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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.Blast-module.html">Package Blast</a> ::
Module NCBIXML
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<h1 class="epydoc">Source Code for <a href="Bio.Blast.NCBIXML-module.html">Module Bio.Blast.NCBIXML</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 2000 by Bertrand Frottier . 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"># Revisions 2005-2006 copyright Michiel de Hoon</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"># Revisions 2006-2008 copyright Peter Cock</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"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</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="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-docstring">"""This module provides code to work with the BLAST XML output</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">following the DTD available on the NCBI FTP</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">ftp://ftp.ncbi.nlm.nih.gov/blast/documents/xml/NCBI_BlastOutput.dtd</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring">Classes:</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring">BlastParser Parses XML output from BLAST.</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring"> This (now) returns a list of Blast records.</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring"> Historically it returned a single Blast record.</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring">_XMLParser Generic SAX parser.</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">parse Incremental parser, this is an iterator that returns</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring"> Blast records.</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">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="Package Bio.Blast=Bio.Blast-module.html,Class Bio.Blast.Record.Blast=Bio.Blast.Record.Blast-class.html"><a title="Bio.Blast
Bio.Blast.Record.Blast" class="py-name" href="#" onclick="return doclink('link-1', 'Blast', 'link-1');">Blast</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name" targets="Module Bio.Blast.Record=Bio.Blast.Record-module.html,Module Bio.CDD.Record=Bio.CDD.Record-module.html,Class Bio.CDD.Record.Record=Bio.CDD.Record.Record-class.html,Class Bio.Cluster.Record=Bio.Cluster.Record-class.html,Class Bio.Compass.Record=Bio.Compass.Record-class.html,Module Bio.ECell.Record=Bio.ECell.Record-module.html,Class Bio.ECell.Record.Record=Bio.ECell.Record.Record-class.html,Class Bio.Fasta.Record=Bio.Fasta.Record-class.html,Module Bio.GenBank.Record=Bio.GenBank.Record-module.html,Class Bio.GenBank.Record.Record=Bio.GenBank.Record.Record-class.html,Module Bio.Geo.Record=Bio.Geo.Record-module.html,Class Bio.Geo.Record.Record=Bio.Geo.Record.Record-class.html,Class Bio.Gobase.Record=Bio.Gobase.Record-class.html,Module Bio.IntelliGenetics.Record=Bio.IntelliGenetics.Record-module.html,Class Bio.IntelliGenetics.Record.Record=Bio.IntelliGenetics.Record.Record-class.html,Class Bio.InterPro.Record=Bio.InterPro.Record-class.html,Class Bio.KEGG.Compound.Record=Bio.KEGG.Compound.Record-class.html,Class Bio.KEGG.Enzyme.Record=Bio.KEGG.Enzyme.Record-class.html,Class Bio.LocusLink.Record=Bio.LocusLink.Record-class.html,Class Bio.LocusLink.web_parse.Record=Bio.LocusLink.web_parse.Record-class.html,Class Bio.Medline.Record=Bio.Medline.Record-class.html,Module Bio.MetaTool.Record=Bio.MetaTool.Record-module.html,Class Bio.MetaTool.Record.Record=Bio.MetaTool.Record.Record-class.html,Module Bio.NBRF.Record=Bio.NBRF.Record-module.html,Class Bio.NBRF.Record.Record=Bio.NBRF.Record.Record-class.html,Class Bio.Ndb.Record=Bio.Ndb.Record-class.html,Class Bio.PopGen.FDist.Record=Bio.PopGen.FDist.Record-class.html,Class Bio.PopGen.GenePop.Record=Bio.PopGen.GenePop.Record-class.html,Class Bio.Prosite.Prodoc.Record=Bio.Prosite.Prodoc.Record-class.html,Class Bio.Prosite.Record=Bio.Prosite.Record-class.html,Class Bio.Rebase.Record=Bio.Rebase.Record-class.html,Class Bio.SCOP.Cla.Record=Bio.SCOP.Cla.Record-class.html,Class Bio.SCOP.Des.Record=Bio.SCOP.Des.Record-class.html,Class Bio.SCOP.Dom.Record=Bio.SCOP.Dom.Record-class.html,Class Bio.SCOP.Hie.Record=Bio.SCOP.Hie.Record-class.html,Module Bio.Saf.Record=Bio.Saf.Record-module.html,Class Bio.Saf.Record.Record=Bio.Saf.Record.Record-class.html,Class Bio.Sequencing.Phd.Record=Bio.Sequencing.Phd.Record-class.html,Class Bio.SwissProt.KeyWList.Record=Bio.SwissProt.KeyWList.Record-class.html,Class Bio.SwissProt.SProt.Record=Bio.SwissProt.SProt.Record-class.html"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-2', 'Record', 'link-2');">Record</a></tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">xml</tt><tt class="py-op">.</tt><tt class="py-name">sax</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">xml</tt><tt class="py-op">.</tt><tt class="py-name">sax</tt><tt class="py-op">.</tt><tt class="py-name">handler</tt> <tt class="py-keyword">import</tt> <tt class="py-name">ContentHandler</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"> </tt>
