="Method Bio.Blast.NCBIStandalone._DescriptionConsumer.no_hits()=Bio.Blast.NCBIStandalone._DescriptionConsumer-class.html#no_hits"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.no_hits" class="py-name" href="#" onclick="return doclink('link-144', 'no_hits', 'link-144');">no_hits</a></tt><tt class="py-op">,</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"> <tt id="link-145" class="py-name"><a title="Bio.Alphabet.Alphabet.contains
Bio.Alphabet.AlphabetEncoder.contains
Bio.Alphabet.Gapped.contains
Bio.Alphabet.HasStopCodon.contains
Bio.Pathway.Rep.HashSet.HashSet.contains
Bio.biblio.Biblio.contains" class="py-name" href="#" onclick="return doclink('link-145', 'contains', 'link-32');">contains</a></tt><tt class="py-op">=</tt><tt class="py-string">'No significant similarity'</tt><tt class="py-op">)</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> <tt id="link-146" class="py-name"><a title="Bio.ParserSupport.read_and_call_while" class="py-name" href="#" onclick="return doclink('link-146', 'read_and_call_while', 'link-33');">read_and_call_while</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-147" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-147', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-148" class="py-name"><a title="Bio.MetaTool.metatool_format.blank" class="py-name" href="#" onclick="return doclink('link-148', 'blank', 'link-35');">blank</a></tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-149" class="py-name" targets="Method Bio.Blast.NCBIStandalone._BlastConsumer.end_descriptions()=Bio.Blast.NCBIStandalone._BlastConsumer-class.html#end_descriptions,Method Bio.Blast.NCBIStandalone._DescriptionConsumer.end_descriptions()=Bio.Blast.NCBIStandalone._DescriptionConsumer-class.html#end_descriptions,Method Bio.Blast.NCBIStandalone._PSIBlastConsumer.end_descriptions()=Bio.Blast.NCBIStandalone._PSIBlastConsumer-class.html#end_descriptions"><a title="Bio.Blast.NCBIStandalone._BlastConsumer.end_descriptions
Bio.Blast.NCBIStandalone._DescriptionConsumer.end_descriptions
Bio.Blast.NCBIStandalone._PSIBlastConsumer.end_descriptions" class="py-name" href="#" onclick="return doclink('link-149', 'end_descriptions', 'link-149');">end_descriptions</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> <tt class="py-comment"># Stop processing.</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"> <tt class="py-comment"># Sequences producing significant alignments: </tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># </tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <a href="http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Ret</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <a href="http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Ret</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># </tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Read the score header lines and a blank line.</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-150" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-150', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-151" class="py-name"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description_header" class="py-name" href="#" onclick="return doclink('link-151', 'description_header', 'link-141');">description_header</a></tt><tt class="py-op">,</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> <tt id="link-152" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-152', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'Sequences producing'</tt><tt class="py-op">)</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"> <tt id="link-153" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-153', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-154" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-154', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-155" class="py-name"><a title="Bio.MetaTool.metatool_format.blank" class="py-name" href="#" onclick="return doclink('link-155', 'blank', 'link-35');">blank</a></tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"> <tt class="py-comment"># Read the descriptions</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># The description contains at least an <a href> into the alignments.</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># What is no alignments are chosen?</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-156" class="py-name"><a title="Bio.ParserSupport.read_and_call_while" class="py-name" href="#" onclick="return doclink('link-156', 'read_and_call_while', 'link-33');">read_and_call_while</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-157" class="py-name" targets="Method Bio.Blast.NCBIStandalone._DescriptionConsumer.description()=Bio.Blast.NCBIStandalone._DescriptionConsumer-class.html#description,Method Bio.Enzyme._RecordConsumer.description()=Bio.Enzyme._RecordConsumer-class.html#description,Method Bio.Prosite._RecordConsumer.description()=Bio.Prosite._RecordConsumer-class.html#description,Function Bio.Std.description()=Bio.Std-module.html#description,Method Bio.SwissProt.SProt._RecordConsumer.description()=Bio.SwissProt.SProt._RecordConsumer-class.html#description,Method Bio.SwissProt.SProt._SequenceConsumer.description()=Bio.SwissProt.SProt._SequenceConsumer-class.html#description,Variable Martel.setup.run_local_tests.description=Martel.setup.run_local_tests-class.html#description"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description
Bio.Enzyme._RecordConsumer.description
Bio.Prosite._RecordConsumer.description
Bio.Std.description
Bio.SwissProt.SProt._RecordConsumer.description
Bio.SwissProt.SProt._SequenceConsumer.description
Martel.setup.run_local_tests.description" class="py-name" href="#" onclick="return doclink('link-157', 'description', 'link-157');">description</a></tt><tt class="py-op">,</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> <tt id="link-158" class="py-name"><a title="Bio.MetaTool.metatool_format.blank" class="py-name" href="#" onclick="return doclink('link-158', 'blank', 'link-35');">blank</a></tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt id="link-159" class="py-name"><a title="Bio.Alphabet.Alphabet.contains
Bio.Alphabet.AlphabetEncoder.contains
Bio.Alphabet.Gapped.contains
Bio.Alphabet.HasStopCodon.contains
Bio.Pathway.Rep.HashSet.HashSet.contains
Bio.biblio.Biblio.contains" class="py-name" href="#" onclick="return doclink('link-159', 'contains', 'link-32');">contains</a></tt><tt class="py-op">=</tt><tt class="py-string">'<a'</tt><tt class="py-op">)</tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"> <tt class="py-comment"># two choices here, either blank lines or a </PRE></tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-160" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-160', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-161" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-161', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> <tt id="link-162" class="py-name"><a title="Bio.Alphabet.Alphabet.contains
Bio.Alphabet.AlphabetEncoder.contains
Bio.Alphabet.Gapped.contains
Bio.Alphabet.HasStopCodon.contains
Bio.Pathway.Rep.HashSet.HashSet.contains
Bio.biblio.Biblio.contains" class="py-name" href="#" onclick="return doclink('link-162', 'contains', 'link-32');">contains</a></tt><tt class="py-op">=</tt><tt class="py-string">'</PRE>'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"> <tt id="link-163" class="py-name"><a title="Bio.ParserSupport.read_and_call_while" class="py-name" href="#" onclick="return doclink('link-163', 'read_and_call_while', 'link-33');">read_and_call_while</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-164" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-164', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-165" class="py-name"><a title="Bio.MetaTool.metatool_format.blank" class="py-name" href="#" onclick="return doclink('link-165', 'blank', 'link-35');">blank</a></tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-166" class="py-name"><a title="Bio.Blast.NCBIStandalone._BlastConsumer.end_descriptions
Bio.Blast.NCBIStandalone._DescriptionConsumer.end_descriptions
Bio.Blast.NCBIStandalone._PSIBlastConsumer.end_descriptions" class="py-name" href="#" onclick="return doclink('link-166', 'end_descriptions', 'link-149');">end_descriptions</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"> </tt>
<a name="_Scanner._scan_alignments"></a><div id="_Scanner._scan_alignments-def"><a name="L283"></a><tt class="py-lineno">283</tt> <a class="py-toggle" href="#" id="_Scanner._scan_alignments-toggle" onclick="return toggle('_Scanner._scan_alignments');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIWWW._Scanner-class.html#_scan_alignments">_scan_alignments</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">uhandle</tt><tt class="py-op">,</tt> <tt class="py-param">consumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Scanner._scan_alignments-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Scanner._scan_alignments-expanded"><a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> <tt class="py-comment"># Check to see whether I'm at an alignment or database report.</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Possibilities:</tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># 1) BLASTP 2.0.14, pairwise alignment</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <CENTER><b><FONT color="green">Alignments</FONT></b></CENTER></tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <PRE></tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># ><a name = 121837></a><a href="http://www.ncbi.nlm.nih.gov:80/entre</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># 2) BLASTP 2.0.10, pairwise alignment</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <PRE></tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <a name = 120291> </a><a href="http://www.ncbi.nlm.nih.gov:80/entre</tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># 3) BLASTP 2.0.10, master-slave</tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <PRE></tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># blast_tmp 1 MFQQIGAVQAKSGTDEPAHPCEKFPPERKCEAVFWKPLPRHEAREILLAARK</tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># 4) BLASTP 2.0.10, 2.0.14, database</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <PRE></tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Database: Non-redundant SwissProt sequences</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># 5) BLASTX 2.2.4, pairwise alignment</tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <CENTER><b><FONT color="green">Alignments</FONT></b></CENTER></tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># </form></tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <script src="blastResult.js"></script><table border="0"><tr><td><FO</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <PRE></tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># 6) Qblast 2.2.10, database (no 'Database' line)</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <PRE></tt> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Lambda K H</tt> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"> <tt class="py-comment"># Get the first two lines and examine them.</tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">line1</tt> <tt class="py-op">=</tt> <tt id="link-167" class="py-name" targets="Function Bio.ParserSupport.safe_readline()=Bio.ParserSupport-module.html#safe_readline"><a title="Bio.ParserSupport.safe_readline" class="py-name" href="#" onclick="return doclink('link-167', 'safe_readline', 'link-167');">safe_readline</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">)</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"> <tt class="py-name">line2</tt> <tt class="py-op">=</tt> <tt id="link-168" class="py-name"><a title="Bio.ParserSupport.safe_readline" class="py-name" href="#" onclick="return doclink('link-168', 'safe_readline', 'link-167');">safe_readline</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">)</tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"> <tt class="py-name">uhandle</tt><tt class="py-op">.</tt><tt id="link-169" class="py-name" targets="Method Bio.File.UndoHandle.saveline()=Bio.File.UndoHandle-class.html#saveline"><a title="Bio.File.UndoHandle.saveline" class="py-name" href="#" onclick="return doclink('link-169', 'saveline', 'link-169');">saveline</a></tt><tt class="py-op">(</tt><tt class="py-name">line2</tt><tt class="py-op">)</tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"> <tt class="py-name">uhandle</tt><tt class="py-op">.</tt><tt id="link-170" class="py-name"><a title="Bio.File.UndoHandle.saveline" class="py-name" href="#" onclick="return doclink('link-170', 'saveline', 'link-169');">saveline</a></tt><tt class="py-op">(</tt><tt class="py-name">line1</tt><tt class="py-op">)</tt> </tt>
<a name="L313"></a><tt class="py-lineno">313</tt> <tt class="py-line"> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"> <tt class="py-name">is_pairwise</tt> <tt class="py-op">=</tt> <tt class="py-name">is_masterslave</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-string">'Alignments'</tt> <tt class="py-keyword">in</tt> <tt class="py-name">line2</tt><tt class="py-op">:</tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"> <tt class="py-name">is_pairwise</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">line2</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">' Database'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">line2</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">'Lambda K H'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L320"></a><tt class="py-lineno">320</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">line2</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">'blast_tmp'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"> <tt class="py-name">is_masterslave</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">line1</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">'<PRE>'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"> <tt class="py-name">is_pairwise</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"Cannot resolve location at lines:\n%s\n%s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">line1</tt><tt class="py-op">,</tt> <tt class="py-name">line2</tt><tt class="py-op">)</tt> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"> </tt>
<a name="L328"></a><tt class="py-lineno">328</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">is_pairwise</tt><tt class="py-op">:</tt> </tt>
<a name="L329"></a><tt class="py-lineno">329</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-171" class="py-name" targets="Method Bio.Blast.NCBIStandalone._Scanner._scan_pairwise_alignments()=Bio.Blast.NCBIStandalone._Scanner-class.html#_scan_pairwise_alignments,Method Bio.Blast.NCBIWWW._Scanner._scan_pairwise_alignments()=Bio.Blast.NCBIWWW._Scanner-class.html#_scan_pairwise_alignments"><a title="Bio.Blast.NCBIStandalone._Scanner._scan_pairwise_alignments
Bio.Blast.NCBIWWW._Scanner._scan_pairwise_alignments" class="py-name" href="#" onclick="return doclink('link-171', '_scan_pairwise_alignments', 'link-171');">_scan_pairwise_alignments</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">)</tt> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">is_masterslave</tt><tt class="py-op">:</tt> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-172" class="py-name" targets="Method Bio.Blast.NCBIStandalone._Scanner._scan_masterslave_alignment()=Bio.Blast.NCBIStandalone._Scanner-class.html#_scan_masterslave_alignment,Method Bio.Blast.NCBIWWW._Scanner._scan_masterslave_alignment()=Bio.Blast.NCBIWWW._Scanner-class.html#_scan_masterslave_alignment"><a title="Bio.Blast.NCBIStandalone._Scanner._scan_masterslave_alignment
Bio.Blast.NCBIWWW._Scanner._scan_masterslave_alignment" class="py-name" href="#" onclick="return doclink('link-172', '_scan_masterslave_alignment', 'link-172');">_scan_masterslave_alignment</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">)</tt> </tt>
</div><a name="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"> </tt>
<a name="_Scanner._scan_pairwise_alignments"></a><div id="_Scanner._scan_pairwise_alignments-def"><a name="L333"></a><tt class="py-lineno">333</tt> <a class="py-toggle" href="#" id="_Scanner._scan_pairwise_alignments-toggle" onclick="return toggle('_Scanner._scan_pairwise_alignments');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIWWW._Scanner-class.html#_scan_pairwise_alignments">_scan_pairwise_alignments</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">uhandle</tt><tt class="py-op">,</tt> <tt class="py-param">consumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Scanner._scan_pairwise_alignments-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Scanner._scan_pairwise_alignments-expanded"><a name="L334"></a><tt class="py-lineno">334</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"> <tt id="link-173" class="py-name"><a title="Bio.ParserSupport.read_and_call_until" class="py-name" href="#" onclick="return doclink('link-173', 'read_and_call_until', 'link-19');">read_and_call_until</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-174" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-174', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-175" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-175', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'<PRE>'</tt><tt class="py-op">)</tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt> <tt class="py-line"> <tt class="py-comment"># The first line is <PRE>. Check the second line to see if</tt> </tt>
<a name="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># I'm still at an alignment.</tt> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">line1</tt> <tt class="py-op">=</tt> <tt id="link-176" class="py-name"><a title="Bio.ParserSupport.safe_readline" class="py-name" href="#" onclick="return doclink('link-176', 'safe_readline', 'link-167');">safe_readline</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">)</tt> </tt>
<a name="L340"></a><tt class="py-lineno">340</tt> <tt class="py-line"> <tt class="py-name">line2</tt> <tt class="py-op">=</tt> <tt id="link-177" class="py-name"><a title="Bio.ParserSupport.safe_readline" class="py-name" href="#" onclick="return doclink('link-177', 'safe_readline', 'link-167');">safe_readline</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">)</tt> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt> <tt class="py-line"> <tt class="py-name">uhandle</tt><tt class="py-op">.</tt><tt id="link-178" class="py-name"><a title="Bio.File.UndoHandle.saveline" class="py-name" href="#" onclick="return doclink('link-178', 'saveline', 'link-169');">saveline</a></tt><tt class="py-op">(</tt><tt class="py-name">line2</tt><tt class="py-op">)</tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt> <tt class="py-line"> <tt class="py-name">uhandle</tt><tt class="py-op">.</tt><tt id="link-179" class="py-name"><a title="Bio.File.UndoHandle.saveline" class="py-name" href="#" onclick="return doclink('link-179', 'saveline', 'link-169');">saveline</a></tt><tt class="py-op">(</tt><tt class="py-name">line1</tt><tt class="py-op">)</tt> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt> <tt class="py-line"> <tt class="py-comment"># Lambda is for Q-blast results, which do not have a Database line</tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">line1</tt><tt class="py-op">.</tt><tt id="link-180" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-180', 'find', 'link-46');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">'Database'</tt><tt class="py-op">)</tt> <tt class="py-op">>=</tt> <tt class="py-number">0</tt> <tt class="py-keyword">or</tt> <tt class="py-name">line2</tt><tt class="py-op">.</tt><tt id="link-181" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-181', 'find', 'link-46');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">"Database"</tt><tt class="py-op">)</tt> <tt class="py-op">>=</tt> <tt class="py-number">0</tt> \ </tt>