<a name="_XMLparser"></a><div id="_XMLparser-def"><a name="L26"></a><tt class="py-lineno"> 26</tt> <a class="py-toggle" href="#" id="_XMLparser-toggle" onclick="return toggle('_XMLparser');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML._XMLparser-class.html">_XMLparser</a><tt class="py-op">(</tt><tt class="py-base-class">ContentHandler</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_XMLparser-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_XMLparser-expanded"><a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"> <tt class="py-docstring">"""Generic SAX Parser</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-docstring"> Just a very basic SAX parser.</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-docstring"> Redefine the methods startElement, characters and endElement.</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="_XMLparser.__init__"></a><div id="_XMLparser.__init__-def"><a name="L33"></a><tt class="py-lineno"> 33</tt> <a class="py-toggle" href="#" id="_XMLparser.__init__-toggle" onclick="return toggle('_XMLparser.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML._XMLparser-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">debug</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_XMLparser.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_XMLparser.__init__-expanded"><a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"> <tt class="py-docstring">"""Constructor</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-docstring"> debug - integer, amount of debug information to print</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-docstring"> """</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">_tag</tt> <tt class="py-op">=</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">_value</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_debug</tt> <tt class="py-op">=</tt> <tt class="py-name">debug</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_debug_ignore_list</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
</div><a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> </tt>
<a name="_XMLparser._secure_name"></a><div id="_XMLparser._secure_name-def"><a name="L43"></a><tt class="py-lineno"> 43</tt> <a class="py-toggle" href="#" id="_XMLparser._secure_name-toggle" onclick="return toggle('_XMLparser._secure_name');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML._XMLparser-class.html#_secure_name">_secure_name</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_XMLparser._secure_name-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_XMLparser._secure_name-expanded"><a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt class="py-docstring">"""Removes 'dangerous' from tag names</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-docstring"> name -- name to be 'secured'</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-comment"># Replace '-' with '_' in XML tag names</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt id="link-3" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.name=Bio.Encodings.IUPACEncoding-module.html#name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-3', 'name', 'link-3');">name</a></tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">'-'</tt><tt class="py-op">,</tt> <tt class="py-string">'_'</tt><tt class="py-op">)</tt> </tt>
</div><a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> </tt>
<a name="_XMLparser.startElement"></a><div id="_XMLparser.startElement-def"><a name="L51"></a><tt class="py-lineno"> 51</tt> <a class="py-toggle" href="#" id="_XMLparser.startElement-toggle" onclick="return toggle('_XMLparser.startElement');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML._XMLparser-class.html#startElement">startElement</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">,</tt> <tt class="py-param">attr</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_XMLparser.startElement-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_XMLparser.startElement-expanded"><a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> <tt class="py-docstring">"""Found XML start tag</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"><tt class="py-docstring"> No real need of attr, BLAST DTD doesn't use them</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"><tt class="py-docstring"> name -- name of the tag</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"><tt class="py-docstring"> attr -- tag attributes</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_tag</tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-class.html#append,Method Bio.EUtils.POM.ElementNode.append()=Bio.EUtils.POM.ElementNode-class.html#append,Method Bio.EUtils.sourcegen.SourceFile.append()=Bio.EUtils.sourcegen.SourceFile-class.html#append,Method Bio.SCOP.Raf.SeqMap.append()=Bio.SCOP.Raf.SeqMap-class.html#append,Method Bio.Seq.MutableSeq.append()=Bio.Seq.MutableSeq-class.html#append,Method Bio.Wise.psw.Alignment.append()=Bio.Wise.psw.Alignment-class.html#append,Method Bio.Wise.psw.AlignmentColumn.append()=Bio.Wise.psw.AlignmentColumn-class.html#append,Method Martel.msre_parse.SubPattern.append()=Martel.msre_parse.SubPattern-class.html#append"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-4', 