<a name="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"> <tt class="py-keyword">or</tt> <tt class="py-name">line2</tt><tt class="py-op">.</tt><tt id="link-182" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-182', 'find', 'link-46');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">'Lambda K H'</tt><tt class="py-op">)</tt> <tt class="py-op">>=</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt> <tt class="py-line"> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"> <tt class="py-comment"># Occasionally, there's a bug where the alignment_header and</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># hsp_header are skipped, leaving only the hsp_alignment.</tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Detect this and handle it accordingly.</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">line2</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">6</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'Query:'</tt><tt class="py-op">:</tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-183" class="py-name" targets="Method Bio.Blast.NCBIWWW._Scanner._scan_abbreviated_pairwise_alignment()=Bio.Blast.NCBIWWW._Scanner-class.html#_scan_abbreviated_pairwise_alignment"><a title="Bio.Blast.NCBIWWW._Scanner._scan_abbreviated_pairwise_alignment" class="py-name" href="#" onclick="return doclink('link-183', '_scan_abbreviated_pairwise_alignment', 'link-183');">_scan_abbreviated_pairwise_alignment</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">)</tt> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-184" class="py-name" targets="Method Bio.Blast.NCBIStandalone._Scanner._scan_one_pairwise_alignment()=Bio.Blast.NCBIStandalone._Scanner-class.html#_scan_one_pairwise_alignment,Method Bio.Blast.NCBIWWW._Scanner._scan_one_pairwise_alignment()=Bio.Blast.NCBIWWW._Scanner-class.html#_scan_one_pairwise_alignment"><a title="Bio.Blast.NCBIStandalone._Scanner._scan_one_pairwise_alignment
Bio.Blast.NCBIWWW._Scanner._scan_one_pairwise_alignment" class="py-name" href="#" onclick="return doclink('link-184', '_scan_one_pairwise_alignment', 'link-184');">_scan_one_pairwise_alignment</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">)</tt> </tt>
</div><a name="L355"></a><tt class="py-lineno">355</tt> <tt class="py-line"> </tt>
<a name="_Scanner._scan_abbreviated_pairwise_alignment"></a><div id="_Scanner._scan_abbreviated_pairwise_alignment-def"><a name="L356"></a><tt class="py-lineno">356</tt> <a class="py-toggle" href="#" id="_Scanner._scan_abbreviated_pairwise_alignment-toggle" onclick="return toggle('_Scanner._scan_abbreviated_pairwise_alignment');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIWWW._Scanner-class.html#_scan_abbreviated_pairwise_alignment">_scan_abbreviated_pairwise_alignment</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">uhandle</tt><tt class="py-op">,</tt> <tt class="py-param">consumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Scanner._scan_abbreviated_pairwise_alignment-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Scanner._scan_abbreviated_pairwise_alignment-expanded"><a name="L357"></a><tt class="py-lineno">357</tt> <tt class="py-line"> <tt class="py-comment"># Sometimes all header information is skipped, leaving</tt> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># only the raw alignments. I believe this is a bug because</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># without the header information, you lose vital information such</tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># as score, target sequence id, etc.</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Format:</tt> </tt>
<a name="L362"></a><tt class="py-lineno">362</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <PRE></tt> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># hsp_alignment</tt> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-185" class="py-name" targets="Method Bio.Blast.NCBIStandalone._AlignmentConsumer.start_alignment()=Bio.Blast.NCBIStandalone._AlignmentConsumer-class.html#start_alignment"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.start_alignment" class="py-name" href="#" onclick="return doclink('link-185', 'start_alignment', 'link-185');">start_alignment</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-186" class="py-name" targets="Method Bio.Blast.NCBIStandalone._HSPConsumer.start_hsp()=Bio.Blast.NCBIStandalone._HSPConsumer-class.html#start_hsp,Method Bio.StdHandler.Handle_hsp.start_hsp()=Bio.StdHandler.Handle_hsp-class.html#start_hsp,Method Bio.StdHandler.Handle_hsp_seqalign.start_hsp()=Bio.StdHandler.Handle_hsp_seqalign-class.html#start_hsp"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.start_hsp
Bio.StdHandler.Handle_hsp.start_hsp
Bio.StdHandler.Handle_hsp_seqalign.start_hsp" class="py-name" href="#" onclick="return doclink('link-186', 'start_hsp', 'link-186');">start_hsp</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt> <tt class="py-line"> <tt id="link-187" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-187', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-188" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-188', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-189" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-189', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'<PRE>'</tt><tt class="py-op">)</tt> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-190" class="py-name" targets="Method Bio.Blast.NCBIStandalone._Scanner._scan_hsp_alignment()=Bio.Blast.NCBIStandalone._Scanner-class.html#_scan_hsp_alignment,Method Bio.Blast.NCBIWWW._Scanner._scan_hsp_alignment()=Bio.Blast.NCBIWWW._Scanner-class.html#_scan_hsp_alignment"><a title="Bio.Blast.NCBIStandalone._Scanner._scan_hsp_alignment
Bio.Blast.NCBIWWW._Scanner._scan_hsp_alignment" class="py-name" href="#" onclick="return doclink('link-190', '_scan_hsp_alignment', 'link-190');">_scan_hsp_alignment</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">)</tt> </tt>
<a name="L369"></a><tt class="py-lineno">369</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-191" class="py-name" targets="Method Bio.Blast.NCBIStandalone._BlastConsumer.end_hsp()=Bio.Blast.NCBIStandalone._BlastConsumer-class.html#end_hsp,Method Bio.Blast.NCBIStandalone._HSPConsumer.end_hsp()=Bio.Blast.NCBIStandalone._HSPConsumer-class.html#end_hsp,Method Bio.Blast.NCBIStandalone._PSIBlastConsumer.end_hsp()=Bio.Blast.NCBIStandalone._PSIBlastConsumer-class.html#end_hsp,Method Bio.StdHandler.Handle_hsp.end_hsp()=Bio.StdHandler.Handle_hsp-class.html#end_hsp,Method Bio.StdHandler.Handle_hsp_seqalign.end_hsp()=Bio.StdHandler.Handle_hsp_seqalign-class.html#end_hsp"><a title="Bio.Blast.NCBIStandalone._BlastConsumer.end_hsp
Bio.Blast.NCBIStandalone._HSPConsumer.end_hsp
Bio.Blast.NCBIStandalone._PSIBlastConsumer.end_hsp
Bio.StdHandler.Handle_hsp.end_hsp
Bio.StdHandler.Handle_hsp_seqalign.end_hsp" class="py-name" href="#" onclick="return doclink('link-191', 'end_hsp', 'link-191');">end_hsp</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L370"></a><tt class="py-lineno">370</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-192" class="py-name" targets="Method Bio.Blast.NCBIStandalone._AlignmentConsumer.end_alignment()=Bio.Blast.NCBIStandalone._AlignmentConsumer-class.html#end_alignment,Method Bio.Blast.NCBIStandalone._BlastConsumer.end_alignment()=Bio.Blast.NCBIStandalone._BlastConsumer-class.html#end_alignment,Method Bio.Blast.NCBIStandalone._PSIBlastConsumer.end_alignment()=Bio.Blast.NCBIStandalone._PSIBlastConsumer-class.html#end_alignment"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.end_alignment
Bio.Blast.NCBIStandalone._BlastConsumer.end_alignment
Bio.Blast.NCBIStandalone._PSIBlastConsumer.end_alignment" class="py-name" href="#" onclick="return doclink('link-192', 'end_alignment', 'link-192');">end_alignment</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L371"></a><tt class="py-lineno">371</tt> <tt class="py-line"> </tt>
<a name="_Scanner._scan_one_pairwise_alignment"></a><div id="_Scanner._scan_one_pairwise_alignment-def"><a name="L372"></a><tt class="py-lineno">372</tt> <a class="py-toggle" href="#" id="_Scanner._scan_one_pairwise_alignment-toggle" onclick="return toggle('_Scanner._scan_one_pairwise_alignment');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIWWW._Scanner-class.html#_scan_one_pairwise_alignment">_scan_one_pairwise_alignment</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">uhandle</tt><tt class="py-op">,</tt> <tt class="py-param">consumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Scanner._scan_one_pairwise_alignment-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Scanner._scan_one_pairwise_alignment-expanded"><a name="L373"></a><tt class="py-lineno">373</tt> <tt class="py-line"> <tt class="py-comment"># Alignment format:</tt> </tt>
<a name="L374"></a><tt class="py-lineno">374</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <CENTER><b><FONT color="green">Alignments</FONT></b></CENTER></tt> </tt>
<a name="L375"></a><tt class="py-lineno">375</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># (BLAST 2.0.14)</tt> </tt>
<a name="L376"></a><tt class="py-lineno">376</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <PRE></tt> </tt>
<a name="L377"></a><tt class="py-lineno">377</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># alignment_header</tt> </tt>
<a name="L378"></a><tt class="py-lineno">378</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># hsp_header</tt> </tt>
<a name="L379"></a><tt class="py-lineno">379</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># hsp_alignment</tt> </tt>
<a name="L380"></a><tt class="py-lineno">380</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># [...]</tt> </tt>
<a name="L381"></a><tt class="py-lineno">381</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># The hsp_header and hsp_alignment blocks can be repeated.</tt> </tt>
<a name="L382"></a><tt class="py-lineno">382</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L383"></a><tt class="py-lineno">383</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-193" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.start_alignment" class="py-name" href="#" onclick="return doclink('link-193', 'start_alignment', 'link-185');">start_alignment</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt> <tt class="py-line"> <tt id="link-194" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-194', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-195" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-195', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-196" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-196', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'<PRE>'</tt><tt class="py-op">)</tt> </tt>
<a name="L385"></a><tt class="py-lineno">385</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-197" class="py-name" targets="Method Bio.Blast.NCBIStandalone._Scanner._scan_alignment_header()=Bio.Blast.NCBIStandalone._Scanner-class.html#_scan_alignment_header,Method Bio.Blast.NCBIWWW._Scanner._scan_alignment_header()=Bio.Blast.NCBIWWW._Scanner-class.html#_scan_alignment_header"><a title="Bio.Blast.NCBIStandalone._Scanner._scan_alignment_header
Bio.Blast.NCBIWWW._Scanner._scan_alignment_header" class="py-name" href="#" onclick="return doclink('link-197', '_scan_alignment_header', 'link-197');">_scan_alignment_header</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">)</tt> </tt>
<a name="L386"></a><tt class="py-lineno">386</tt> <tt class="py-line"> </tt>
<a name="L387"></a><tt class="py-lineno">387</tt> <tt class="py-line"> <tt class="py-comment"># Scan a bunch of score/alignment's.</tt> </tt>
<a name="L388"></a><tt class="py-lineno">388</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L389"></a><tt class="py-lineno">389</tt> <tt class="py-line"> <tt class="py-comment"># An HSP header starts with ' Score'.</tt> </tt>
<a name="L390"></a><tt class="py-lineno">390</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># However, if the HSP header is not the first one in the</tt> </tt>
<a name="L391"></a><tt class="py-lineno">391</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># alignment, there will be a '<PRE>' line first. Therefore,</tt> </tt>
<a name="L392"></a><tt class="py-lineno">392</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># I will need to check either of the first two lines to</tt> </tt>
<a name="L393"></a><tt class="py-lineno">393</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># see if I'm at an HSP header.</tt> </tt>
<a name="L394"></a><tt class="py-lineno">394</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">line1</tt> <tt class="py-op">=</tt> <tt id="link-198" class="py-name"><a title="Bio.ParserSupport.safe_readline" class="py-name" href="#" onclick="return doclink('link-198', 'safe_readline', 'link-167');">safe_readline</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">)</tt> </tt>
<a name="L395"></a><tt class="py-lineno">395</tt> <tt class="py-line"> <tt class="py-name">line2</tt> <tt class="py-op">=</tt> <tt id="link-199" class="py-name"><a title="Bio.ParserSupport.safe_readline" class="py-name" href="#" onclick="return doclink('link-199', 'safe_readline', 'link-167');">safe_readline</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">)</tt> </tt>
<a name="L396"></a><tt class="py-lineno">396</tt> <tt class="py-line"> <tt class="py-name">line3</tt> <tt class="py-op">=</tt> <tt id="link-200" class="py-name"><a title="Bio.ParserSupport.safe_readline" class="py-name" href="#" onclick="return doclink('link-200', 'safe_readline', 'link-167');">safe_readline</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">)</tt> </tt>
<a name="L397"></a><tt class="py-lineno">397</tt> <tt class="py-line"> <tt class="py-name">uhandle</tt><tt class="py-op">.</tt><tt id="link-201" class="py-name"><a title="Bio.File.UndoHandle.saveline" class="py-name" href="#" onclick="return doclink('link-201', 'saveline', 'link-169');">saveline</a></tt><tt class="py-op">(</tt><tt class="py-name">line3</tt><tt class="py-op">)</tt> </tt>
<a name="L398"></a><tt class="py-lineno">398</tt> <tt class="py-line"> <tt class="py-name">uhandle</tt><tt class="py-op">.</tt><tt id="link-202" class="py-name"><a title="Bio.File.UndoHandle.saveline" class="py-name" href="#" onclick="return doclink('link-202', 'saveline', 'link-169');">saveline</a></tt><tt class="py-op">(</tt><tt class="py-name">line2</tt><tt class="py-op">)</tt> </tt>
<a name="L399"></a><tt class="py-lineno">399</tt> <tt class="py-line"> <tt class="py-name">uhandle</tt><tt class="py-op">.</tt><tt id="link-203" class="py-name"><a title="Bio.File.UndoHandle.saveline" class="py-name" href="#" onclick="return doclink('link-203', 'saveline', 'link-169');">saveline</a></tt><tt class="py-op">(</tt><tt class="py-name">line1</tt><tt class="py-op">)</tt> </tt>
<a name="L400"></a><tt class="py-lineno">400</tt> <tt class="py-line"> <tt class="py-comment"># There can be <a> links in front of 'Score'</tt> </tt>
<a name="L401"></a><tt class="py-lineno">401</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">rea</tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-204" class="py-name"><a title="Bio.Prosite.Pattern.compile" class="py-name" href="#" onclick="return doclink('link-204', 'compile', 'link-21');">compile</a></tt><tt class="py-op">(</tt><tt class="py-string">r"</?a[^>]*>"</tt><tt class="py-op">)</tt> </tt>
<a name="L402"></a><tt class="py-lineno">402</tt> <tt class="py-line"> <tt class="py-name">line1</tt> <tt class="py-op">=</tt> <tt class="py-name">rea</tt><tt class="py-op">.</tt><tt class="py-name">sub</tt><tt class="py-op">(</tt><tt class="py-string">""</tt><tt class="py-op">,</tt> <tt class="py-name">line1</tt><tt class="py-op">)</tt> </tt>
<a name="L403"></a><tt class="py-lineno">403</tt> <tt class="py-line"> <tt class="py-name">line2</tt> <tt class="py-op">=</tt> <tt class="py-name">rea</tt><tt class="py-op">.</tt><tt class="py-name">sub</tt><tt class="py-op">(</tt><tt class="py-string">""</tt><tt class="py-op">,</tt> <tt class="py-name">line2</tt><tt class="py-op">)</tt> </tt>
<a name="L404"></a><tt class="py-lineno">404</tt> <tt class="py-line"> <tt class="py-name">line3</tt> <tt class="py-op">=</tt> <tt class="py-name">rea</tt><tt class="py-op">.</tt><tt class="py-name">sub</tt><tt class="py-op">(</tt><tt class="py-string">""</tt><tt class="py-op">,</tt> <tt class="py-name">line3</tt><tt class="py-op">)</tt> </tt>
<a name="L405"></a><tt class="py-lineno">405</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line1</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">6</tt><tt class="py-op">]</tt> <tt class="py-op">!=</tt> <tt class="py-string">' Score'</tt> <tt class="py-keyword">and</tt> <tt class="py-name">line2</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">6</tt><tt class="py-op">]</tt> <tt class="py-op">!=</tt> <tt class="py-string">' Score'</tt> <tt class="py-keyword">and</tt> \ </tt>
<a name="L406"></a><tt class="py-lineno">406</tt> <tt class="py-line"> <tt class="py-name">line3</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">6</tt><tt class="py-op">]</tt> <tt class="py-op">!=</tt> <tt class="py-string">' Score'</tt><tt class="py-op">:</tt> </tt>
<a name="L407"></a><tt class="py-lineno">407</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L408"></a><tt class="py-lineno">408</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-205" class="py-name" targets="Method Bio.Blast.NCBIStandalone._Scanner._scan_hsp()=Bio.Blast.NCBIStandalone._Scanner-class.html#_scan_hsp,Method Bio.Blast.NCBIWWW._Scanner._scan_hsp()=Bio.Blast.NCBIWWW._Scanner-class.html#_scan_hsp"><a title="Bio.Blast.NCBIStandalone._Scanner._scan_hsp
Bio.Blast.NCBIWWW._Scanner._scan_hsp" class="py-name" href="#" onclick="return doclink('link-205', '_scan_hsp', 'link-205');">_scan_hsp</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">)</tt> </tt>
<a name="L409"></a><tt class="py-lineno">409</tt> <tt class="py-line"> </tt>
<a name="L410"></a><tt class="py-lineno">410</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-206" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.end_alignment
Bio.Blast.NCBIStandalone._BlastConsumer.end_alignment
Bio.Blast.NCBIStandalone._PSIBlastConsumer.end_alignment" class="py-name" href="#" onclick="return doclink('link-206', 'end_alignment', 'link-192');">end_alignment</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L411"></a><tt class="py-lineno">411</tt> <tt class="py-line"> </tt>
<a name="_Scanner._scan_alignment_header"></a><div id="_Scanner._scan_alignment_header-def"><a name="L412"></a><tt class="py-lineno">412</tt> <a class="py-toggle" href="#" id="_Scanner._scan_alignment_header-toggle" onclick="return toggle('_Scanner._scan_alignment_header');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIWWW._Scanner-class.html#_scan_alignment_header">_scan_alignment_header</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">uhandle</tt><tt class="py-op">,</tt> <tt class="py-param">consumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Scanner._scan_alignment_header-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Scanner._scan_alignment_header-expanded"><a name="L413"></a><tt class="py-lineno">413</tt> <tt class="py-line"> <tt class="py-comment"># <a name = 120291> </a><a href="http://www.ncbi.nlm.nih.gov:80/entrez/</tt> </tt>
<a name="L414"></a><tt class="py-lineno">414</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Length = 141</tt> </tt>
<a name="L415"></a><tt class="py-lineno">415</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt>
<a name="L416"></a><tt class="py-lineno">416</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L417"></a><tt class="py-lineno">417</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt id="link-207" class="py-name"><a title="Bio.ParserSupport.safe_readline" class="py-name" href="#" onclick="return doclink('link-207', 'safe_readline', 'link-167');">safe_readline</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">)</tt> </tt>
<a name="L418"></a><tt class="py-lineno">418</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">lstrip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">'Length ='</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L419"></a><tt class="py-lineno">419</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-208" class="py-name" targets="Method Bio.Blast.NCBIStandalone._AlignmentConsumer.length()=Bio.Blast.NCBIStandalone._AlignmentConsumer-class.html#length,Method Bio.GFF.easy.Location.length()=Bio.GFF.easy.Location-class.html#length"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-208', 'length', 'link-208');">length</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L420"></a><tt class="py-lineno">420</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L421"></a><tt class="py-lineno">421</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-209" class="py-name"><a title="Bio.ParserSupport.is_blank_line" class="py-name" href="#" onclick="return doclink('link-209', 'is_blank_line', 'link-59');">is_blank_line</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L422"></a><tt class="py-lineno">422</tt> <tt class="py-line"> <tt class="py-comment"># Check to make sure I haven't missed the Length line</tt> </tt>
<a name="L423"></a><tt class="py-lineno">423</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"I missed the Length in an alignment header"</tt> </tt>
<a name="L424"></a><tt class="py-lineno">424</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-210" class="py-name" targets="Method Bio.Blast.NCBIStandalone._AlignmentConsumer.title()=Bio.Blast.NCBIStandalone._AlignmentConsumer-class.html#title,Method Bio.GenBank._FeatureConsumer.title()=Bio.GenBank._FeatureConsumer-class.html#title,Method Bio.GenBank._RecordConsumer.title()=Bio.GenBank._RecordConsumer-class.html#title,Method Bio.Medline._RecordConsumer.title()=Bio.Medline._RecordConsumer-class.html#title,Variable Bio.expressions.fasta.title=Bio.expressions.fasta-module.html#title"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title
Bio.Medline._RecordConsumer.title
Bio.expressions.fasta.title" class="py-name" href="#" onclick="return doclink('link-210', 'title', 'link-210');">title</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L425"></a><tt class="py-lineno">425</tt> <tt class="py-line"> </tt>
<a name="L426"></a><tt class="py-lineno">426</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-211" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-211', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-212" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-212', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> </tt>
<a name="L427"></a><tt class="py-lineno">427</tt> <tt class="py-line"> <tt id="link-213" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-213', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">' '</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L428"></a><tt class="py-lineno">428</tt> <tt class="py-line"> <tt id="link-214" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-214', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-215" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-215', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-216" class="py-name"><a title="Bio.MetaTool.metatool_format.blank" class="py-name" href="#" onclick="return doclink('link-216', 'blank', 'link-35');">blank</a></tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
</div><a name="L429"></a><tt class="py-lineno">429</tt> <tt class="py-line"> </tt>
<a name="_Scanner._scan_hsp"></a><div id="_Scanner._scan_hsp-def"><a name="L430"></a><tt class="py-lineno">430</tt> <a class="py-toggle" href="#" id="_Scanner._scan_hsp-toggle" onclick="return toggle('_Scanner._scan_hsp');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIWWW._Scanner-class.html#_scan_hsp">_scan_hsp</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">uhandle</tt><tt class="py-op">,</tt> <tt class="py-param">consumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Scanner._scan_hsp-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Scanner._scan_hsp-expanded"><a name="L431"></a><tt class="py-lineno">431</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-217" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.start_hsp
Bio.StdHandler.Handle_hsp.start_hsp
Bio.StdHandler.Handle_hsp_seqalign.start_hsp" class="py-name" href="#" onclick="return doclink('link-217', 'start_hsp', 'link-186');">start_hsp</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L432"></a><tt class="py-lineno">432</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-218" class="py-name" targets="Method Bio.Blast.NCBIStandalone._Scanner._scan_hsp_header()=Bio.Blast.NCBIStandalone._Scanner-class.html#_scan_hsp_header,Method Bio.Blast.NCBIWWW._Scanner._scan_hsp_header()=Bio.Blast.NCBIWWW._Scanner-class.html#_scan_hsp_header"><a title="Bio.Blast.NCBIStandalone._Scanner._scan_hsp_header
Bio.Blast.NCBIWWW._Scanner._scan_hsp_header" class="py-name" href="#" onclick="return doclink('link-218', '_scan_hsp_header', 'link-218');">_scan_hsp_header</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">)</tt> </tt>
<a name="L433"></a><tt class="py-lineno">433</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-219" class="py-name"><a title="Bio.Blast.NCBIStandalone._Scanner._scan_hsp_alignment
Bio.Blast.NCBIWWW._Scanner._scan_hsp_alignment" class="py-name" href="#" onclick="return doclink('link-219', '_scan_hsp_alignment', 'link-190');">_scan_hsp_alignment</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">)</tt> </tt>
<a name="L434"></a><tt class="py-lineno">434</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-220" class="py-name"><a title="Bio.Blast.NCBIStandalone._BlastConsumer.end_hsp
Bio.Blast.NCBIStandalone._HSPConsumer.end_hsp
Bio.Blast.NCBIStandalone._PSIBlastConsumer.end_hsp
Bio.StdHandler.Handle_hsp.end_hsp
Bio.StdHandler.Handle_hsp_seqalign.end_hsp" class="py-name" href="#" onclick="return doclink('link-220', 'end_hsp', 'link-191');">end_hsp</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L435"></a><tt class="py-lineno">435</tt> <tt class="py-line"> </tt>
<a name="_Scanner._scan_hsp_header"></a><div id="_Scanner._scan_hsp_header-def"><a name="L436"></a><tt class="py-lineno">436</tt> <a class="py-toggle" href="#" id="_Scanner._scan_hsp_header-toggle" onclick="return toggle('_Scanner._scan_hsp_header');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIWWW._Scanner-class.html#_scan_hsp_header">_scan_hsp_header</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">uhandle</tt><tt class="py-op">,</tt> <tt class="py-param">consumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Scanner._scan_hsp_header-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Scanner._scan_hsp_header-expanded"><a name="L437"></a><tt class="py-lineno">437</tt> <tt class="py-line"> <tt class="py-comment"># If the HSP is not the first one within an alignment, includes:</tt> </tt>
<a name="L438"></a><tt class="py-lineno">438</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <PRE></tt> </tt>
<a name="L439"></a><tt class="py-lineno">439</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L440"></a><tt class="py-lineno">440</tt> <tt class="py-line"> <tt class="py-comment"># Score = 22.7 bits (47), Expect = 2.5</tt> </tt>
<a name="L441"></a><tt class="py-lineno">441</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Identities = 10/36 (27%), Positives = 18/36 (49%)</tt> </tt>
<a name="L442"></a><tt class="py-lineno">442</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Strand = Plus / Plus</tt> </tt>
<a name="L443"></a><tt class="py-lineno">443</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Frame = +3</tt> </tt>
<a name="L444"></a><tt class="py-lineno">444</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt>
<a name="L445"></a><tt class="py-lineno">445</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L446"></a><tt class="py-lineno">446</tt> <tt class="py-line"> <tt id="link-221" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-221', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-222" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-222', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-223" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-223', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'<PRE>'</tt><tt class="py-op">)</tt> </tt>
<a name="L447"></a><tt class="py-lineno">447</tt> <tt class="py-line"> <tt id="link-224" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-224', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-225" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-225', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-226" class="py-name"><a title="Bio.MetaTool.metatool_format.blank" class="py-name" href="#" onclick="return doclink('link-226', 'blank', 'link-35');">blank</a></tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L448"></a><tt class="py-lineno">448</tt> <tt class="py-line"> <tt id="link-227" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-227', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-228" class="py-name" targets="Method Bio.Blast.NCBIStandalone._HSPConsumer.score()=Bio.Blast.NCBIStandalone._HSPConsumer-class.html#score,Variable Bio.expressions.blast.ncbiblast.score=Bio.expressions.blast.ncbiblast-module.html#score"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-228', 'score', 'link-228');">score</a></tt><tt class="py-op">,</tt> </tt>
<a name="L449"></a><tt class="py-lineno">449</tt> <tt class="py-line"> <tt class="py-name">has_re</tt><tt class="py-op">=</tt><tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-229" class="py-name"><a title="Bio.Prosite.Pattern.compile" class="py-name" href="#" onclick="return doclink('link-229', 'compile', 'link-21');">compile</a></tt><tt class="py-op">(</tt><tt class="py-string">r'^ (<a[^>]*></a>)*Score'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L450"></a><tt class="py-lineno">450</tt> <tt class="py-line"> <tt id="link-230" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-230', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-231" class="py-name" targets="Method Bio.Blast.NCBIStandalone._HSPConsumer.identities()=Bio.Blast.NCBIStandalone._HSPConsumer-class.html#identities,Variable Bio.expressions.blast.wublast.identities=Bio.expressions.blast.wublast-module.html#identities"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.identities
Bio.expressions.blast.wublast.identities" class="py-name" href="#" onclick="return doclink('link-231', 'identities', 'link-231');">identities</a></tt><tt class="py-op">,</tt> <tt id="link-232" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-232', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">' Identities'</tt><tt class="py-op">)</tt> </tt>
<a name="L451"></a><tt class="py-lineno">451</tt> <tt class="py-line"> <tt class="py-comment"># BLASTN</tt> </tt>
<a name="L452"></a><tt class="py-lineno">452</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-233" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-233', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-234" class="py-name" targets="Method Bio.Blast.NCBIStandalone._HSPConsumer.strand()=Bio.Blast.NCBIStandalone._HSPConsumer-class.html#strand,Variable Bio.expressions.blast.ncbiblast.strand=Bio.expressions.blast.ncbiblast-module.html#strand"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.strand
Bio.expressions.blast.ncbiblast.strand" class="py-name" href="#" onclick="return doclink('link-234', 'strand', 'link-234');">strand</a></tt><tt class="py-op">,</tt> <tt id="link-235" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-235', 'start', 'link-42');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-string">' Strand'</tt><tt class="py-op">)</tt> </tt>
<a name="L453"></a><tt class="py-lineno">453</tt> <tt class="py-line"> <tt class="py-comment"># BLASTX, TBLASTN, TBLASTX</tt> </tt>
<a name="L454"></a><tt class="py-lineno">454</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-236" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-236', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-237" class="py-name" targets="Method Bio.Blast.NCBIStandalone._HSPConsumer.frame()=Bio.Blast.NCBIStandalone._HSPConsumer-class.html#frame,Variable Bio.expressions.blast.ncbiblast.frame=Bio.expressions.blast.ncbiblast-module.html#frame"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.frame
Bio.expressions.blast.ncbiblast.frame" class="py-name" href="#" onclick="return doclink('link-237', 'frame', 'link-237');">frame</a></tt><tt class="py-op">,</tt> <tt id="link-238" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-238', 'start', 'link-42');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-string">' Frame'</tt><tt class="py-op">)</tt> </tt>
<a name="L455"></a><tt class="py-lineno">455</tt> <tt class="py-line"> <tt id="link-239" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-239', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-240" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-240', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-241" class="py-name"><a title="Bio.MetaTool.metatool_format.blank" class="py-name" href="#" onclick="return doclink('link-241', 'blank', 'link-35');">blank</a></tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
</div><a name="L456"></a><tt class="py-lineno">456</tt> <tt class="py-line"> </tt>
<a name="_Scanner._scan_hsp_alignment"></a><div id="_Scanner._scan_hsp_alignment-def"><a name="L457"></a><tt class="py-lineno">457</tt> <a class="py-toggle" href="#" id="_Scanner._scan_hsp_alignment-toggle" onclick="return toggle('_Scanner._scan_hsp_alignment');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIWWW._Scanner-class.html#_scan_hsp_alignment">_scan_hsp_alignment</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">uhandle</tt><tt class="py-op">,</tt> <tt class="py-param">consumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Scanner._scan_hsp_alignment-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Scanner._scan_hsp_alignment-expanded"><a name="L458"></a><tt class="py-lineno">458</tt> <tt class="py-line"> <tt class="py-comment"># Query: 11 GRGVSACA-------TCDGFFYRNQKVAVIGGGNTAVEEALYLSNIASEVHLIHRRDGF</tt> </tt>
<a name="L459"></a><tt class="py-lineno">459</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># GRGVS+ TC Y + + V GGG+ + EE L + I R+</tt> </tt>
<a name="L460"></a><tt class="py-lineno">460</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Sbjct: 12 GRGVSSVVRRCIHKPTCKE--YAVKIIDVTGGGSFSAEEVQELREATLKEVDILRKVSG</tt> </tt>
<a name="L461"></a><tt class="py-lineno">461</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># </tt> </tt>
<a name="L462"></a><tt class="py-lineno">462</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Query: 64 AEKILIKR 71</tt> </tt>
<a name="L463"></a><tt class="py-lineno">463</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># I +K </tt> </tt>
<a name="L464"></a><tt class="py-lineno">464</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Sbjct: 70 PNIIQLKD 77</tt> </tt>
<a name="L465"></a><tt class="py-lineno">465</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># </PRE></tt> </tt>
<a name="L466"></a><tt class="py-lineno">466</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt>
<a name="L467"></a><tt class="py-lineno">467</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># </tt> </tt>
<a name="L468"></a><tt class="py-lineno">468</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L469"></a><tt class="py-lineno">469</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L470"></a><tt class="py-lineno">470</tt> <tt class="py-line"> <tt class="py-comment"># Blastn adds an extra line filled with spaces before Query</tt> </tt>
<a name="L471"></a><tt class="py-lineno">471</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-242" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-242', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-243" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-243', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-244" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-244', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">' '</tt><tt class="py-op">)</tt> </tt>
<a name="L472"></a><tt class="py-lineno">472</tt> <tt class="py-line"> <tt id="link-245" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-245', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-246" class="py-name" targets="Method Bio.Blast.NCBIStandalone._HSPConsumer.query()=Bio.Blast.NCBIStandalone._HSPConsumer-class.html#query,Function Bio.Entrez.query()=Bio.Entrez-module.html#query,Function Bio.WWW.NCBI.query()=Bio.WWW.NCBI-module.html#query"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.query
Bio.Entrez.query
Bio.WWW.NCBI.query" class="py-name" href="#" onclick="return doclink('link-246', 'query', 'link-246');">query</a></tt><tt class="py-op">,</tt> <tt id="link-247" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-247', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'Query'</tt><tt class="py-op">)</tt> </tt>
<a name="L473"></a><tt class="py-lineno">473</tt> <tt class="py-line"> <tt id="link-248" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-248', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-249" class="py-name" targets="Method Bio.Blast.NCBIStandalone._HSPConsumer.align()=Bio.Blast.NCBIStandalone._HSPConsumer-class.html#align,Class Bio.FSSP.fssp_rec.align=Bio.FSSP.fssp_rec.align-class.html,Function Bio.Wise.align()=Bio.Wise-module.html#align,Function Bio.Wise.dnal.align()=Bio.Wise.dnal-module.html#align,Function Bio.Wise.psw.align()=Bio.Wise.psw-module.html#align,Variable Bio.pairwise2.align=Bio.pairwise2-module.html#align"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.align
Bio.FSSP.fssp_rec.align
Bio.Wise.align
Bio.Wise.dnal.align
Bio.Wise.psw.align
Bio.pairwise2.align" class="py-name" href="#" onclick="return doclink('link-249', 'align', 'link-249');">align</a></tt><tt class="py-op">,</tt> <tt id="link-250" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-250', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">' '</tt><tt class="py-op">)</tt> </tt>
<a name="L474"></a><tt class="py-lineno">474</tt> <tt class="py-line"> <tt id="link-251" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-251', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-252" class="py-name" targets="Method Bio.Blast.NCBIStandalone._HSPConsumer.sbjct()=Bio.Blast.NCBIStandalone._HSPConsumer-class.html#sbjct"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.sbjct" class="py-name" href="#" onclick="return doclink('link-252', 'sbjct', 'link-252');">sbjct</a></tt><tt class="py-op">,</tt> <tt id="link-253" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-253', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'Sbjct'</tt><tt class="py-op">)</tt> </tt>
<a name="L475"></a><tt class="py-lineno">475</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-254" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-254', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-255" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-255', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-256" class="py-name"><a title="Bio.MetaTool.metatool_format.blank" class="py-name" href="#" onclick="return doclink('link-256', 'blank', 'link-35');">blank</a></tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L476"></a><tt class="py-lineno">476</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L477"></a><tt class="py-lineno">477</tt> <tt class="py-line"> <tt id="link-257" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-257', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-258" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-258', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-259" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-259', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'</PRE>'</tt><tt class="py-op">)</tt> </tt>
<a name="L478"></a><tt class="py-lineno">478</tt> <tt class="py-line"> <tt id="link-260" class="py-name"><a title="Bio.ParserSupport.read_and_call_while" class="py-name" href="#" onclick="return doclink('link-260', 'read_and_call_while', 'link-33');">read_and_call_while</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-261" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-261', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-262" class="py-name"><a title="Bio.MetaTool.metatool_format.blank" class="py-name" href="#" onclick="return doclink('link-262', 'blank', 'link-35');">blank</a></tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
</div><a name="L479"></a><tt class="py-lineno">479</tt> <tt class="py-line"> </tt>