'append', 'link-4');">append</a></tt><tt class="py-op">(</tt><tt id="link-5" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-5', 'name', 'link-3');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-comment"># Try to call a method (defined in subclasses)</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">method</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-6" class="py-name" targets="Method Bio.Blast.NCBIXML._XMLparser._secure_name()=Bio.Blast.NCBIXML._XMLparser-class.html#_secure_name"><a title="Bio.Blast.NCBIXML._XMLparser._secure_name" class="py-name" href="#" onclick="return doclink('link-6', '_secure_name', 'link-6');">_secure_name</a></tt><tt class="py-op">(</tt><tt class="py-string">'_start_'</tt> <tt class="py-op">+</tt> <tt id="link-7" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-7', 'name', 'link-3');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-comment">#Note could use try / except AttributeError</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#BUT I found often triggered by nested errors...</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">hasattr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">method</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-name">eval</tt><tt class="py-op">(</tt><tt class="py-string">"self.%s()"</tt> <tt class="py-op">%</tt> <tt class="py-name">method</tt><tt class="py-op">)</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_debug</tt> <tt class="py-op">></tt> <tt class="py-number">4</tt> <tt class="py-op">:</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"NCBIXML: Parsed: "</tt> <tt class="py-op">+</tt> <tt class="py-name">method</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-comment"># Doesn't exist (yet)</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">method</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_debug_ignore_list</tt> <tt class="py-op">:</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_debug</tt> <tt class="py-op">></tt> <tt class="py-number">3</tt> <tt class="py-op">:</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"NCBIXML: Ignored: "</tt> <tt class="py-op">+</tt> <tt class="py-name">method</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_debug_ignore_list</tt><tt class="py-op">.</tt><tt id="link-8" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-8', 'append', 'link-4');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">method</tt><tt class="py-op">)</tt> </tt>
</div><a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> </tt>
<a name="_XMLparser.characters"></a><div id="_XMLparser.characters-def"><a name="L78"></a><tt class="py-lineno"> 78</tt> <a class="py-toggle" href="#" id="_XMLparser.characters-toggle" onclick="return toggle('_XMLparser.characters');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML._XMLparser-class.html#characters">characters</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">ch</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_XMLparser.characters-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_XMLparser.characters-expanded"><a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-docstring">"""Found some text</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"><tt class="py-docstring"> ch -- characters read</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt> <tt class="py-op">+=</tt> <tt class="py-name">ch</tt> <tt class="py-comment"># You don't ever get the whole string</tt> </tt>
</div><a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> </tt>
<a name="_XMLparser.endElement"></a><div id="_XMLparser.endElement-def"><a name="L85"></a><tt class="py-lineno"> 85</tt> <a class="py-toggle" href="#" id="_XMLparser.endElement-toggle" onclick="return toggle('_XMLparser.endElement');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML._XMLparser-class.html#endElement">endElement</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_XMLparser.endElement-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_XMLparser.endElement-expanded"><a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-docstring">"""Found XML end tag</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"><tt class="py-docstring"> name -- tag name</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-comment"># Strip character buffer</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt><tt class="py-op">.</tt><tt id="link-9" 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-9', 'strip', 'link-9');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-comment"># Try to call a method (defined in subclasses)</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">method</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-10" class="py-name"><a title="Bio.Blast.NCBIXML._XMLparser._secure_name" class="py-name" href="#" onclick="return doclink('link-10', '_secure_name', 'link-6');">_secure_name</a></tt><tt class="py-op">(</tt><tt class="py-string">'_end_'</tt> <tt class="py-op">+</tt> <tt id="link-11" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-11', 'name', 'link-3');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-comment">#Note could use try / except AttributeError</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#BUT I found often triggered by nested errors...</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">hasattr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">method</tt><tt class="py-op">)</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">eval</tt><tt class="py-op">(</tt><tt class="py-string">"self.%s()"</tt> <tt class="py-op">%</tt> <tt class="py-name">method</tt><tt class="py-op">)</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_debug</tt> <tt class="py-op">></tt> <tt class="py-number">2</tt> <tt class="py-op">:</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"NCBIXML: Parsed: "</tt> <tt class="py-op">+</tt> <tt class="py-name">method</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-comment"># Doesn't exist (yet)</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">method</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_debug_ignore_list</tt> <tt class="py-op">:</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_debug</tt> <tt class="py-op">></tt> <tt class="py-number">1</tt> <tt class="py-op">:</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"NCBIXML: Ignored: "</tt> <tt class="py-op">+</tt> <tt class="py-name">method</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_debug_ignore_list</tt><tt class="py-op">.</tt><tt id="link-12" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-12', 'append', 'link-4');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">method</tt><tt class="py-op">)</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-comment"># Reset character buffer</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
</div></div><a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> </tt>
<a name="BlastParser"></a><div id="BlastParser-def"><a name="L111"></a><tt class="py-lineno">111</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.NCBIXML.BlastParser-class.html">BlastParser</a><tt class="py-op">(</tt><tt class="py-base-class">_XMLparser</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="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-docstring">"""Parse XML BLAST data into a Record.Blast object</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"><tt class="py-docstring"> All XML 'action' methods are private methods and may be:</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"><tt class="py-docstring"> _start_TAG called when the start tag is found</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"><tt class="py-docstring"> _end_TAG called when the end tag is found</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> </tt>
<a name="BlastParser.__init__"></a><div id="BlastParser.__init__-def"><a name="L119"></a><tt class="py-lineno">119</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.NCBIXML.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-param">debug</tt><tt class="py-op">=</tt><tt class="py-number">0</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="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-docstring">"""Constructor</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"><tt class="py-docstring"> debug - integer, amount of debug information to print</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-comment"># Calling superclass method</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-13" class="py-name" targets="Class Bio.Blast.NCBIXML._XMLparser=Bio.Blast.NCBIXML._XMLparser-class.html"><a title="Bio.Blast.NCBIXML._XMLparser" class="py-name" href="#" onclick="return doclink('link-13', '_XMLparser', 'link-13');">_XMLparser</a></tt><tt class="py-op">.</tt><tt id="link-14" class="py-name" targets="Method Bio.Affy.CelFile.CelConsumer.__init__()=Bio.Affy.CelFile.CelConsumer-class.html#__init__,Method Bio.Affy.CelFile.CelParser.__init__()=Bio.Affy.CelFile.CelParser-class.html#__init__,Method Bio.Affy.CelFile.CelRecord.__init__()=Bio.Affy.CelFile.CelRecord-class.html#__init__,Method Bio.Ais.Immune.__init__()=Bio.Ais.Immune-class.html#__init__,Method Bio.Ais.Lymphocyte.__init__()=Bio.Ais.Lymphocyte-class.html#__init__,Method Bio.Align.AlignInfo.PSSM.__init__()=Bio.Align.AlignInfo.PSSM-class.html#__init__,Method Bio.Align.AlignInfo.SummaryInfo.__init__()=Bio.Align.AlignInfo.SummaryInfo-class.html#__init__,Method Bio.Align.FormatConvert.FormatConverter.__init__()=Bio.Align.FormatConvert.FormatConverter-class.html#__init__,Method Bio.Align.Generic.Alignment.__init__()=Bio.Align.Generic.Alignment-class.html#__init__,Method Bio.AlignAce.Applications.AlignAceCommandline.__init__()=Bio.AlignAce.Applications.AlignAceCommandline-class.html#__init__,Method Bio.AlignAce.Applications.CompareAceCommandline.__init__()=Bio.AlignAce.Applications.CompareAceCommandline-class.html#__init__,Method Bio.AlignAce.Motif.Motif.__init__()=Bio.AlignAce.Motif.Motif-class.html#__init__,Method Bio.AlignAce.Parser.AlignAceConsumer.__init__()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#__init__,Method Bio.AlignAce.Parser.AlignAceParser.__init__()=Bio.AlignAce.Parser.AlignAceParser-class.html#__init__,Method Bio.AlignAce.Parser.CompareAceConsumer.