<a name="_Scanner._scan_masterslave_alignment"></a><div id="_Scanner._scan_masterslave_alignment-def"><a name="L480"></a><tt class="py-lineno">480</tt> <a class="py-toggle" href="#" id="_Scanner._scan_masterslave_alignment-toggle" onclick="return toggle('_Scanner._scan_masterslave_alignment');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIWWW._Scanner-class.html#_scan_masterslave_alignment">_scan_masterslave_alignment</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">uhandle</tt><tt class="py-op">,</tt> <tt class="py-param">consumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Scanner._scan_masterslave_alignment-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Scanner._scan_masterslave_alignment-expanded"><a name="L481"></a><tt class="py-lineno">481</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-263" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.start_alignment" class="py-name" href="#" onclick="return doclink('link-263', 'start_alignment', 'link-185');">start_alignment</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L482"></a><tt class="py-lineno">482</tt> <tt class="py-line"> <tt id="link-264" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-264', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-265" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-265', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-266" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-266', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'<PRE>'</tt><tt class="py-op">)</tt> </tt>
<a name="L483"></a><tt class="py-lineno">483</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L484"></a><tt class="py-lineno">484</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt id="link-267" class="py-name"><a title="Bio.ParserSupport.safe_readline" class="py-name" href="#" onclick="return doclink('link-267', 'safe_readline', 'link-167');">safe_readline</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">)</tt> </tt>
<a name="L485"></a><tt class="py-lineno">485</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-268" class="py-name"><a title="Bio.ParserSupport.is_blank_line" class="py-name" href="#" onclick="return doclink('link-268', 'is_blank_line', 'link-59');">is_blank_line</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L486"></a><tt class="py-lineno">486</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-269" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-269', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L487"></a><tt class="py-lineno">487</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">6</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'</PRE>'</tt><tt class="py-op">:</tt> </tt>
<a name="L488"></a><tt class="py-lineno">488</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-270" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-270', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L489"></a><tt class="py-lineno">489</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L490"></a><tt class="py-lineno">490</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L491"></a><tt class="py-lineno">491</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-271" class="py-name" targets="Method Bio.Blast.NCBIStandalone._AlignmentConsumer.multalign()=Bio.Blast.NCBIStandalone._AlignmentConsumer-class.html#multalign"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.multalign" class="py-name" href="#" onclick="return doclink('link-271', 'multalign', 'link-271');">multalign</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L492"></a><tt class="py-lineno">492</tt> <tt class="py-line"> <tt id="link-272" class="py-name"><a title="Bio.ParserSupport.read_and_call_while" class="py-name" href="#" onclick="return doclink('link-272', 'read_and_call_while', 'link-33');">read_and_call_while</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-273" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-273', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-274" class="py-name"><a title="Bio.MetaTool.metatool_format.blank" class="py-name" href="#" onclick="return doclink('link-274', 'blank', 'link-35');">blank</a></tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L493"></a><tt class="py-lineno">493</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-275" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.end_alignment
Bio.Blast.NCBIStandalone._BlastConsumer.end_alignment
Bio.Blast.NCBIStandalone._PSIBlastConsumer.end_alignment" class="py-name" href="#" onclick="return doclink('link-275', 'end_alignment', 'link-192');">end_alignment</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L494"></a><tt class="py-lineno">494</tt> <tt class="py-line"> </tt>
<a name="_Scanner._scan_database_report"></a><div id="_Scanner._scan_database_report-def"><a name="L495"></a><tt class="py-lineno">495</tt> <a class="py-toggle" href="#" id="_Scanner._scan_database_report-toggle" onclick="return toggle('_Scanner._scan_database_report');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIWWW._Scanner-class.html#_scan_database_report">_scan_database_report</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">uhandle</tt><tt class="py-op">,</tt> <tt class="py-param">consumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Scanner._scan_database_report-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Scanner._scan_database_report-expanded"><a name="L496"></a><tt class="py-lineno">496</tt> <tt class="py-line"> <tt class="py-comment"># <PRE></tt> </tt>
<a name="L497"></a><tt class="py-lineno">497</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Database: Non-redundant SwissProt sequences</tt> </tt>
<a name="L498"></a><tt class="py-lineno">498</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Posted date: Dec 18, 1999 8:26 PM</tt> </tt>
<a name="L499"></a><tt class="py-lineno">499</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Number of letters in database: 29,652,561</tt> </tt>
<a name="L500"></a><tt class="py-lineno">500</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Number of sequences in database: 82,258</tt> </tt>
<a name="L501"></a><tt class="py-lineno">501</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># </tt> </tt>
<a name="L502"></a><tt class="py-lineno">502</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Lambda K H</tt> </tt>
<a name="L503"></a><tt class="py-lineno">503</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># 0.317 0.133 0.395 </tt> </tt>
<a name="L504"></a><tt class="py-lineno">504</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># </tt> </tt>
<a name="L505"></a><tt class="py-lineno">505</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Gapped</tt> </tt>
<a name="L506"></a><tt class="py-lineno">506</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Lambda K H</tt> </tt>
<a name="L507"></a><tt class="py-lineno">507</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># 0.270 0.0470 0.230 </tt> </tt>
<a name="L508"></a><tt class="py-lineno">508</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># </tt> </tt>
<a name="L509"></a><tt class="py-lineno">509</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L510"></a><tt class="py-lineno">510</tt> <tt class="py-line"> <tt class="py-comment"># qblast (BLASTN 2.2.10) does not give the Database: bits before the Lambda</tt> </tt>
<a name="L511"></a><tt class="py-lineno">511</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># information, so that needs to be skipped</tt> </tt>
<a name="L512"></a><tt class="py-lineno">512</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L513"></a><tt class="py-lineno">513</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-276" class="py-name" targets="Method Bio.Blast.NCBIStandalone._DatabaseReportConsumer.start_database_report()=Bio.Blast.NCBIStandalone._DatabaseReportConsumer-class.html#start_database_report"><a title="Bio.Blast.NCBIStandalone._DatabaseReportConsumer.start_database_report" class="py-name" href="#" onclick="return doclink('link-276', 'start_database_report', 'link-276');">start_database_report</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L514"></a><tt class="py-lineno">514</tt> <tt class="py-line"> </tt>
<a name="L515"></a><tt class="py-lineno">515</tt> <tt class="py-line"> <tt class="py-comment"># TBALSTN 2.2.6</tt> </tt>
<a name="L516"></a><tt class="py-lineno">516</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <PRE> Database: /tmp/affyA.fasta</tt> </tt>
<a name="L517"></a><tt class="py-lineno">517</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">uhandle</tt><tt class="py-op">.</tt><tt id="link-277" class="py-name"><a title="Bio.File.UndoHandle.peekline" class="py-name" href="#" onclick="return doclink('link-277', 'peekline', 'link-26');">peekline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L518"></a><tt class="py-lineno">518</tt> <tt class="py-line"> <tt class="py-comment"># only look for database information if we aren't already at the</tt> </tt>
<a name="L519"></a><tt class="py-lineno">519</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Lambda bits</tt> </tt>
<a name="L520"></a><tt class="py-lineno">520</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-278" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-278', 'find', 'link-46');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">"Database"</tt><tt class="py-op">)</tt> <tt class="py-op"><</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L521"></a><tt class="py-lineno">521</tt> <tt class="py-line"> <tt id="link-279" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-279', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-280" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-280', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-281" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-281', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'<PRE>'</tt><tt class="py-op">)</tt> </tt>
<a name="L522"></a><tt class="py-lineno">522</tt> <tt class="py-line"> <tt class="py-name">line2</tt> <tt class="py-op">=</tt> <tt class="py-name">uhandle</tt><tt class="py-op">.</tt><tt id="link-282" class="py-name"><a title="Bio.File.UndoHandle.peekline" class="py-name" href="#" onclick="return doclink('link-282', 'peekline', 'link-26');">peekline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L523"></a><tt class="py-lineno">523</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line2</tt><tt class="py-op">.</tt><tt id="link-283" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-283', 'find', 'link-46');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">"Lambda K H"</tt><tt class="py-op">)</tt> <tt class="py-op"><</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L524"></a><tt class="py-lineno">524</tt> <tt class="py-line"> <tt id="link-284" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-284', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-285" class="py-name" targets="Method Bio.Blast.NCBIStandalone._DatabaseReportConsumer.database()=Bio.Blast.NCBIStandalone._DatabaseReportConsumer-class.html#database"><a title="Bio.Blast.NCBIStandalone._DatabaseReportConsumer.database" class="py-name" href="#" onclick="return doclink('link-285', 'database', 'link-285');">database</a></tt><tt class="py-op">,</tt> <tt id="link-286" class="py-name"><a title="Bio.Alphabet.Alphabet.contains
Bio.Alphabet.AlphabetEncoder.contains
Bio.Alphabet.Gapped.contains
Bio.Alphabet.HasStopCodon.contains
Bio.Pathway.Rep.HashSet.HashSet.contains
Bio.biblio.Biblio.contains" class="py-name" href="#" onclick="return doclink('link-286', 'contains', 'link-32');">contains</a></tt><tt class="py-op">=</tt><tt class="py-string">' Database'</tt><tt class="py-op">)</tt> </tt>
<a name="L525"></a><tt class="py-lineno">525</tt> <tt class="py-line"> <tt id="link-287" class="py-name"><a title="Bio.ParserSupport.read_and_call_until" class="py-name" href="#" onclick="return doclink('link-287', 'read_and_call_until', 'link-19');">read_and_call_until</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-288" class="py-name"><a title="Bio.Blast.NCBIStandalone._DatabaseReportConsumer.database" class="py-name" href="#" onclick="return doclink('link-288', 'database', 'link-285');">database</a></tt><tt class="py-op">,</tt> <tt id="link-289" class="py-name"><a title="Bio.Alphabet.Alphabet.contains
Bio.Alphabet.AlphabetEncoder.contains
Bio.Alphabet.Gapped.contains
Bio.Alphabet.HasStopCodon.contains
Bio.Pathway.Rep.HashSet.HashSet.contains
Bio.biblio.Biblio.contains" class="py-name" href="#" onclick="return doclink('link-289', 'contains', 'link-32');">contains</a></tt><tt class="py-op">=</tt><tt class="py-string">"Posted"</tt><tt class="py-op">)</tt> </tt>
<a name="L526"></a><tt class="py-lineno">526</tt> <tt class="py-line"> <tt id="link-290" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-290', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-291" class="py-name" targets="Method Bio.Blast.NCBIStandalone._DatabaseReportConsumer.posted_date()=Bio.Blast.NCBIStandalone._DatabaseReportConsumer-class.html#posted_date"><a title="Bio.Blast.NCBIStandalone._DatabaseReportConsumer.posted_date" class="py-name" href="#" onclick="return doclink('link-291', 'posted_date', 'link-291');">posted_date</a></tt><tt class="py-op">,</tt> <tt id="link-292" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-292', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">' Posted'</tt><tt class="py-op">)</tt> </tt>
<a name="L527"></a><tt class="py-lineno">527</tt> <tt class="py-line"> <tt id="link-293" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-293', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-294" class="py-name" targets="Method Bio.Blast.NCBIStandalone._DatabaseReportConsumer.num_letters_in_database()=Bio.Blast.NCBIStandalone._DatabaseReportConsumer-class.html#num_letters_in_database"><a title="Bio.Blast.NCBIStandalone._DatabaseReportConsumer.num_letters_in_database" class="py-name" href="#" onclick="return doclink('link-294', 'num_letters_in_database', 'link-294');">num_letters_in_database</a></tt><tt class="py-op">,</tt> </tt>
<a name="L528"></a><tt class="py-lineno">528</tt> <tt class="py-line"> <tt id="link-295" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-295', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">' Number of letters'</tt><tt class="py-op">)</tt> </tt>
<a name="L529"></a><tt class="py-lineno">529</tt> <tt class="py-line"> <tt id="link-296" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-296', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-297" class="py-name" targets="Method Bio.Blast.NCBIStandalone._DatabaseReportConsumer.num_sequences_in_database()=Bio.Blast.NCBIStandalone._DatabaseReportConsumer-class.html#num_sequences_in_database"><a title="Bio.Blast.NCBIStandalone._DatabaseReportConsumer.num_sequences_in_database" class="py-name" href="#" onclick="return doclink('link-297', 'num_sequences_in_database', 'link-297');">num_sequences_in_database</a></tt><tt class="py-op">,</tt> </tt>
<a name="L530"></a><tt class="py-lineno">530</tt> <tt class="py-line"> <tt id="link-298" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-298', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">' Number of sequences'</tt><tt class="py-op">)</tt> </tt>
<a name="L531"></a><tt class="py-lineno">531</tt> <tt class="py-line"> <tt id="link-299" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-299', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-300" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-300', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-301" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-301', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">' '</tt><tt class="py-op">)</tt> </tt>
<a name="L532"></a><tt class="py-lineno">532</tt> <tt class="py-line"> </tt>
<a name="L533"></a><tt class="py-lineno">533</tt> <tt class="py-line"> <tt id="link-302" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-302', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-303" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-303', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-304" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-304', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'Lambda'</tt><tt class="py-op">)</tt> </tt>
<a name="L534"></a><tt class="py-lineno">534</tt> <tt class="py-line"> <tt id="link-305" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-305', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-306" class="py-name" targets="Method Bio.Blast.NCBIStandalone._DatabaseReportConsumer.ka_params()=Bio.Blast.NCBIStandalone._DatabaseReportConsumer-class.html#ka_params"><a title="Bio.Blast.NCBIStandalone._DatabaseReportConsumer.ka_params" class="py-name" href="#" onclick="return doclink('link-306', 'ka_params', 'link-306');">ka_params</a></tt><tt class="py-op">)</tt> </tt>
<a name="L535"></a><tt class="py-lineno">535</tt> <tt class="py-line"> <tt id="link-307" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-307', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-308" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-308', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-309" class="py-name"><a title="Bio.MetaTool.metatool_format.blank" class="py-name" href="#" onclick="return doclink('link-309', 'blank', 'link-35');">blank</a></tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L536"></a><tt class="py-lineno">536</tt> <tt class="py-line"> </tt>
<a name="L537"></a><tt class="py-lineno">537</tt> <tt class="py-line"> <tt class="py-comment"># not BLASTP</tt> </tt>
<a name="L538"></a><tt class="py-lineno">538</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-310" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-310', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-311" class="py-name" targets="Method Bio.Blast.NCBIStandalone._DatabaseReportConsumer.gapped()=Bio.Blast.NCBIStandalone._DatabaseReportConsumer-class.html#gapped"><a title="Bio.Blast.NCBIStandalone._DatabaseReportConsumer.gapped" class="py-name" href="#" onclick="return doclink('link-311', 'gapped', 'link-311');">gapped</a></tt><tt class="py-op">,</tt> <tt id="link-312" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-312', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'Gapped'</tt><tt class="py-op">)</tt> </tt>
<a name="L539"></a><tt class="py-lineno">539</tt> <tt class="py-line"> <tt class="py-comment"># not TBLASTX</tt> </tt>
<a name="L540"></a><tt class="py-lineno">540</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt id="link-313" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-313', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-314" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-314', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-315" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-315', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'Lambda'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L541"></a><tt class="py-lineno">541</tt> <tt class="py-line"> <tt id="link-316" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-316', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-317" class="py-name" targets="Method Bio.Blast.NCBIStandalone._DatabaseReportConsumer.ka_params_gap()=Bio.Blast.NCBIStandalone._DatabaseReportConsumer-class.html#ka_params_gap"><a title="Bio.Blast.NCBIStandalone._DatabaseReportConsumer.ka_params_gap" class="py-name" href="#" onclick="return doclink('link-317', 'ka_params_gap', 'link-317');">ka_params_gap</a></tt><tt class="py-op">)</tt> </tt>
<a name="L542"></a><tt class="py-lineno">542</tt> <tt class="py-line"> <tt id="link-318" class="py-name"><a title="Bio.ParserSupport.read_and_call_while" class="py-name" href="#" onclick="return doclink('link-318', 'read_and_call_while', 'link-33');">read_and_call_while</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-319" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-319', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-320" class="py-name"><a title="Bio.MetaTool.metatool_format.blank" class="py-name" href="#" onclick="return doclink('link-320', 'blank', 'link-35');">blank</a></tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L543"></a><tt class="py-lineno">543</tt> <tt class="py-line"> </tt>
<a name="L544"></a><tt class="py-lineno">544</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-321" class="py-name" targets="Method Bio.Blast.NCBIStandalone._BlastConsumer.end_database_report()=Bio.Blast.NCBIStandalone._BlastConsumer-class.html#end_database_report,Method Bio.Blast.NCBIStandalone._DatabaseReportConsumer.end_database_report()=Bio.Blast.NCBIStandalone._DatabaseReportConsumer-class.html#end_database_report,Method Bio.Blast.NCBIStandalone._PSIBlastConsumer.end_database_report()=Bio.Blast.NCBIStandalone._PSIBlastConsumer-class.html#end_database_report"><a title="Bio.Blast.NCBIStandalone._BlastConsumer.end_database_report
Bio.Blast.NCBIStandalone._DatabaseReportConsumer.end_database_report
Bio.Blast.NCBIStandalone._PSIBlastConsumer.end_database_report" class="py-name" href="#" onclick="return doclink('link-321', 'end_database_report', 'link-321');">end_database_report</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L545"></a><tt class="py-lineno">545</tt> <tt class="py-line"> </tt>
<a name="_Scanner._scan_parameters"></a><div id="_Scanner._scan_parameters-def"><a name="L546"></a><tt class="py-lineno">546</tt> <a class="py-toggle" href="#" id="_Scanner._scan_parameters-toggle" onclick="return toggle('_Scanner._scan_parameters');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIWWW._Scanner-class.html#_scan_parameters">_scan_parameters</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">uhandle</tt><tt class="py-op">,</tt> <tt class="py-param">consumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Scanner._scan_parameters-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Scanner._scan_parameters-expanded"><a name="L547"></a><tt class="py-lineno">547</tt> <tt class="py-line"> <tt class="py-comment"># Matrix: BLOSUM62</tt> </tt>
<a name="L548"></a><tt class="py-lineno">548</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Number of Hits to DB: 1st pass: 41542626, 2nd pass: 9765</tt> </tt>
<a name="L549"></a><tt class="py-lineno">549</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Number of Sequences: 1st pass: 89405, 2nd pass: 84</tt> </tt>
<a name="L550"></a><tt class="py-lineno">550</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Number of extensions: 1st pass: 500847, 2nd pass: 6747</tt> </tt>
<a name="L551"></a><tt class="py-lineno">551</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Number of successful extensions: 1st pass: 14, 2nd pass: 49</tt> </tt>
<a name="L552"></a><tt class="py-lineno">552</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Number of sequences better than 10.0: 20</tt> </tt>
<a name="L553"></a><tt class="py-lineno">553</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># length of query: 205</tt> </tt>
<a name="L554"></a><tt class="py-lineno">554</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># length of database: 10,955,950</tt> </tt>
<a name="L555"></a><tt class="py-lineno">555</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># effective HSP length: 46</tt> </tt>
<a name="L556"></a><tt class="py-lineno">556</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># effective length of query: 158</tt> </tt>
<a name="L557"></a><tt class="py-lineno">557</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># effective length of database: 6,843,320</tt> </tt>
<a name="L558"></a><tt class="py-lineno">558</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># effective search space: 1081244560</tt> </tt>
<a name="L559"></a><tt class="py-lineno">559</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># effective search space used: 1081244560</tt> </tt>
<a name="L560"></a><tt class="py-lineno">560</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># frameshift window, decay const: 50, 0.5</tt> </tt>
<a name="L561"></a><tt class="py-lineno">561</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># T: 13</tt> </tt>
<a name="L562"></a><tt class="py-lineno">562</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># A: 40</tt> </tt>
<a name="L563"></a><tt class="py-lineno">563</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># X1: 16 ( 7.3 bits)</tt> </tt>
<a name="L564"></a><tt class="py-lineno">564</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># X2: 0 ( 0.0 bits)</tt> </tt>
<a name="L565"></a><tt class="py-lineno">565</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># S1: 41 (21.7 bits)</tt> </tt>
<a name="L566"></a><tt class="py-lineno">566</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># S2: 52 (26.7 bits)</tt> </tt>
<a name="L567"></a><tt class="py-lineno">567</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># </tt> </tt>
<a name="L568"></a><tt class="py-lineno">568</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># </PRE></tt> </tt>
<a name="L569"></a><tt class="py-lineno">569</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L570"></a><tt class="py-lineno">570</tt> <tt class="py-line"> <tt class="py-comment"># 6/3/2001, </PRE> is gone, replaced by </form></tt> </tt>
<a name="L571"></a><tt class="py-lineno">571</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L572"></a><tt class="py-lineno">572</tt> <tt class="py-line"> </tt>
<a name="L573"></a><tt class="py-lineno">573</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-322" class="py-name" targets="Method Bio.Blast.NCBIStandalone._ParametersConsumer.start_parameters()=Bio.Blast.NCBIStandalone._ParametersConsumer-class.html#start_parameters"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.start_parameters" class="py-name" href="#" onclick="return doclink('link-322', 'start_parameters', 'link-322');">start_parameters</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L574"></a><tt class="py-lineno">574</tt> <tt class="py-line"> </tt>
<a name="L575"></a><tt class="py-lineno">575</tt> <tt class="py-line"> <tt class="py-comment"># qblast doesn't have Matrix line</tt> </tt>
<a name="L576"></a><tt class="py-lineno">576</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-323" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-323', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-324" class="py-name" targets="Method Bio.Blast.NCBIStandalone._ParametersConsumer.matrix()=Bio.Blast.NCBIStandalone._ParametersConsumer-class.html#matrix,Variable Bio.MetaTool.metatool_format.matrix=Bio.MetaTool.metatool_format-module.html#matrix,Method Bio.Prosite._RecordConsumer.matrix()=Bio.Prosite._RecordConsumer-class.html#matrix"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.matrix
Bio.MetaTool.metatool_format.matrix
Bio.Prosite._RecordConsumer.matrix" class="py-name" href="#" onclick="return doclink('link-324', 'matrix', 'link-324');">matrix</a></tt><tt class="py-op">,</tt> <tt id="link-325" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-325', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'Matrix'</tt><tt class="py-op">)</tt> </tt>
<a name="L577"></a><tt class="py-lineno">577</tt> <tt class="py-line"> <tt class="py-comment"># not TBLASTX</tt> </tt>
<a name="L578"></a><tt class="py-lineno">578</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-326" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-326', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-327" class="py-name" targets="Method Bio.Blast.NCBIStandalone._ParametersConsumer.gap_penalties()=Bio.Blast.NCBIStandalone._ParametersConsumer-class.html#gap_penalties"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.gap_penalties" class="py-name" href="#" onclick="return doclink('link-327', 'gap_penalties', 'link-327');">gap_penalties</a></tt><tt class="py-op">,</tt> <tt id="link-328" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-328', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'Gap'</tt><tt class="py-op">)</tt> </tt>
<a name="L579"></a><tt class="py-lineno">579</tt> <tt class="py-line"> </tt>
<a name="L580"></a><tt class="py-lineno">580</tt> <tt class="py-line"> <tt class="py-comment"># in qblast the Number of Hits and Number of Sequences lines are</tt> </tt>
<a name="L581"></a><tt class="py-lineno">581</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># reversed</tt> </tt>
<a name="L582"></a><tt class="py-lineno">582</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt id="link-329" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-329', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-330" class="py-name" targets="Method Bio.Blast.NCBIStandalone._ParametersConsumer.num_hits()=Bio.Blast.NCBIStandalone._ParametersConsumer-class.html#num_hits"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.num_hits" class="py-name" href="#" onclick="return doclink('link-330', 'num_hits', 'link-330');">num_hits</a></tt><tt class="py-op">,</tt> </tt>
<a name="L583"></a><tt class="py-lineno">583</tt> <tt class="py-line"> <tt id="link-331" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-331', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'Number of Hits'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L584"></a><tt class="py-lineno">584</tt> <tt class="py-line"> <tt id="link-332" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-332', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-333" class="py-name" targets="Method Bio.Blast.NCBIStandalone._ParametersConsumer.num_sequences()=Bio.Blast.NCBIStandalone._ParametersConsumer-class.html#num_sequences"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.num_sequences" class="py-name" href="#" onclick="return doclink('link-333', 'num_sequences', 'link-333');">num_sequences</a></tt><tt class="py-op">,</tt> </tt>
<a name="L585"></a><tt class="py-lineno">585</tt> <tt class="py-line"> <tt id="link-334" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-334', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'Number of Sequences'</tt><tt class="py-op">)</tt> </tt>
<a name="L586"></a><tt class="py-lineno">586</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L587"></a><tt class="py-lineno">587</tt> <tt class="py-line"> <tt id="link-335" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-335', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-336" class="py-name"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.num_sequences" class="py-name" href="#" onclick="return doclink('link-336', 'num_sequences', 'link-333');">num_sequences</a></tt><tt class="py-op">,</tt> </tt>
<a name="L588"></a><tt class="py-lineno">588</tt> <tt class="py-line"> <tt id="link-337" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-337', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'Number of Sequences'</tt><tt class="py-op">)</tt> </tt>
<a name="L589"></a><tt class="py-lineno">589</tt> <tt class="py-line"> <tt id="link-338" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-338', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-339" class="py-name"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.num_hits" class="py-name" href="#" onclick="return doclink('link-339', 'num_hits', 'link-330');">num_hits</a></tt><tt class="py-op">,</tt> </tt>
<a name="L590"></a><tt class="py-lineno">590</tt> <tt class="py-line"> <tt id="link-340" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-340', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'Number of Hits'</tt><tt class="py-op">)</tt> </tt>
<a name="L591"></a><tt class="py-lineno">591</tt> <tt class="py-line"> </tt>
<a name="L592"></a><tt class="py-lineno">592</tt> <tt class="py-line"> <tt id="link-341" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-341', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-342" class="py-name" targets="Method Bio.Blast.NCBIStandalone._ParametersConsumer.num_extends()=Bio.Blast.NCBIStandalone._ParametersConsumer-class.html#num_extends"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.num_extends" class="py-name" href="#" onclick="return doclink('link-342', 'num_extends', 'link-342');">num_extends</a></tt><tt class="py-op">,</tt> </tt>
<a name="L593"></a><tt class="py-lineno">593</tt> <tt class="py-line"> <tt id="link-343" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-343', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'Number of extensions'</tt><tt class="py-op">)</tt> </tt>
<a name="L594"></a><tt class="py-lineno">594</tt> <tt class="py-line"> <tt id="link-344" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-344', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-345" class="py-name" targets="Method Bio.Blast.NCBIStandalone._ParametersConsumer.num_good_extends()=Bio.Blast.NCBIStandalone._ParametersConsumer-class.html#num_good_extends"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.num_good_extends" class="py-name" href="#" onclick="return doclink('link-345', 'num_good_extends', 'link-345');">num_good_extends</a></tt><tt class="py-op">,</tt> </tt>
<a name="L595"></a><tt class="py-lineno">595</tt> <tt class="py-line"> <tt id="link-346" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-346', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'Number of successful'</tt><tt class="py-op">)</tt> </tt>
<a name="L596"></a><tt class="py-lineno">596</tt> <tt class="py-line"> </tt>
<a name="L597"></a><tt class="py-lineno">597</tt> <tt class="py-line"> <tt id="link-347" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-347', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-348" class="py-name" targets="Method Bio.Blast.NCBIStandalone._ParametersConsumer.num_seqs_better_e()=Bio.Blast.NCBIStandalone._ParametersConsumer-class.html#num_seqs_better_e"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.num_seqs_better_e" class="py-name" href="#" onclick="return doclink('link-348', 'num_seqs_better_e', 'link-348');">num_seqs_better_e</a></tt><tt class="py-op">,</tt> </tt>
<a name="L598"></a><tt class="py-lineno">598</tt> <tt class="py-line"> <tt id="link-349" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-349', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'Number of sequences'</tt><tt class="py-op">)</tt> </tt>
<a name="L599"></a><tt class="py-lineno">599</tt> <tt class="py-line"> </tt>
<a name="L600"></a><tt class="py-lineno">600</tt> <tt class="py-line"> <tt class="py-comment"># not BLASTN, TBLASTX</tt> </tt>
<a name="L601"></a><tt class="py-lineno">601</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt id="link-350" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-350', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-351" class="py-name" targets="Method Bio.Blast.NCBIStandalone._ParametersConsumer.hsps_no_gap()=Bio.Blast.NCBIStandalone._ParametersConsumer-class.html#hsps_no_gap"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.hsps_no_gap" class="py-name" href="#" onclick="return doclink('link-351', 'hsps_no_gap', 'link-351');">hsps_no_gap</a></tt><tt class="py-op">,</tt> </tt>
<a name="L602"></a><tt class="py-lineno">602</tt> <tt class="py-line"> <tt id="link-352" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-352', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">"Number of HSP's better"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L603"></a><tt class="py-lineno">603</tt> <tt class="py-line"> <tt class="py-comment"># for qblast order of HSP info is changed</tt> </tt>
<a name="L604"></a><tt class="py-lineno">604</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt id="link-353" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-353', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-354" class="py-name" targets="Method Bio.Blast.NCBIStandalone._ParametersConsumer.hsps_prelim_gapped()=Bio.Blast.NCBIStandalone._ParametersConsumer-class.html#hsps_prelim_gapped"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.hsps_prelim_gapped" class="py-name" href="#" onclick="return doclink('link-354', 'hsps_prelim_gapped', 'link-354');">hsps_prelim_gapped</a></tt><tt class="py-op">,</tt> </tt>
<a name="L605"></a><tt class="py-lineno">605</tt> <tt class="py-line"> <tt id="link-355" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-355', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">"Number of HSP's successfully"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L606"></a><tt class="py-lineno">606</tt> <tt class="py-line"> <tt id="link-356" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-356', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt class="py-name">hsps_prelim_gap_attempted</tt><tt class="py-op">,</tt> </tt>
<a name="L607"></a><tt class="py-lineno">607</tt> <tt class="py-line"> <tt id="link-357" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-357', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">"Number of HSP's that"</tt><tt class="py-op">)</tt> </tt>
<a name="L608"></a><tt class="py-lineno">608</tt> <tt class="py-line"> <tt id="link-358" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-358', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-359" class="py-name" targets="Method Bio.Blast.NCBIStandalone._ParametersConsumer.hsps_gapped()=Bio.Blast.NCBIStandalone._ParametersConsumer-class.html#hsps_gapped"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.hsps_gapped" class="py-name" href="#" onclick="return doclink('link-359', 'hsps_gapped', 'link-359');">hsps_gapped</a></tt><tt class="py-op">,</tt> </tt>
<a name="L609"></a><tt class="py-lineno">609</tt> <tt class="py-line"> <tt id="link-360" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-360', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">"Number of HSP's gapped"</tt><tt class="py-op">)</tt> </tt>
<a name="L610"></a><tt class="py-lineno">610</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L611"></a><tt class="py-lineno">611</tt> <tt class="py-line"> <tt id="link-361" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-361', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt class="py-name">no_event</tt><tt class="py-op">,</tt> </tt>
<a name="L612"></a><tt class="py-lineno">612</tt> <tt class="py-line"> <tt id="link-362" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-362', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">"Number of HSP's gapped"</tt><tt class="py-op">)</tt> </tt>
<a name="L613"></a><tt class="py-lineno">613</tt> <tt class="py-line"> <tt id="link-363" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-363', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt class="py-name">no_event</tt><tt class="py-op">,</tt> </tt>
<a name="L614"></a><tt class="py-lineno">614</tt> <tt class="py-line"> <tt id="link-364" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-364', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">"Number of HSP's successfully"</tt><tt class="py-op">)</tt> </tt>
<a name="L615"></a><tt class="py-lineno">615</tt> <tt class="py-line"> <tt id="link-365" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-365', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt class="py-name">no_event</tt><tt class="py-op">,</tt> </tt>
<a name="L616"></a><tt class="py-lineno">616</tt> <tt class="py-line"> <tt id="link-366" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-366', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">"Number of extra gapped"</tt><tt class="py-op">)</tt> </tt>
<a name="L617"></a><tt class="py-lineno">617</tt> <tt class="py-line"> </tt>
<a name="L618"></a><tt class="py-lineno">618</tt> <tt class="py-line"> <tt class="py-comment"># QBlast has different capitalization on the Length info:</tt> </tt>
<a name="L619"></a><tt class="py-lineno">619</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt id="link-367" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-367', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-368" class="py-name" targets="Method Bio.Blast.NCBIStandalone._ParametersConsumer.query_length()=Bio.Blast.NCBIStandalone._ParametersConsumer-class.html#query_length"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.query_length" class="py-name" href="#" onclick="return doclink('link-368', 'query_length', 'link-368');">query_length</a></tt><tt class="py-op">,</tt> </tt>
<a name="L620"></a><tt class="py-lineno">620</tt> <tt class="py-line"> <tt id="link-369" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-369', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'Length of query'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L621"></a><tt class="py-lineno">621</tt> <tt class="py-line"> <tt id="link-370" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-370', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-371" class="py-name" targets="Method Bio.Blast.NCBIStandalone._ParametersConsumer.database_length()=Bio.Blast.NCBIStandalone._ParametersConsumer-class.html#database_length"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.database_length" class="py-name" href="#" onclick="return doclink('link-371', 'database_length', 'link-371');">database_length</a></tt><tt class="py-op">,</tt> </tt>
<a name="L622"></a><tt class="py-lineno">622</tt> <tt class="py-line"> <tt id="link-372" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-372', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'Length of database'</tt><tt class="py-op">)</tt> </tt>
<a name="L623"></a><tt class="py-lineno">623</tt> <tt class="py-line"> <tt id="link-373" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-373', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt class="py-name">no_event</tt><tt class="py-op">,</tt> </tt>