__init__()=Bio.AlignAce.Parser.CompareAceConsumer-class.html#__init__,Method Bio.AlignAce.Parser.CompareAceParser.__init__()=Bio.AlignAce.Parser.CompareAceParser-class.html#__init__,Method Bio.AlignIO.Interfaces.AlignmentIterator.__init__()=Bio.AlignIO.Interfaces.AlignmentIterator-class.html#__init__,Method Bio.AlignIO.Interfaces.AlignmentWriter.__init__()=Bio.AlignIO.Interfaces.AlignmentWriter-class.html#__init__,Method Bio.AlignIO.Interfaces.SequentialAlignmentWriter.__init__()=Bio.AlignIO.Interfaces.SequentialAlignmentWriter-class.html#__init__,Method Bio.Alphabet.AlphabetEncoder.__init__()=Bio.Alphabet.AlphabetEncoder-class.html#__init__,Method Bio.Alphabet.Gapped.__init__()=Bio.Alphabet.Gapped-class.html#__init__,Method Bio.Alphabet.HasStopCodon.__init__()=Bio.Alphabet.HasStopCodon-class.html#__init__,Method Bio.Application.AbstractCommandline.__init__()=Bio.Application.AbstractCommandline-class.html#__init__,Method Bio.Application.ApplicationResult.__init__()=Bio.Application.ApplicationResult-class.html#__init__,Method Bio.Application._AbstractParameter.__init__()=Bio.Application._AbstractParameter-class.html#__init__,Method Bio.Blast.Applications.BlastallCommandline.__init__()=Bio.Blast.Applications.BlastallCommandline-class.html#__init__,Method Bio.Blast.Applications.FastacmdCommandline.__init__()=Bio.Blast.Applications.FastacmdCommandline-class.html#__init__,Method Bio.Blast.NCBIStandalone.BlastErrorParser.__init__()=Bio.Blast.NCBIStandalone.BlastErrorParser-class.html#__init__,Method Bio.Blast.NCBIStandalone.BlastParser.__init__()=Bio.Blast.NCBIStandalone.BlastParser-class.html#__init__,Method Bio.Blast.NCBIStandalone.Iterator.__init__()=Bio.Blast.NCBIStandalone.Iterator-class.html#__init__,Method Bio.Blast.NCBIStandalone.PSIBlastParser.__init__()=Bio.Blast.NCBIStandalone.PSIBlastParser-class.html#__init__,Method Bio.Blast.NCBIStandalone._BlastConsumer.__init__()=Bio.Blast.NCBIStandalone._BlastConsumer-class.html#__init__,Method Bio.Blast.NCBIStandalone._BlastErrorConsumer.__init__()=Bio.Blast.NCBIStandalone._BlastErrorConsumer-class.html#__init__,Method Bio.Blast.NCBIStandalone._PSIBlastConsumer.__init__()=Bio.Blast.NCBIStandalone._PSIBlastConsumer-class.html#__init__,Method Bio.Blast.NCBIWWW.BlastParser.__init__()=Bio.Blast.NCBIWWW.BlastParser-class.html#__init__,Method Bio.Blast.NCBIXML.BlastParser.__init__()=Bio.Blast.NCBIXML.BlastParser-class.html#__init__,Method Bio.Blast.NCBIXML._XMLparser.__init__()=Bio.Blast.NCBIXML._XMLparser-class.html#__init__,Method Bio.Blast.ParseBlastTable.BlastTableEntry.__init__()=Bio.Blast.ParseBlastTable.BlastTableEntry-class.html#__init__,Method Bio.Blast.ParseBlastTable.BlastTableReader.__init__()=Bio.Blast.ParseBlastTable.BlastTableReader-class.html#__init__,Method Bio.Blast.ParseBlastTable.BlastTableRec.__init__()=Bio.Blast.ParseBlastTable.BlastTableRec-class.html#__init__,Method Bio.Blast.Record.Alignment.__init__()=Bio.Blast.Record.Alignment-class.html#__init__,Method Bio.Blast.Record.Blast.__init__()=Bio.Blast.Record.Blast-class.html#__init__,Method Bio.Blast.Record.DatabaseReport.__init__()=Bio.Blast.Record.DatabaseReport-class.html#__init__,Method Bio.Blast.Record.Description.__init__()=Bio.Blast.Record.Description-class.html#__init__,Method Bio.Blast.Record.HSP.__init__()=Bio.Blast.Record.HSP-class.html#__init__,Method Bio.Blast.Record.Header.__init__()=Bio.Blast.Record.Header-class.html#__init__,Method Bio.Blast.Record.MultipleAlignment.__init__()=Bio.Blast.Record.MultipleAlignment-class.html#__init__,Method Bio.Blast.Record.PSIBlast.__init__()=Bio.Blast.Record.PSIBlast-class.html#__init__,Method Bio.Blast.Record.Parameters.__init__()=Bio.Blast.Record.Parameters-class.html#__init__,Method Bio.Blast.Record.Round.__init__()=Bio.Blast.Record.Round-class.html#__init__,Method Bio.CAPS.CAPSMap.__init__()=Bio.CAPS.CAPSMap-class.html#__init__,Method Bio.CAPS.DifferentialCutsite.__init__()=Bio.CAPS.DifferentialCutsite-class.html#__init__,Method Bio.CDD.Iterator.__init__()=Bio.CDD.Iterator-class.html#__init__,Method Bio.CDD.Record.Record.__init__()=Bio.CDD.Record.Record-class.html#__init__,Method Bio.CDD.RecordParser.__init__()=Bio.CDD.RecordParser-class.html#__init__,Method Bio.CDD._RecordConsumer.__init__()=Bio.CDD._RecordConsumer-class.html#__init__,Method Bio.CDD._Scanner.__init__()=Bio.CDD._Scanner-class.html#__init__,Method Bio.Clustalw.ClustalAlignment.__init__()=Bio.Clustalw.ClustalAlignment-class.html#__init__,Method Bio.Clustalw.MultipleAlignCL.__init__()=Bio.Clustalw.MultipleAlignCL-class.html#__init__,Method Bio.Cluster.DataFile.__init__()=Bio.Cluster.DataFile-class.html#__init__,Method Bio.Cluster.Record.__init__()=Bio.Cluster.Record-class.html#__init__,Method 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Bio.Blast.NCBIStandalone._BlastConsumer.__init__
Bio.Blast.NCBIStandalone._BlastErrorConsumer.__init__
Bio.Blast.NCBIStandalone._PSIBlastConsumer.__init__
Bio.Blast.NCBIWWW.BlastParser.__init__
Bio.Blast.NCBIXML.BlastParser.__init__
Bio.Blast.NCBIXML._XMLparser.__init__
Bio.Blast.ParseBlastTable.BlastTableEntry.__init__
Bio.Blast.ParseBlastTable.BlastTableReader.__init__