<a name="L624"></a><tt class="py-lineno">624</tt> <tt class="py-line"> <tt id="link-374" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-374', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'Length adjustment'</tt><tt class="py-op">)</tt> </tt>
<a name="L625"></a><tt class="py-lineno">625</tt> <tt class="py-line"> <tt id="link-375" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-375', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-376" class="py-name" targets="Method Bio.Blast.NCBIStandalone._ParametersConsumer.effective_query_length()=Bio.Blast.NCBIStandalone._ParametersConsumer-class.html#effective_query_length"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.effective_query_length" class="py-name" href="#" onclick="return doclink('link-376', 'effective_query_length', 'link-376');">effective_query_length</a></tt><tt class="py-op">,</tt> </tt>
<a name="L626"></a><tt class="py-lineno">626</tt> <tt class="py-line"> <tt id="link-377" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-377', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'Effective length of query'</tt><tt class="py-op">)</tt> </tt>
<a name="L627"></a><tt class="py-lineno">627</tt> <tt class="py-line"> <tt id="link-378" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-378', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-379" class="py-name" targets="Method Bio.Blast.NCBIStandalone._ParametersConsumer.effective_database_length()=Bio.Blast.NCBIStandalone._ParametersConsumer-class.html#effective_database_length"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.effective_database_length" class="py-name" href="#" onclick="return doclink('link-379', 'effective_database_length', 'link-379');">effective_database_length</a></tt><tt class="py-op">,</tt> </tt>
<a name="L628"></a><tt class="py-lineno">628</tt> <tt class="py-line"> <tt id="link-380" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-380', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'Effective length of database'</tt><tt class="py-op">)</tt> </tt>
<a name="L629"></a><tt class="py-lineno">629</tt> <tt class="py-line"> <tt id="link-381" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-381', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-382" class="py-name" targets="Method Bio.Blast.NCBIStandalone._ParametersConsumer.effective_search_space()=Bio.Blast.NCBIStandalone._ParametersConsumer-class.html#effective_search_space"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.effective_search_space" class="py-name" href="#" onclick="return doclink('link-382', 'effective_search_space', 'link-382');">effective_search_space</a></tt><tt class="py-op">,</tt> </tt>
<a name="L630"></a><tt class="py-lineno">630</tt> <tt class="py-line"> <tt id="link-383" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-383', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'Effective search space:'</tt><tt class="py-op">)</tt> </tt>
<a name="L631"></a><tt class="py-lineno">631</tt> <tt class="py-line"> <tt id="link-384" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-384', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-385" class="py-name" targets="Method Bio.Blast.NCBIStandalone._ParametersConsumer.effective_search_space_used()=Bio.Blast.NCBIStandalone._ParametersConsumer-class.html#effective_search_space_used"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.effective_search_space_used" class="py-name" href="#" onclick="return doclink('link-385', 'effective_search_space_used', 'link-385');">effective_search_space_used</a></tt><tt class="py-op">,</tt> </tt>
<a name="L632"></a><tt class="py-lineno">632</tt> <tt class="py-line"> <tt id="link-386" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-386', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'Effective search space used'</tt><tt class="py-op">)</tt> </tt>
<a name="L633"></a><tt class="py-lineno">633</tt> <tt class="py-line"> </tt>
<a name="L634"></a><tt class="py-lineno">634</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L635"></a><tt class="py-lineno">635</tt> <tt class="py-line"> <tt id="link-387" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-387', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-388" class="py-name"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.query_length" class="py-name" href="#" onclick="return doclink('link-388', 'query_length', 'link-368');">query_length</a></tt><tt class="py-op">,</tt> </tt>
<a name="L636"></a><tt class="py-lineno">636</tt> <tt class="py-line"> <tt id="link-389" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-389', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'length of query'</tt><tt class="py-op">)</tt> </tt>
<a name="L637"></a><tt class="py-lineno">637</tt> <tt class="py-line"> <tt id="link-390" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-390', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-391" class="py-name"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.database_length" class="py-name" href="#" onclick="return doclink('link-391', 'database_length', 'link-371');">database_length</a></tt><tt class="py-op">,</tt> </tt>
<a name="L638"></a><tt class="py-lineno">638</tt> <tt class="py-line"> <tt id="link-392" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-392', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'length of database'</tt><tt class="py-op">)</tt> </tt>
<a name="L639"></a><tt class="py-lineno">639</tt> <tt class="py-line"> <tt id="link-393" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-393', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-394" class="py-name" targets="Method Bio.Blast.NCBIStandalone._ParametersConsumer.effective_hsp_length()=Bio.Blast.NCBIStandalone._ParametersConsumer-class.html#effective_hsp_length"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.effective_hsp_length" class="py-name" href="#" onclick="return doclink('link-394', 'effective_hsp_length', 'link-394');">effective_hsp_length</a></tt><tt class="py-op">,</tt> </tt>
<a name="L640"></a><tt class="py-lineno">640</tt> <tt class="py-line"> <tt id="link-395" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-395', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'effective HSP'</tt><tt class="py-op">)</tt> </tt>
<a name="L641"></a><tt class="py-lineno">641</tt> <tt class="py-line"> <tt id="link-396" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-396', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-397" class="py-name"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.effective_query_length" class="py-name" href="#" onclick="return doclink('link-397', 'effective_query_length', 'link-376');">effective_query_length</a></tt><tt class="py-op">,</tt> </tt>
<a name="L642"></a><tt class="py-lineno">642</tt> <tt class="py-line"> <tt id="link-398" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-398', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'effective length of query'</tt><tt class="py-op">)</tt> </tt>
<a name="L643"></a><tt class="py-lineno">643</tt> <tt class="py-line"> <tt id="link-399" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-399', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-400" class="py-name"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.effective_database_length" class="py-name" href="#" onclick="return doclink('link-400', 'effective_database_length', 'link-379');">effective_database_length</a></tt><tt class="py-op">,</tt> </tt>
<a name="L644"></a><tt class="py-lineno">644</tt> <tt class="py-line"> <tt id="link-401" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-401', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'effective length of database'</tt><tt class="py-op">)</tt> </tt>
<a name="L645"></a><tt class="py-lineno">645</tt> <tt class="py-line"> <tt id="link-402" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-402', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-403" class="py-name"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.effective_search_space" class="py-name" href="#" onclick="return doclink('link-403', 'effective_search_space', 'link-382');">effective_search_space</a></tt><tt class="py-op">,</tt> </tt>
<a name="L646"></a><tt class="py-lineno">646</tt> <tt class="py-line"> <tt id="link-404" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-404', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'effective search space:'</tt><tt class="py-op">)</tt> </tt>
<a name="L647"></a><tt class="py-lineno">647</tt> <tt class="py-line"> <tt id="link-405" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-405', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-406" class="py-name"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.effective_search_space_used" class="py-name" href="#" onclick="return doclink('link-406', 'effective_search_space_used', 'link-385');">effective_search_space_used</a></tt><tt class="py-op">,</tt> </tt>
<a name="L648"></a><tt class="py-lineno">648</tt> <tt class="py-line"> <tt id="link-407" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-407', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'effective search space used'</tt><tt class="py-op">)</tt> </tt>
<a name="L649"></a><tt class="py-lineno">649</tt> <tt class="py-line"> </tt>
<a name="L650"></a><tt class="py-lineno">650</tt> <tt class="py-line"> <tt class="py-comment"># BLASTX, TBLASTN, TBLASTX</tt> </tt>
<a name="L651"></a><tt class="py-lineno">651</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-408" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-408', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-409" class="py-name" targets="Method Bio.Blast.NCBIStandalone._ParametersConsumer.frameshift()=Bio.Blast.NCBIStandalone._ParametersConsumer-class.html#frameshift"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.frameshift" class="py-name" href="#" onclick="return doclink('link-409', 'frameshift', 'link-409');">frameshift</a></tt><tt class="py-op">,</tt> <tt id="link-410" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-410', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'frameshift'</tt><tt class="py-op">)</tt> </tt>
<a name="L652"></a><tt class="py-lineno">652</tt> <tt class="py-line"> <tt id="link-411" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-411', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-412" class="py-name" targets="Method Bio.Blast.NCBIStandalone._ParametersConsumer.threshold()=Bio.Blast.NCBIStandalone._ParametersConsumer-class.html#threshold,Method Bio.Compass._Consumer.threshold()=Bio.Compass._Consumer-class.html#threshold"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.threshold
Bio.Compass._Consumer.threshold" class="py-name" href="#" onclick="return doclink('link-412', 'threshold', 'link-412');">threshold</a></tt><tt class="py-op">,</tt> <tt id="link-413" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-413', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'T'</tt><tt class="py-op">)</tt> </tt>
<a name="L653"></a><tt class="py-lineno">653</tt> <tt class="py-line"> <tt id="link-414" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-414', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-415" class="py-name" targets="Method Bio.Blast.NCBIStandalone._ParametersConsumer.window_size()=Bio.Blast.NCBIStandalone._ParametersConsumer-class.html#window_size"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.window_size" class="py-name" href="#" onclick="return doclink('link-415', 'window_size', 'link-415');">window_size</a></tt><tt class="py-op">,</tt> <tt id="link-416" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-416', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'A'</tt><tt class="py-op">)</tt> </tt>
<a name="L654"></a><tt class="py-lineno">654</tt> <tt class="py-line"> <tt id="link-417" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-417', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-418" class="py-name" targets="Method Bio.Blast.NCBIStandalone._ParametersConsumer.dropoff_1st_pass()=Bio.Blast.NCBIStandalone._ParametersConsumer-class.html#dropoff_1st_pass"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.dropoff_1st_pass" class="py-name" href="#" onclick="return doclink('link-418', 'dropoff_1st_pass', 'link-418');">dropoff_1st_pass</a></tt><tt class="py-op">,</tt> <tt id="link-419" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-419', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'X1'</tt><tt class="py-op">)</tt> </tt>
<a name="L655"></a><tt class="py-lineno">655</tt> <tt class="py-line"> <tt id="link-420" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-420', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-421" class="py-name" targets="Method Bio.Blast.NCBIStandalone._ParametersConsumer.gap_x_dropoff()=Bio.Blast.NCBIStandalone._ParametersConsumer-class.html#gap_x_dropoff"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.gap_x_dropoff" class="py-name" href="#" onclick="return doclink('link-421', 'gap_x_dropoff', 'link-421');">gap_x_dropoff</a></tt><tt class="py-op">,</tt> <tt id="link-422" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-422', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'X2'</tt><tt class="py-op">)</tt> </tt>
<a name="L656"></a><tt class="py-lineno">656</tt> <tt class="py-line"> <tt class="py-comment"># not BLASTN, TBLASTX</tt> </tt>
<a name="L657"></a><tt class="py-lineno">657</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-423" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-423', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-424" class="py-name" targets="Method Bio.Blast.NCBIStandalone._ParametersConsumer.gap_x_dropoff_final()=Bio.Blast.NCBIStandalone._ParametersConsumer-class.html#gap_x_dropoff_final"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.gap_x_dropoff_final" class="py-name" href="#" onclick="return doclink('link-424', 'gap_x_dropoff_final', 'link-424');">gap_x_dropoff_final</a></tt><tt class="py-op">,</tt> </tt>
<a name="L658"></a><tt class="py-lineno">658</tt> <tt class="py-line"> <tt id="link-425" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-425', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'X3'</tt><tt class="py-op">)</tt> </tt>
<a name="L659"></a><tt class="py-lineno">659</tt> <tt class="py-line"> <tt id="link-426" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-426', 'read_and_call', 'link-27');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-427" class="py-name" targets="Method Bio.Blast.NCBIStandalone._ParametersConsumer.gap_trigger()=Bio.Blast.NCBIStandalone._ParametersConsumer-class.html#gap_trigger"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.gap_trigger" class="py-name" href="#" onclick="return doclink('link-427', 'gap_trigger', 'link-427');">gap_trigger</a></tt><tt class="py-op">,</tt> <tt id="link-428" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-428', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'S1'</tt><tt class="py-op">)</tt> </tt>
<a name="L660"></a><tt class="py-lineno">660</tt> <tt class="py-line"> <tt id="link-429" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-429', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-430" class="py-name" targets="Method Bio.Blast.NCBIStandalone._ParametersConsumer.blast_cutoff()=Bio.Blast.NCBIStandalone._ParametersConsumer-class.html#blast_cutoff"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.blast_cutoff" class="py-name" href="#" onclick="return doclink('link-430', 'blast_cutoff', 'link-430');">blast_cutoff</a></tt><tt class="py-op">,</tt> <tt id="link-431" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-431', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'S2'</tt><tt class="py-op">)</tt> </tt>
<a name="L661"></a><tt class="py-lineno">661</tt> <tt class="py-line"> </tt>
<a name="L662"></a><tt class="py-lineno">662</tt> <tt class="py-line"> <tt id="link-432" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-432', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-433" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-433', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-434" class="py-name"><a title="Bio.MetaTool.metatool_format.blank" class="py-name" href="#" onclick="return doclink('link-434', 'blank', 'link-35');">blank</a></tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L663"></a><tt class="py-lineno">663</tt> <tt class="py-line"> <tt id="link-435" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-435', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-436" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-436', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-437" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-437', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">"</PRE>"</tt><tt class="py-op">)</tt> </tt>
<a name="L664"></a><tt class="py-lineno">664</tt> <tt class="py-line"> <tt id="link-438" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-438', 'attempt_read_and_call', 'link-40');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-439" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-439', 'noevent', 'link-20');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-440" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-440', 'start', 'link-42');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">"</form>"</tt><tt class="py-op">)</tt> </tt>
<a name="L665"></a><tt class="py-lineno">665</tt> <tt class="py-line"> </tt>
<a name="L666"></a><tt class="py-lineno">666</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-441" class="py-name" targets="Method Bio.Blast.NCBIStandalone._BlastConsumer.end_parameters()=Bio.Blast.NCBIStandalone._BlastConsumer-class.html#end_parameters,Method Bio.Blast.NCBIStandalone._PSIBlastConsumer.end_parameters()=Bio.Blast.NCBIStandalone._PSIBlastConsumer-class.html#end_parameters,Method Bio.Blast.NCBIStandalone._ParametersConsumer.end_parameters()=Bio.Blast.NCBIStandalone._ParametersConsumer-class.html#end_parameters"><a title="Bio.Blast.NCBIStandalone._BlastConsumer.end_parameters
Bio.Blast.NCBIStandalone._PSIBlastConsumer.end_parameters
Bio.Blast.NCBIStandalone._ParametersConsumer.end_parameters" class="py-name" href="#" onclick="return doclink('link-441', 'end_parameters', 'link-441');">end_parameters</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L667"></a><tt class="py-lineno">667</tt> <tt class="py-line"> </tt>
<a name="qblast"></a><div id="qblast-def"><a name="L668"></a><tt class="py-lineno">668</tt> <a class="py-toggle" href="#" id="qblast-toggle" onclick="return toggle('qblast');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIWWW-module.html#qblast">qblast</a><tt class="py-op">(</tt><tt class="py-param">program</tt><tt class="py-op">,</tt> <tt class="py-param">database</tt><tt class="py-op">,</tt> <tt class="py-param">sequence</tt><tt class="py-op">,</tt> </tt>
<a name="L669"></a><tt class="py-lineno">669</tt> <tt class="py-line"> <tt class="py-param">auto_format</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-param">composition_based_statistics</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L670"></a><tt class="py-lineno">670</tt> <tt class="py-line"> <tt class="py-param">db_genetic_code</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-param">endpoints</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-param">entrez_query</tt><tt class="py-op">=</tt><tt class="py-string">'(none)'</tt><tt class="py-op">,</tt> </tt>