Bio.Blast.ParseBlastTable.BlastTableRec.__init__
Bio.Blast.Record.Alignment.__init__
Bio.Blast.Record.Blast.__init__
Bio.Blast.Record.DatabaseReport.__init__
Bio.Blast.Record.Description.__init__
Bio.Blast.Record.HSP.__init__
Bio.Blast.Record.Header.__init__
Bio.Blast.Record.MultipleAlignment.__init__
Bio.Blast.Record.PSIBlast.__init__
Bio.Blast.Record.Parameters.__init__
Bio.Blast.Record.Round.__init__
Bio.CAPS.CAPSMap.__init__
Bio.CAPS.DifferentialCutsite.__init__
Bio.CDD.Iterator.__init__
Bio.CDD.Record.Record.__init__
Bio.CDD.RecordParser.__init__
Bio.CDD._RecordConsumer.__init__
Bio.CDD._Scanner.__init__
Bio.Clustalw.ClustalAlignment.__init__
Bio.Clustalw.MultipleAlignCL.__init__
Bio.Cluster.DataFile.__init__
Bio.Cluster.Record.__init__
Bio.Compass.Iterator.__init__
Bio.Compass.Record.__init__
Bio.Compass.RecordParser.__init__
Bio.Compass._Consumer.__init__
Bio.Crystal.Chain.__init__
Bio.Crystal.Crystal.__init__
Bio.Crystal.CrystalError.__init__
Bio.Crystal.Error.__init__
Bio.Crystal.Hetero.__init__
Bio.DBXRef.DBXRef.__init__
Bio.Data.CodonTable.AmbiguousCodonTable.__init__
Bio.Data.CodonTable.AmbiguousForwardTable.__init__
Bio.Data.CodonTable.CodonTable.__init__
Bio.Data.CodonTable.NCBICodonTable.__init__
Bio.Decode.DecodeParser.__init__
Bio.Decode.DecodeScanner.__init__
Bio.Decode.Float.__init__
Bio.Decode.Function.__init__
Bio.Decode.FunctionCall.__init__
Bio.Decode.FunctionCallChain.__init__
Bio.Decode.FunctionName.__init__
Bio.Decode.Integer.__init__
Bio.Decode.String.__init__
Bio.Decode.Token.__init__
Bio.Decode.ValueToken.__init__
Bio.DocSQL.Create.__init__
Bio.DocSQL.Insert.__init__
Bio.DocSQL.IterationCursor.__init__
Bio.DocSQL.Query.__init__
Bio.DocSQL.QueryAll.__init__
Bio.DocSQL.QueryGeneric.__init__
Bio.DocSQL.QueryRow.__init__
Bio.DocSQL.QuerySingle.__init__
Bio.ECell.ECellError.__init__
Bio.ECell.Error.__init__
Bio.ECell.Iterator.__init__
Bio.ECell.Record.Record.__init__
Bio.ECell.RecordParser.__init__
Bio.ECell._RecordConsumer.__init__
Bio.ECell._Scanner.__init__
Bio.EUtils.Config.DatabaseInfo.__init__
Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet.__init__
Bio.EUtils.DBIdsClient.DBIdsClient.__init__
Bio.EUtils.DBIdsClient.DBIdsLookup.__init__
Bio.EUtils.Datatypes.BinaryOp.__init__
Bio.EUtils.Datatypes.CheckLinkSet.__init__
Bio.EUtils.Datatypes.DBIds.__init__
Bio.EUtils.Datatypes.Date.__init__
Bio.EUtils.Datatypes.DateRange.__init__
Bio.EUtils.Datatypes.EUtilsSearchError.__init__
Bio.EUtils.Datatypes.IdCheck.__init__
Bio.EUtils.Datatypes.IdUrlSet.__init__
Bio.EUtils.Datatypes.Link.__init__
Bio.EUtils.Datatypes.LinkSetDb.__init__
Bio.EUtils.Datatypes.LinksLinkSet.__init__
Bio.EUtils.Datatypes.NeighborLinkSet.__init__
Bio.EUtils.Datatypes.ObjUrl.__init__
Bio.EUtils.Datatypes.PostResult.__init__
Bio.EUtils.Datatypes.Problem.__init__
Bio.EUtils.Datatypes.Provider.__init__
Bio.EUtils.Datatypes.Range.__init__
Bio.EUtils.Datatypes.SearchResult.__init__
Bio.EUtils.Datatypes.Summary.__init__
Bio.EUtils.Datatypes.Term.__init__
Bio.EUtils.Datatypes.WithinNDays.__init__
Bio.EUtils.HistoryClient.BaseHistoryRecordSet.__init__
Bio.EUtils.HistoryClient.HistoryClient.__init__
Bio.EUtils.HistoryClient.HistoryCookie.__init__
Bio.EUtils.HistoryClient.HistoryLookup.__init__
Bio.EUtils.HistoryClient.HistoryRecord.__init__
Bio.EUtils.MultiDict.OrderedMultiDict.__init__
Bio.EUtils.MultiDict.UnorderedMultiDict.__init__
Bio.EUtils.POM.Comment.__init__
Bio.EUtils.POM.ContentModel.__init__
Bio.EUtils.POM.DTDConsumerForSourceGeneration.__init__
Bio.EUtils.POM.ElementNode.__init__
Bio.EUtils.POM.IndentedText.__init__
Bio.EUtils.POM.ObjectParserHandler.__init__
Bio.EUtils.POM.POMDocument.__init__
Bio.EUtils.POM.XMLAttribute.__init__
Bio.EUtils.POM._ContentModelGenerator.__init__
Bio.EUtils.ReseekFile.ReseekFile.__init__
Bio.EUtils.ThinClient.ThinClient.__init__
Bio.EUtils.parse.UsePOMParser.__init__
Bio.EUtils.sourcegen.ClassHolder.__init__
Bio.EUtils.sourcegen.FunctionHolder.__init__
Bio.EUtils.sourcegen.MethodHolder.__init__
Bio.EUtils.sourcegen.SourceFile.__init__
Bio.EUtils.sourcegen.SourceGen.__init__
Bio.Emboss.Applications.EConsenseCommandline.__init__
Bio.Emboss.Applications.EInvertedCommandline.__init__
Bio.Emboss.Applications.ENeighborCommandline.__init__
Bio.Emboss.Applications.EProtDistCommandline.__init__
Bio.Emboss.Applications.EProtParsCommandline.__init__
Bio.Emboss.Applications.ESeqBootCommandline.__init__
Bio.Emboss.Applications.ETandemCommandline.__init__
Bio.Emboss.Applications.Est2GenomeCommandline.__init__
Bio.Emboss.Applications.FuzznucCommandline.__init__
Bio.Emboss.Applications.PalindromeCommandline.__init__
Bio.Emboss.Applications.Primer3Commandline.__init__
Bio.Emboss.Applications.PrimerSearchCommandline.__init__
Bio.Emboss.Applications.TranalignCommandline.__init__
Bio.Emboss.Applications.WaterCommandline.__init__
Bio.Emboss.Primer.Primer3Parser.__init__
Bio.Emboss.Primer.Primer3Primers.__init__
Bio.Emboss.Primer.Primer3Record.__init__
Bio.Emboss.Primer.PrimerSearchAmplifier.__init__
Bio.Emboss.Primer.PrimerSearchInputRecord.__init__
Bio.Emboss.Primer.PrimerSearchOutputRecord.__init__
Bio.Emboss.Primer.PrimerSearchParser.__init__
Bio.Emboss.Primer._Primer3RecordConsumer.__init__
Bio.Emboss.Primer._Primer3Scanner.__init__
Bio.Emboss.Primer._PrimerSearchRecordConsumer.__init__
Bio.Emboss.Primer._PrimerSearchScanner.__init__
Bio.Entrez.Parser.DataHandler.__init__
Bio.Entrez.Parser.StructureElement.__init__
Bio.Enzyme.DataRecord.__init__
Bio.Enzyme.EnzymeRecord.__init__
Bio.Enzyme.Iterator.__init__
Bio.Enzyme.RecordParser.__init__
Bio.Enzyme._RecordConsumer.__init__
Bio.FSSP.FSSPAlignDict.__init__
Bio.FSSP.FSSPAlignRec.__init__
Bio.FSSP.FSSPHeader.__init__
Bio.FSSP.FSSPSumRec.__init__
Bio.FSSP.FSSPTools.FSSPMultAlign.__init__
Bio.FSSP.PosAlign.__init__
Bio.FSSP.fssp_rec.fff_rec.__init__
Bio.Fasta.FastaAlign.FastaAlignment.__init__
Bio.Fasta.Iterator.__init__
Bio.Fasta.Record.__init__
Bio.Fasta.RecordParser.__init__
Bio.Fasta.SequenceParser.__init__
Bio.File.SGMLHandle.__init__
Bio.File.SGMLStripper.MyParser.__init__
Bio.File.SGMLStripper.__init__
Bio.File.UndoHandle.__init__
Bio.FilteredReader.FilteredReader.__init__
Bio.GA.Crossover.General.SafeFitnessCrossover.__init__
Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover.__init__
Bio.GA.Crossover.GeneralPoint.InterleaveCrossover.__init__
Bio.GA.Crossover.Point.SinglePointCrossover.__init__
Bio.GA.Crossover.TwoPoint.TwoPointCrossover.__init__
Bio.GA.Crossover.Uniform.UniformCrossover.__init__
Bio.GA.Evolver.GenerationEvolver.__init__
Bio.GA.Evolver.SteadyStateEvolver.__init__
Bio.GA.Mutation.General.SafeFitnessMutation.__init__
Bio.GA.Mutation.Simple.ConversionMutation.__init__
Bio.GA.Mutation.Simple.SinglePositionMutation.__init__
Bio.GA.Organism.Organism.__init__
Bio.GA.Repair.Stabilizing.AmbiguousRepair.__init__
Bio.GA.Selection.Abstract.AbstractSelection.__init__
Bio.GA.Selection.Diversity.DiversitySelection.__init__
Bio.GA.Selection.RouletteWheel.RouletteWheelSelection.__init__
Bio.GA.Selection.Tournament.TournamentSelection.__init__
Bio.GFF.Connection.__init__
Bio.GFF.Feature.__init__
Bio.GFF.FeatureAggregate.__init__
Bio.GFF.FeatureQuery.__init__
Bio.GFF.FeatureQueryRow.__init__
Bio.GFF.GenericTools.ArgsParser.__init__
Bio.GFF.GenericTools.Surrogate.__init__
Bio.GFF.GenericTools.TempFile.__init__
Bio.GFF.RetrieveSeqname.__init__
Bio.GFF.Segment.__init__
Bio.GFF.easy.FeatureDict.__init__
Bio.GFF.easy.Location.__init__
Bio.GFF.easy.LocationFromCoords.__init__
Bio.GFF.easy.LocationFromString.__init__
Bio.GFF.easy.LocationJoin.__init__
Bio.GenBank.FeatureParser.__init__
Bio.GenBank.Iterator.__init__
Bio.GenBank.LocationParser.AbsoluteLocation.__init__
Bio.GenBank.LocationParser.Between.__init__
Bio.GenBank.LocationParser.FeatureName.__init__
Bio.GenBank.LocationParser.Function.__init__
Bio.GenBank.LocationParser.HighBound.__init__
Bio.GenBank.LocationParser.Integer.__init__
Bio.GenBank.LocationParser.LocationParser.__init__
Bio.GenBank.LocationParser.LocationScanner.__init__
Bio.GenBank.LocationParser.LowBound.__init__
Bio.GenBank.LocationParser.Path.__init__
Bio.GenBank.LocationParser.Range.__init__
Bio.GenBank.LocationParser.Symbol.__init__
Bio.GenBank.LocationParser.Token.__init__
Bio.GenBank.LocationParser.TwoBound.__init__
Bio.GenBank.NCBIDictionary.__init__
Bio.GenBank.Record.Feature.__init__
Bio.GenBank.Record.Qualifier.__init__
Bio.GenBank.Record.Record.__init__
Bio.GenBank.Record.Reference.__init__
Bio.GenBank.RecordParser.__init__
Bio.GenBank.Scanner.InsdcScanner.__init__
Bio.GenBank._BaseGenBankConsumer.__init__
Bio.GenBank._FeatureConsumer.__init__
Bio.GenBank._RecordConsumer.__init__
Bio.GenBank.utils.FeatureValueCleaner.__init__
Bio.Geo.Record.Record.__init__
Bio.Gobase.Dictionary.__init__
Bio.Gobase.GeneRecord.__init__
Bio.Gobase.Iterator.__init__
Bio.Gobase.ProteinRecord.__init__
Bio.Gobase.Record.__init__
Bio.Gobase.RecordParser.__init__
Bio.Gobase.SequenceRecord.__init__
Bio.Gobase._RecordConsumer.__init__
Bio.Graphics.BasicChromosome.Chromosome.__init__
Bio.Graphics.BasicChromosome.ChromosomeSegment.__init__
Bio.Graphics.BasicChromosome.Organism.__init__
Bio.Graphics.BasicChromosome.TelomereSegment.__init__
Bio.Graphics.BasicChromosome._ChromosomeComponent.__init__
Bio.Graphics.Comparative.ComparativeScatterPlot.__init__
Bio.Graphics.DisplayRepresentation.ChromosomeCounts.__init__
Bio.Graphics.Distribution.BarChartDistribution.__init__
Bio.Graphics.Distribution.DistributionPage.__init__
Bio.Graphics.Distribution.LineDistribution.__init__
Bio.HMM.DynamicProgramming.AbstractDPAlgorithms.__init__
Bio.HMM.DynamicProgramming.LogDPAlgorithms.__init__
Bio.HMM.DynamicProgramming.ScaledDPAlgorithms.__init__
Bio.HMM.MarkovModel.HiddenMarkovModel.__init__
Bio.HMM.MarkovModel.MarkovModelBuilder.__init__
Bio.HMM.Trainer.AbstractTrainer.__init__
Bio.HMM.Trainer.BaumWelchTrainer.__init__
Bio.HMM.Trainer.KnownStateTrainer.__init__
Bio.HMM.Trainer.TrainingSequence.__init__
Bio.HotRand.HotCache.__init__
Bio.HotRand.HotRandom.__init__
Bio.Index._InMemoryIndex.__init__
Bio.Index._ShelveIndex.__init__
Bio.IntelliGenetics.IntelliGeneticsReader.__init__
Bio.IntelliGenetics.Iterator.__init__
Bio.IntelliGenetics.Record.Record.__init__
Bio.IntelliGenetics.RecordParser.__init__
Bio.IntelliGenetics._RecordConsumer.__init__
Bio.IntelliGenetics._Scanner.__init__