<a name="L671"></a><tt class="py-lineno">671</tt> <tt class="py-line"> <tt class="py-param">expect</tt><tt class="py-op">=</tt><tt class="py-number">10.0</tt><tt class="py-op">,</tt><tt class="py-param">filter</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-param">gapcosts</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-param">genetic_code</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L672"></a><tt class="py-lineno">672</tt> <tt class="py-line"> <tt class="py-param">hitlist_size</tt><tt class="py-op">=</tt><tt class="py-number">50</tt><tt class="py-op">,</tt><tt class="py-param">i_thresh</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-param">layout</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-param">lcase_mask</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L673"></a><tt class="py-lineno">673</tt> <tt class="py-line"> <tt class="py-param">matrix_name</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-param">nucl_penalty</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-param">nucl_reward</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L674"></a><tt class="py-lineno">674</tt> <tt class="py-line"> <tt class="py-param">other_advanced</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-param">perc_ident</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-param">phi_pattern</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L675"></a><tt class="py-lineno">675</tt> <tt class="py-line"> <tt class="py-param">query_file</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-param">query_believe_defline</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-param">query_from</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L676"></a><tt class="py-lineno">676</tt> <tt class="py-line"> <tt class="py-param">query_to</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-param">searchsp_eff</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-param">service</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-param">threshold</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L677"></a><tt class="py-lineno">677</tt> <tt class="py-line"> <tt class="py-param">ungapped_alignment</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-param">word_size</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L678"></a><tt class="py-lineno">678</tt> <tt class="py-line"> <tt class="py-param">alignments</tt><tt class="py-op">=</tt><tt class="py-number">500</tt><tt class="py-op">,</tt><tt class="py-param">alignment_view</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-param">descriptions</tt><tt class="py-op">=</tt><tt class="py-number">500</tt><tt class="py-op">,</tt> </tt>
<a name="L679"></a><tt class="py-lineno">679</tt> <tt class="py-line"> <tt class="py-param">entrez_links_new_window</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-param">expect_low</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-param">expect_high</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L680"></a><tt class="py-lineno">680</tt> <tt class="py-line"> <tt class="py-param">format_entrez_query</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-param">format_object</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-param">format_type</tt><tt class="py-op">=</tt><tt class="py-string">'XML'</tt><tt class="py-op">,</tt> </tt>
<a name="L681"></a><tt class="py-lineno">681</tt> <tt class="py-line"> <tt class="py-param">ncbi_gi</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-param">results_file</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-param">show_overview</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L682"></a><tt class="py-lineno">682</tt> <tt class="py-line"> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="qblast-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="qblast-expanded"><a name="L683"></a><tt class="py-lineno">683</tt> <tt class="py-line"> <tt class="py-docstring">"""Do a BLAST search using the QBLAST server at NCBI.</tt> </tt>
<a name="L684"></a><tt class="py-lineno">684</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L685"></a><tt class="py-lineno">685</tt> <tt class="py-line"><tt class="py-docstring"> Supports all parameters of the qblast API for Put and Get.</tt> </tt>
<a name="L686"></a><tt class="py-lineno">686</tt> <tt class="py-line"><tt class="py-docstring"> Some useful parameters:</tt> </tt>
<a name="L687"></a><tt class="py-lineno">687</tt> <tt class="py-line"><tt class="py-docstring"> program blastn, blastp, blastx, tblastn, or tblastx (lower case)</tt> </tt>
<a name="L688"></a><tt class="py-lineno">688</tt> <tt class="py-line"><tt class="py-docstring"> database Which database to search against (e.g. "nr").</tt> </tt>
<a name="L689"></a><tt class="py-lineno">689</tt> <tt class="py-line"><tt class="py-docstring"> sequence The sequence to search.</tt> </tt>
<a name="L690"></a><tt class="py-lineno">690</tt> <tt class="py-line"><tt class="py-docstring"> ncbi_gi TRUE/FALSE whether to give 'gi' identifier.</tt> </tt>
<a name="L691"></a><tt class="py-lineno">691</tt> <tt class="py-line"><tt class="py-docstring"> descriptions Number of descriptions to show. Def 500.</tt> </tt>
<a name="L692"></a><tt class="py-lineno">692</tt> <tt class="py-line"><tt class="py-docstring"> alignments Number of alignments to show. Def 500.</tt> </tt>
<a name="L693"></a><tt class="py-lineno">693</tt> <tt class="py-line"><tt class="py-docstring"> expect An expect value cutoff. Def 10.0.</tt> </tt>
<a name="L694"></a><tt class="py-lineno">694</tt> <tt class="py-line"><tt class="py-docstring"> matrix_name Specify an alt. matrix (PAM30, PAM70, BLOSUM80, BLOSUM45).</tt> </tt>
<a name="L695"></a><tt class="py-lineno">695</tt> <tt class="py-line"><tt class="py-docstring"> filter "none" turns off filtering. Default no filtering</tt> </tt>
<a name="L696"></a><tt class="py-lineno">696</tt> <tt class="py-line"><tt class="py-docstring"> format_type "HTML", "Text", "ASN.1", or "XML". Def. "XML".</tt> </tt>
<a name="L697"></a><tt class="py-lineno">697</tt> <tt class="py-line"><tt class="py-docstring"> entrez_query Entrez query to limit Blast search</tt> </tt>
<a name="L698"></a><tt class="py-lineno">698</tt> <tt class="py-line"><tt class="py-docstring"> hitlist_size Number of hits to return. Default 50</tt> </tt>
<a name="L699"></a><tt class="py-lineno">699</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L700"></a><tt class="py-lineno">700</tt> <tt class="py-line"><tt class="py-docstring"> This function does no checking of the validity of the parameters</tt> </tt>
<a name="L701"></a><tt class="py-lineno">701</tt> <tt class="py-line"><tt class="py-docstring"> and passes the values to the server as is. More help is available at:</tt> </tt>
<a name="L702"></a><tt class="py-lineno">702</tt> <tt class="py-line"><tt class="py-docstring"> http://www.ncbi.nlm.nih.gov/BLAST/blast_overview.html</tt> </tt>
<a name="L703"></a><tt class="py-lineno">703</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L704"></a><tt class="py-lineno">704</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L705"></a><tt class="py-lineno">705</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">urllib</tt><tt class="py-op">,</tt> <tt class="py-name">urllib2</tt> </tt>
<a name="L706"></a><tt class="py-lineno">706</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt id="link-442" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-442', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-443" class="py-name" targets="Package Bio.WWW=Bio.WWW-module.html"><a title="Bio.WWW" class="py-name" href="#" onclick="return doclink('link-443', 'WWW', 'link-443');">WWW</a></tt> <tt class="py-keyword">import</tt> <tt id="link-444" class="py-name" targets="Class Bio.WWW.RequestLimiter=Bio.WWW.RequestLimiter-class.html"><a title="Bio.WWW.RequestLimiter" class="py-name" href="#" onclick="return doclink('link-444', 'RequestLimiter', 'link-444');">RequestLimiter</a></tt> </tt>
<a name="L707"></a><tt class="py-lineno">707</tt> <tt class="py-line"> </tt>
<a name="L708"></a><tt class="py-lineno">708</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">program</tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt><tt class="py-string">'blastn'</tt><tt class="py-op">,</tt> <tt class="py-string">'blastp'</tt><tt class="py-op">,</tt> <tt class="py-string">'blastx'</tt><tt class="py-op">,</tt> <tt class="py-string">'tblastn'</tt><tt class="py-op">,</tt> <tt class="py-string">'tblastx'</tt><tt class="py-op">]</tt> </tt>
<a name="L709"></a><tt class="py-lineno">709</tt> <tt class="py-line"> </tt>
<a name="L710"></a><tt class="py-lineno">710</tt> <tt class="py-line"> <tt class="py-comment"># Format the "Put" command, which sends search requests to qblast.</tt> </tt>
<a name="L711"></a><tt class="py-lineno">711</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Parameters taken from http://www.ncbi.nlm.nih.gov/BLAST/Doc/node5.html on 9 July 2007</tt> </tt>
<a name="L712"></a><tt class="py-lineno">712</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-445" class="py-name" targets="Method Bio.AlignAce.Parser.AlignAceConsumer.parameters()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#parameters,Variable Bio.expressions.blast.wublast.parameters=Bio.expressions.blast.wublast-module.html#parameters"><a title="Bio.AlignAce.Parser.AlignAceConsumer.parameters
Bio.expressions.blast.wublast.parameters" class="py-name" href="#" onclick="return doclink('link-445', 'parameters', 'link-445');">parameters</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> </tt>
<a name="L713"></a><tt class="py-lineno">713</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'AUTO_FORMAT'</tt><tt class="py-op">,</tt><tt class="py-name">auto_format</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L714"></a><tt class="py-lineno">714</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'COMPOSITION_BASED_STATISTICS'</tt><tt class="py-op">,</tt><tt class="py-name">composition_based_statistics</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L715"></a><tt class="py-lineno">715</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'DATABASE'</tt><tt class="py-op">,</tt><tt id="link-446" class="py-name"><a title="Bio.Blast.NCBIStandalone._DatabaseReportConsumer.database" class="py-name" href="#" onclick="return doclink('link-446', 'database', 'link-285');">database</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L716"></a><tt class="py-lineno">716</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'DB_GENETIC_CODE'</tt><tt class="py-op">,</tt><tt class="py-name">db_genetic_code</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L717"></a><tt class="py-lineno">717</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'ENDPOINTS'</tt><tt class="py-op">,</tt><tt class="py-name">endpoints</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L718"></a><tt class="py-lineno">718</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'ENTREZ_QUERY'</tt><tt class="py-op">,</tt><tt class="py-name">entrez_query</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L719"></a><tt class="py-lineno">719</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'EXPECT'</tt><tt class="py-op">,</tt><tt id="link-447" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.expect=Bio.expressions.blast.ncbiblast-module.html#expect"><a title="Bio.expressions.blast.ncbiblast.expect" class="py-name" href="#" onclick="return doclink('link-447', 'expect', 'link-447');">expect</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L720"></a><tt class="py-lineno">720</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'FILTER'</tt><tt class="py-op">,</tt><tt id="link-448" class="py-name" targets="Function Bio.FSSP.FSSPTools.filter()=Bio.FSSP.FSSPTools-module.html#filter,Method Bio.FilteredReader.FilteredReader.filter()=Bio.FilteredReader.FilteredReader-class.html#filter,Variable Bio.expressions.swissprot.filter=Bio.expressions.swissprot-module.html#filter"><a title="Bio.FSSP.FSSPTools.filter
Bio.FilteredReader.FilteredReader.filter
Bio.expressions.swissprot.filter" class="py-name" href="#" onclick="return doclink('link-448', 'filter', 'link-448');">filter</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L721"></a><tt class="py-lineno">721</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'GAPCOSTS'</tt><tt class="py-op">,</tt><tt class="py-name">gapcosts</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L722"></a><tt class="py-lineno">722</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'GENETIC_CODE'</tt><tt class="py-op">,</tt><tt class="py-name">genetic_code</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L723"></a><tt class="py-lineno">723</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'HITLIST_SIZE'</tt><tt class="py-op">,</tt><tt class="py-name">hitlist_size</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L724"></a><tt class="py-lineno">724</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'I_THRESH'</tt><tt class="py-op">,</tt><tt class="py-name">i_thresh</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L725"></a><tt class="py-lineno">725</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'LAYOUT'</tt><tt class="py-op">,</tt><tt class="py-name">layout</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L726"></a><tt class="py-lineno">726</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'LCASE_MASK'</tt><tt class="py-op">,</tt><tt class="py-name">lcase_mask</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L727"></a><tt class="py-lineno">727</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'MATRIX_NAME'</tt><tt class="py-op">,</tt><tt class="py-name">matrix_name</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L728"></a><tt class="py-lineno">728</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'NUCL_PENALTY'</tt><tt class="py-op">,</tt><tt class="py-name">nucl_penalty</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L729"></a><tt class="py-lineno">729</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'NUCL_REWARD'</tt><tt class="py-op">,</tt><tt class="py-name">nucl_reward</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L730"></a><tt class="py-lineno">730</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'OTHER_ADVANCED'</tt><tt class="py-op">,</tt><tt class="py-name">other_advanced</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L731"></a><tt class="py-lineno">731</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'PERC_IDENT'</tt><tt class="py-op">,</tt><tt class="py-name">perc_ident</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L732"></a><tt class="py-lineno">732</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'PHI_PATTERN'</tt><tt class="py-op">,</tt><tt class="py-name">phi_pattern</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L733"></a><tt class="py-lineno">733</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'PROGRAM'</tt><tt class="py-op">,</tt><tt class="py-name">program</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L734"></a><tt class="py-lineno">734</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'QUERY'</tt><tt class="py-op">,</tt><tt id="link-449" class="py-name" targets="Method Bio.AlignAce.Parser.AlignAceConsumer.sequence()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#sequence,Variable Bio.Emboss.primer3_format.sequence=Bio.Emboss.primer3_format-module.html#sequence,Method Bio.FSSP.FSSPAlignDict.sequence()=Bio.FSSP.FSSPAlignDict-class.html#sequence,Method Bio.GenBank._FeatureConsumer.sequence()=Bio.GenBank._FeatureConsumer-class.html#sequence,Method Bio.GenBank._RecordConsumer.sequence()=Bio.GenBank._RecordConsumer-class.html#sequence,Method Bio.IntelliGenetics._RecordConsumer.sequence()=Bio.IntelliGenetics._RecordConsumer-class.html#sequence,Method Bio.Rebase._RecordConsumer.sequence()=Bio.Rebase._RecordConsumer-class.html#sequence,Function Bio.Std.sequence()=Bio.Std-module.html#sequence,Module Bio.builders.SeqRecord.sequence=Bio.builders.SeqRecord.sequence-module.html,Variable Bio.expressions.fasta.sequence=Bio.expressions.fasta-module.html#sequence,Variable Bio.expressions.genbank.sequence=Bio.expressions.genbank-module.html#sequence,Variable Bio.expressions.swissprot.sprot38.sequence=Bio.expressions.swissprot.sprot38-module.html#sequence,Module Bio.formatdefs.sequence=Bio.formatdefs.sequence-module.html,Variable Bio.formatdefs.sequence.sequence=Bio.formatdefs.sequence-module.html#sequence,Variable Martel.test.test_swissprot38.sequence=Martel.test.test_swissprot38-module.html#sequence,Variable Martel.test.testformats.swissprot38.sequence=Martel.test.testformats.swissprot38-module.html#sequence"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-449', 'sequence', 'link-449');">sequence</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L735"></a><tt class="py-lineno">735</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'QUERY_FILE'</tt><tt class="py-op">,</tt><tt class="py-name">query_file</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L736"></a><tt class="py-lineno">736</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'QUERY_BELIEVE_DEFLINE'</tt><tt class="py-op">,</tt><tt class="py-name">query_believe_defline</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L737"></a><tt class="py-lineno">737</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'QUERY_FROM'</tt><tt class="py-op">,</tt><tt class="py-name">query_from</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L738"></a><tt class="py-lineno">738</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'QUERY_TO'</tt><tt class="py-op">,</tt><tt class="py-name">query_to</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L739"></a><tt class="py-lineno">739</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'SEARCHSP_EFF'</tt><tt class="py-op">,</tt><tt class="py-name">searchsp_eff</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L740"></a><tt class="py-lineno">740</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'SERVICE'</tt><tt class="py-op">,</tt><tt class="py-name">service</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L741"></a><tt class="py-lineno">741</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'THRESHOLD'</tt><tt class="py-op">,</tt><tt id="link-450" class="py-name"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.threshold
Bio.Compass._Consumer.threshold" class="py-name" href="#" onclick="return doclink('link-450', 'threshold', 'link-412');">threshold</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L742"></a><tt class="py-lineno">742</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'UNGAPPED_ALIGNMENT'</tt><tt class="py-op">,</tt><tt class="py-name">ungapped_alignment</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L743"></a><tt class="py-lineno">743</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'WORD_SIZE'</tt><tt class="py-op">,</tt><tt class="py-name">word_size</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L744"></a><tt class="py-lineno">744</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'CMD'</tt><tt class="py-op">,</tt> <tt class="py-string">'Put'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L745"></a><tt class="py-lineno">745</tt> <tt class="py-line"> <tt class="py-op">]</tt> </tt>
<a name="L746"></a><tt class="py-lineno">746</tt> <tt class="py-line"> <tt id="link-451" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.query
Bio.Entrez.query
Bio.WWW.NCBI.query" class="py-name" href="#" onclick="return doclink('link-451', 'query', 'link-246');">query</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-452" class="py-name" targets="Variable Bio.MarkovModel.x=Bio.MarkovModel-module.html#x,Variable Bio.Statistics.lowess.x=Bio.Statistics.lowess-module.html#x"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-452', 'x', 'link-452');">x</a></tt> <tt class="py-keyword">for</tt> <tt id="link-453" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-453', 'x', 'link-452');">x</a></tt> <tt class="py-keyword">in</tt> <tt id="link-454" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.parameters
Bio.expressions.blast.wublast.parameters" class="py-name" href="#" onclick="return doclink('link-454', 'parameters', 'link-445');">parameters</a></tt> <tt class="py-keyword">if</tt> <tt id="link-455" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-455', 'x', 'link-452');">x</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">]</tt> </tt>
<a name="L747"></a><tt class="py-lineno">747</tt> <tt class="py-line"> <tt id="link-456" class="py-name" targets="Variable Bio.DocSQL.Query.message=Bio.DocSQL.Query-class.html#message"><a title="Bio.DocSQL.Query.message" class="py-name" href="#" onclick="return doclink('link-456', 'message', 'link-456');">message</a></tt> <tt class="py-op">=</tt> <tt class="py-name">urllib</tt><tt class="py-op">.</tt><tt class="py-name">urlencode</tt><tt class="py-op">(</tt><tt id="link-457" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.query
Bio.Entrez.query
Bio.WWW.NCBI.query" class="py-name" href="#" onclick="return doclink('link-457', 'query', 'link-246');">query</a></tt><tt class="py-op">)</tt> </tt>
<a name="L748"></a><tt class="py-lineno">748</tt> <tt class="py-line"> </tt>
<a name="L749"></a><tt class="py-lineno">749</tt> <tt class="py-line"> <tt class="py-comment"># Send off the initial query to qblast.</tt> </tt>
<a name="L750"></a><tt class="py-lineno">750</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">request</tt> <tt class="py-op">=</tt> <tt class="py-name">urllib2</tt><tt class="py-op">.</tt><tt class="py-name">Request</tt><tt class="py-op">(</tt><tt class="py-string">"http://blast.ncbi.nlm.nih.gov/Blast.cgi"</tt><tt class="py-op">,</tt> </tt>
<a name="L751"></a><tt class="py-lineno">751</tt> <tt class="py-line"> <tt id="link-458" class="py-name"><a title="Bio.DocSQL.Query.message" class="py-name" href="#" onclick="return doclink('link-458', 'message', 'link-456');">message</a></tt><tt class="py-op">,</tt> </tt>
<a name="L752"></a><tt class="py-lineno">752</tt> <tt class="py-line"> <tt class="py-op">{</tt><tt class="py-string">"User-Agent"</tt><tt class="py-op">:</tt><tt class="py-string">"BiopythonClient"</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> </tt>
<a name="L753"></a><tt class="py-lineno">753</tt> <tt class="py-line"> <tt id="link-459" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-459', 'handle', 'link-8');">handle</a></tt> <tt class="py-op">=</tt> <tt class="py-name">urllib2</tt><tt class="py-op">.</tt><tt class="py-name">urlopen</tt><tt class="py-op">(</tt><tt class="py-name">request</tt><tt class="py-op">)</tt> </tt>
<a name="L754"></a><tt class="py-lineno">754</tt> <tt class="py-line"> </tt>
<a name="L755"></a><tt class="py-lineno">755</tt> <tt class="py-line"> <tt class="py-comment"># Format the "Get" command, which gets the formatted results from qblast</tt> </tt>
<a name="L756"></a><tt class="py-lineno">756</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Parameters taken from http://www.ncbi.nlm.nih.gov/BLAST/Doc/node6.html on 9 July 2007 </tt> </tt>
<a name="L757"></a><tt class="py-lineno">757</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">rid</tt><tt class="py-op">,</tt> <tt class="py-name">rtoe</tt> <tt class="py-op">=</tt> <tt id="link-460" class="py-name" targets="Function Bio.Blast.NCBIWWW._parse_qblast_ref_page()=Bio.Blast.NCBIWWW-module.html#_parse_qblast_ref_page"><a title="Bio.Blast.NCBIWWW._parse_qblast_ref_page" class="py-name" href="#" onclick="return doclink('link-460', '_parse_qblast_ref_page', 'link-460');">_parse_qblast_ref_page</a></tt><tt class="py-op">(</tt><tt id="link-461" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-461', 'handle', 'link-8');">handle</a></tt><tt class="py-op">)</tt> </tt>
<a name="L758"></a><tt class="py-lineno">758</tt> <tt class="py-line"> <tt id="link-462" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.parameters
Bio.expressions.blast.wublast.parameters" class="py-name" href="#" onclick="return doclink('link-462', 'parameters', 'link-445');">parameters</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> </tt>
<a name="L759"></a><tt class="py-lineno">759</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'ALIGNMENTS'</tt><tt class="py-op">,</tt><tt class="py-name">alignments</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L760"></a><tt class="py-lineno">760</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'ALIGNMENT_VIEW'</tt><tt class="py-op">,</tt><tt class="py-name">alignment_view</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L761"></a><tt class="py-lineno">761</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'DESCRIPTIONS'</tt><tt class="py-op">,</tt><tt class="py-name">descriptions</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L762"></a><tt class="py-lineno">762</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'ENTREZ_LINKS_NEW_WINDOW'</tt><tt class="py-op">,</tt><tt class="py-name">entrez_links_new_window</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L763"></a><tt class="py-lineno">763</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'EXPECT_LOW'</tt><tt class="py-op">,</tt><tt class="py-name">expect_low</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L764"></a><tt class="py-lineno">764</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'EXPECT_HIGH'</tt><tt class="py-op">,</tt><tt class="py-name">expect_high</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L765"></a><tt class="py-lineno">765</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'FORMAT_ENTREZ_QUERY'</tt><tt class="py-op">,</tt><tt class="py-name">format_entrez_query</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L766"></a><tt class="py-lineno">766</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'FORMAT_OBJECT'</tt><tt class="py-op">,</tt><tt class="py-name">format_object</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L767"></a><tt class="py-lineno">767</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'FORMAT_TYPE'</tt><tt class="py-op">,</tt><tt class="py-name">format_type</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L768"></a><tt class="py-lineno">768</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'NCBI_GI'</tt><tt class="py-op">,</tt><tt class="py-name">ncbi_gi</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L769"></a><tt class="py-lineno">769</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'RID'</tt><tt class="py-op">,</tt><tt class="py-name">rid</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L770"></a><tt class="py-lineno">770</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'RESULTS_FILE'</tt><tt class="py-op">,</tt><tt class="py-name">results_file</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L771"></a><tt class="py-lineno">771</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'SERVICE'</tt><tt class="py-op">,</tt><tt class="py-name">service</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L772"></a><tt class="py-lineno">772</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'SHOW_OVERVIEW'</tt><tt class="py-op">,</tt><tt class="py-name">show_overview</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L773"></a><tt class="py-lineno">773</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">'CMD'</tt><tt class="py-op">,</tt> <tt class="py-string">'Get'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L774"></a><tt class="py-lineno">774</tt> <tt class="py-line"> <tt class="py-op">]</tt> </tt>
<a name="L775"></a><tt class="py-lineno">775</tt> <tt class="py-line"> <tt id="link-463" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.query
Bio.Entrez.query
Bio.WWW.NCBI.query" class="py-name" href="#" onclick="return doclink('link-463', 'query', 'link-246');">query</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-464" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-464', 'x', 'link-452');">x</a></tt> <tt class="py-keyword">for</tt> <tt id="link-465" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-465', 'x', 'link-452');">x</a></tt> <tt class="py-keyword">in</tt> <tt id="link-466" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.parameters
Bio.expressions.blast.wublast.parameters" class="py-name" href="#" onclick="return doclink('link-466', 'parameters', 'link-445');">parameters</a></tt> <tt class="py-keyword">if</tt> <tt id="link-467" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-467', 'x', 'link-452');">x</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">]</tt> </tt>
<a name="L776"></a><tt class="py-lineno">776</tt> <tt class="py-line"> <tt id="link-468" class="py-name"><a title="Bio.DocSQL.Query.message" class="py-name" href="#" onclick="return doclink('link-468', 'message', 'link-456');">message</a></tt> <tt class="py-op">=</tt> <tt class="py-name">urllib</tt><tt class="py-op">.</tt><tt class="py-name">urlencode</tt><tt class="py-op">(</tt><tt id="link-469" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.query
Bio.Entrez.query
Bio.WWW.NCBI.query" class="py-name" href="#" onclick="return doclink('link-469', 'query', 'link-246');">query</a></tt><tt class="py-op">)</tt> </tt>
<a name="L777"></a><tt class="py-lineno">777</tt> <tt class="py-line"> </tt>
<a name="L778"></a><tt class="py-lineno">778</tt> <tt class="py-line"> <tt class="py-comment"># Poll NCBI until the results are ready.</tt> </tt>
<a name="L779"></a><tt class="py-lineno">779</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">limiter</tt> <tt class="py-op">=</tt> <tt id="link-470" class="py-name"><a title="Bio.WWW.RequestLimiter" class="py-name" href="#" onclick="return doclink('link-470', 'RequestLimiter', 'link-444');">RequestLimiter</a></tt><tt class="py-op">(</tt><tt class="py-number">3</tt><tt class="py-op">)</tt> </tt>
<a name="L780"></a><tt class="py-lineno">780</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L781"></a><tt class="py-lineno">781</tt> <tt class="py-line"> <tt class="py-name">limiter</tt><tt class="py-op">.</tt><tt id="link-471" class="py-name" targets="Method Bio.WWW.RequestLimiter.wait()=Bio.WWW.RequestLimiter-class.html#wait"><a title="Bio.WWW.RequestLimiter.wait" class="py-name" href="#" onclick="return doclink('link-471', 'wait', 'link-471');">wait</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L782"></a><tt class="py-lineno">782</tt> <tt class="py-line"> <tt class="py-name">request</tt> <tt class="py-op">=</tt> <tt class="py-name">urllib2</tt><tt class="py-op">.</tt><tt class="py-name">Request</tt><tt class="py-op">(</tt><tt class="py-string">"http://blast.ncbi.nlm.nih.gov/Blast.cgi"</tt><tt class="py-op">,</tt> </tt>
<a name="L783"></a><tt class="py-lineno">783</tt> <tt class="py-line"> <tt id="link-472" class="py-name"><a title="Bio.DocSQL.Query.message" class="py-name" href="#" onclick="return doclink('link-472', 'message', 'link-456');">message</a></tt><tt class="py-op">,</tt> </tt>
<a name="L784"></a><tt class="py-lineno">784</tt> <tt class="py-line"> <tt class="py-op">{</tt><tt class="py-string">"User-Agent"</tt><tt class="py-op">:</tt><tt class="py-string">"BiopythonClient"</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> </tt>
<a name="L785"></a><tt class="py-lineno">785</tt> <tt class="py-line"> <tt id="link-473" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-473', 'handle', 'link-8');">handle</a></tt> <tt class="py-op">=</tt> <tt class="py-name">urllib2</tt><tt class="py-op">.</tt><tt class="py-name">urlopen</tt><tt class="py-op">(</tt><tt class="py-name">request</tt><tt class="py-op">)</tt> </tt>
<a name="L786"></a><tt class="py-lineno">786</tt> <tt class="py-line"> <tt class="py-name">results</tt> <tt class="py-op">=</tt> <tt id="link-474" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-474', 'handle', 'link-8');">handle</a></tt><tt class="py-op">.</tt><tt id="link-475" class="py-name" targets="Method Bio.AlignAce.Motif.Motif.read()=Bio.AlignAce.Motif.Motif-class.html#read,Function Bio.AlignIO.read()=Bio.AlignIO-module.html#read,Function Bio.Cluster.read()=Bio.Cluster-module.html#read,Method Bio.EUtils.ReseekFile.ReseekFile.read()=Bio.EUtils.ReseekFile.ReseekFile-class.html#read,Function Bio.Entrez.read()=Bio.Entrez-module.html#read,Method Bio.File.SGMLHandle.read()=Bio.File.SGMLHandle-class.html#read,Method Bio.File.UndoHandle.read()=Bio.File.UndoHandle-class.html#read,Method Bio.FilteredReader.FilteredReader.read()=Bio.FilteredReader.FilteredReader-class.html#read,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.read()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#read,Method Bio.Nexus.Nexus.Nexus.read()=Bio.Nexus.Nexus.Nexus-class.html#read,Function Bio.Prosite.Prodoc.read()=Bio.Prosite.Prodoc-module.html#read,Function Bio.Prosite.read()=Bio.Prosite-module.html#read,Method Bio.SGMLExtractor.SGMLExtractorHandle.read()=Bio.SGMLExtractor.SGMLExtractorHandle-class.html#read,Function Bio.SeqIO.read()=Bio.SeqIO-module.html#read,Function Bio.SwissProt.read()=Bio.SwissProt-module.html#read"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-475', 'read', 'link-475');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L787"></a><tt class="py-lineno">787</tt> <tt class="py-line"> <tt class="py-comment"># XML results don't have the Status tag when finished</tt> </tt>
<a name="L788"></a><tt class="py-lineno">788</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">results</tt><tt class="py-op">.</tt><tt id="link-476" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-476', 'find', 'link-46');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">"Status="</tt><tt class="py-op">)</tt> <tt class="py-op"><</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L789"></a><tt class="py-lineno">789</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L790"></a><tt class="py-lineno">790</tt> <tt class="py-line"> <tt id="link-477" class="py-name" targets="Variable Bio.PDB.Polypeptide.i=Bio.PDB.Polypeptide-module.html#i"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-477', 'i', 'link-477');">i</a></tt> <tt class="py-op">=</tt> <tt class="py-name">results</tt><tt class="py-op">.</tt><tt id="link-478" class="py-name" targets="Method Bio.Crystal.Chain.index()=Bio.Crystal.Chain-class.html#index,Method Bio.EUtils.POM.ElementNode.index()=Bio.EUtils.POM.ElementNode-class.html#index,Method Bio.SCOP.Raf.SeqMap.index()=Bio.SCOP.Raf.SeqMap-class.html#index,Method Bio.Seq.MutableSeq.index()=Bio.Seq.MutableSeq-class.html#index"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-478', 'index', 'link-478');">index</a></tt><tt class="py-op">(</tt><tt class="py-string">"Status="</tt><tt class="py-op">)</tt> </tt>
<a name="L791"></a><tt class="py-lineno">791</tt> <tt class="py-line"> <tt class="py-name">j</tt> <tt class="py-op">=</tt> <tt class="py-name">results</tt><tt class="py-op">.</tt><tt id="link-479" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-479', 'index', 'link-478');">index</a></tt><tt class="py-op">(</tt><tt class="py-string">"\n"</tt><tt class="py-op">,</tt> <tt id="link-480" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-480', 'i', 'link-477');">i</a></tt><tt class="py-op">)</tt> </tt>
<a name="L792"></a><tt class="py-lineno">792</tt> <tt class="py-line"> <tt class="py-name">status</tt> <tt class="py-op">=</tt> <tt class="py-name">results</tt><tt class="py-op">[</tt><tt id="link-481" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-481', 'i', 'link-477');">i</a></tt><tt class="py-op">+</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-string">"Status="</tt><tt class="py-op">)</tt><tt class="py-op">:</tt><tt class="py-name">j</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-482" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-482', 'strip', 'link-37');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L793"></a><tt class="py-lineno">793</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">status</tt><tt class="py-op">.</tt><tt class="py-name">upper</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-string">"READY"</tt><tt class="py-op">:</tt> </tt>
<a name="L794"></a><tt class="py-lineno">794</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L795"></a><tt class="py-lineno">795</tt> <tt class="py-line"> </tt>
<a name="L796"></a><tt class="py-lineno">796</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">StringIO</tt><tt class="py-op">.</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-name">results</tt><tt class="py-op">)</tt> </tt>
</div><a name="L797"></a><tt class="py-lineno">797</tt> <tt class="py-line"> </tt>
<a name="_parse_qblast_ref_page"></a><div id="_parse_qblast_ref_page-def"><a name="L798"></a><tt class="py-lineno">798</tt> <a class="py-toggle" href="#" id="_parse_qblast_ref_page-toggle" onclick="return toggle('_parse_qblast_ref_page');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIWWW-module.html#_parse_qblast_ref_page">_parse_qblast_ref_page</a><tt class="py-op">(</tt><tt class="py-param">handle</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_parse_qblast_ref_page-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_parse_qblast_ref_page-expanded"><a name="L799"></a><tt class="py-lineno">799</tt> <tt class="py-line"> <tt class="py-docstring">"""Return tuple of RID, RTOE."""</tt> </tt>
<a name="L800"></a><tt class="py-lineno">800</tt> <tt class="py-line"> <tt id="link-483" class="py-name" targets="Variable Martel.test.test_swissprot38.s=Martel.test.test_swissprot38-module.html#s"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-483', 's', 'link-483');">s</a></tt> <tt class="py-op">=</tt> <tt id="link-484" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-484', 'handle', 'link-8');">handle</a></tt><tt class="py-op">.</tt><tt id="link-485" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-485', 'read', 'link-475');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L801"></a><tt class="py-lineno">801</tt> <tt class="py-line"> <tt id="link-486" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-486', 'i', 'link-477');">i</a></tt> <tt class="py-op">=</tt> <tt id="link-487" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-487', 's', 'link-483');">s</a></tt><tt class="py-op">.</tt><tt id="link-488" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-488', 'find', 'link-46');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">"RID ="</tt><tt class="py-op">)</tt> </tt>
<a name="L802"></a><tt class="py-lineno">802</tt> <tt class="py-line"> <tt class="py-name">j</tt> <tt class="py-op">=</tt> <tt id="link-489" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-489', 's', 'link-483');">s</a></tt><tt class="py-op">.</tt><tt id="link-490" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-490', 'find', 'link-46');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">"\n"</tt><tt class="py-op">,</tt> <tt id="link-491" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-491', 'i', 'link-477');">i</a></tt><tt class="py-op">)</tt> </tt>
<a name="L803"></a><tt class="py-lineno">803</tt> <tt class="py-line"> <tt class="py-name">rid</tt> <tt class="py-op">=</tt> <tt id="link-492" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-492', 's', 'link-483');">s</a></tt><tt class="py-op">[</tt><tt id="link-493" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-493', 'i', 'link-477');">i</a></tt><tt class="py-op">+</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-string">"RID ="</tt><tt class="py-op">)</tt><tt class="py-op">:</tt><tt class="py-name">j</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-494" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-494', 'strip', 'link-37');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L804"></a><tt class="py-lineno">804</tt> <tt class="py-line"> </tt>
<a name="L805"></a><tt class="py-lineno">805</tt> <tt class="py-line"> <tt id="link-495" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-495', 'i', 'link-477');">i</a></tt> <tt class="py-op">=</tt> <tt id="link-496" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-496', 's', 'link-483');">s</a></tt><tt class="py-op">.</tt><tt id="link-497" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-497', 'find', 'link-46');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">"RTOE ="</tt><tt class="py-op">)</tt> </tt>
<a name="L806"></a><tt class="py-lineno">806</tt> <tt class="py-line"> <tt class="py-name">j</tt> <tt class="py-op">=</tt> <tt id="link-498" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-498', 's', 'link-483');">s</a></tt><tt class="py-op">.</tt><tt id="link-499" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-499', 'find', 'link-46');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">"\n"</tt><tt class="py-op">,</tt> <tt id="link-500" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-500', 'i', 'link-477');">i</a></tt><tt class="py-op">)</tt> </tt>
<a name="L807"></a><tt class="py-lineno">807</tt> <tt class="py-line"> <tt class="py-name">rtoe</tt> <tt class="py-op">=</tt> <tt id="link-501" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-501', 's', 'link-483');">s</a></tt><tt class="py-op">[</tt><tt id="link-502" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-502', 'i', 'link-477');">i</a></tt><tt class="py-op">+</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-string">"RTOE ="</tt><tt class="py-op">)</tt><tt class="py-op">:</tt><tt class="py-name">j</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-503" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-503', 'strip', 'link-37');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L808"></a><tt class="py-lineno">808</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">rid</tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">rtoe</tt><tt class="py-op">)</tt> </tt>
</div><a name="L809"></a><tt class="py-lineno">809</tt> <tt class="py-line"> </tt><script type="text/javascript">
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