Bio.KDTree.CKDTree.KDTree.__init__
Bio.KDTree.CKDTree.KDTreePtr.__init__
Bio.KDTree.KDTree.KDTree.__init__
Bio.KEGG.Compound.Record.__init__
Bio.KEGG.Enzyme.Record.__init__
Bio.LocusLink.Iterator.__init__
Bio.LocusLink.Record.__init__
Bio.LocusLink.RecordParser.__init__
Bio.LocusLink._RecordConsumer.__init__
Bio.LocusLink._Scanner.__init__
Bio.LocusLink.web_parse.Record.__init__
Bio.LocusLink.web_parse.Token.__init__
Bio.LocusLink.web_parse.Url.__init__
Bio.LogisticRegression.LogisticRegression.__init__
Bio.MEME.Motif.Instance.__init__
Bio.MEME.Motif.MEMEMotif.__init__
Bio.MEME.Motif.Motif.__init__
Bio.MEME.Parser.MASTParser.__init__
Bio.MEME.Parser.MASTRecord.__init__
Bio.MEME.Parser.MEMEParser.__init__
Bio.MEME.Parser.MEMERecord.__init__
Bio.MEME.Parser._MASTConsumer.__init__
Bio.MEME.Parser._MEMEConsumer.__init__
Bio.MarkovModel.MarkovModel.__init__
Bio.MaxEntropy.MaxEntropy.__init__
Bio.Medline.Iterator.__init__
Bio.Medline.Record.__init__
Bio.Medline.RecordParser.__init__
Bio.Medline._RecordConsumer.__init__
Bio.MetaTool.Iterator.__init__
Bio.MetaTool.Record.Metabolite.__init__
Bio.MetaTool.Record.MetaboliteRole.__init__
Bio.MetaTool.Record.PathwayTransform.__init__
Bio.MetaTool.Record.Record.__init__
Bio.MetaTool.RecordParser.__init__
Bio.MetaTool._RecordConsumer.__init__
Bio.MetaTool._Scanner.__init__
Bio.Mindy.BaseDB.OpenDB.__init__
Bio.Mindy.BerkeleyDB.BerkeleyDB.__init__
Bio.Mindy.BerkeleyDB.PrimaryNamespace.__init__
Bio.Mindy.BerkeleyDB.SecondaryNamespace.__init__
Bio.Mindy.FlatDB.BaseFlatDB.__init__
Bio.Mindy.FlatDB.BisectFile.__init__
Bio.Mindy.FlatDB.DiskFlatDB.__init__
Bio.Mindy.FlatDB.MemoryFlatDB.__init__
Bio.Mindy.FlatDB.PrimaryNamespace.__init__
Bio.Mindy.FlatDB.PrimaryTable.__init__
Bio.Mindy.FlatDB.SecondaryNamespace.__init__
Bio.Mindy.FlatDB.SecondaryTable.__init__
Bio.Mindy.Location.Location.__init__
Bio.Mindy.SimpleSeqRecord.BaseSeqRecordIndexer.__init__
Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder.__init__
Bio.Mindy.SimpleSeqRecord.FunctionIndexer.__init__
Bio.Mindy.SimpleSeqRecord.SimpleIndexer.__init__
Bio.Mindy.XPath.GrabXPathNodes.__init__
Bio.NBRF.Iterator.__init__
Bio.NBRF.Record.Record.__init__
Bio.NBRF.RecordParser.__init__
Bio.NBRF._RecordConsumer.__init__
Bio.NBRF._Scanner.__init__
Bio.NMR.xpktools.Peaklist.__init__
Bio.NMR.xpktools.XpkEntry.__init__
Bio.NaiveBayes.NaiveBayes.__init__
Bio.Ndb.Record.__init__
Bio.NetCatch.ExtractUrls.__init__
Bio.NetCatch.NetCatch.__init__
Bio.NetCatch.Url.__init__
Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.__init__
Bio.NeuralNetwork.BackPropagation.Network.BasicNetwork.__init__
Bio.NeuralNetwork.Gene.Motif.MotifCoder.__init__
Bio.NeuralNetwork.Gene.Motif.MotifFinder.__init__
Bio.NeuralNetwork.Gene.Pattern.PatternIO.__init__
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.__init__
Bio.NeuralNetwork.Gene.Schema.DifferentialSchemaFitness.__init__
Bio.NeuralNetwork.Gene.Schema.GeneticAlgorithmFinder.__init__
Bio.NeuralNetwork.Gene.Schema.MostCountSchemaFitness.__init__
Bio.NeuralNetwork.Gene.Schema.RandomMotifGenerator.__init__
Bio.NeuralNetwork.Gene.Schema.Schema.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaCoder.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaFactory.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.__init__
Bio.NeuralNetwork.Gene.Schema.SimpleFinisher.__init__
Bio.NeuralNetwork.Gene.Signature.SignatureCoder.__init__
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.__init__
Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop.__init__
Bio.NeuralNetwork.Training.ExampleManager.__init__
Bio.NeuralNetwork.Training.TrainingExample.__init__
Bio.Nexus.Nexus.Block.__init__
Bio.Nexus.Nexus.CharBuffer.__init__
Bio.Nexus.Nexus.Commandline.__init__
Bio.Nexus.Nexus.Nexus.__init__
Bio.Nexus.Nexus.StepMatrix.__init__
Bio.Nexus.Nodes.Chain.__init__
Bio.Nexus.Nodes.Node.__init__
Bio.Nexus.Trees.NodeData.__init__
Bio.Nexus.Trees.Tree.__init__
Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap.__init__
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__init__
Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap.__init__
Bio.PDB.Atom.Atom.__init__
Bio.PDB.Atom.DisorderedAtom.__init__
Bio.PDB.Chain.Chain.__init__
Bio.PDB.DSSP'.DSSP.__init__
Bio.PDB.Dice.ChainSelector.__init__
Bio.PDB.Entity.DisorderedEntityWrapper.__init__
Bio.PDB.Entity.Entity.__init__
Bio.PDB.FragmentMapper'.Fragment.__init__
Bio.PDB.FragmentMapper'.FragmentMapper.__init__
Bio.PDB.HSExposure.ExposureCN.__init__
Bio.PDB.HSExposure.HSExposureCA.__init__
Bio.PDB.HSExposure.HSExposureCB.__init__
Bio.PDB.HSExposure._AbstractHSExposure.__init__
Bio.PDB.MMCIF2Dict.MMCIF2Dict.__init__
Bio.PDB.Model.Model.__init__
Bio.PDB.NACCESS.NACCESS.__init__
Bio.PDB.NACCESS.NACCESS_atomic.__init__
Bio.PDB.NeighborSearch.NeighborSearch.__init__
Bio.PDB.PDBIO'.PDBIO.__init__
Bio.PDB.PDBList'.PDBList.__init__
Bio.PDB.PDBParser'.PDBParser.__init__
Bio.PDB.PSEA.PSEA.__init__
Bio.PDB.Polypeptide.CaPPBuilder.__init__
Bio.PDB.Polypeptide.PPBuilder.__init__
Bio.PDB.Polypeptide._PPBuilder.__init__
Bio.PDB.Residue.DisorderedResidue.__init__
Bio.PDB.Residue.Residue.__init__
Bio.PDB.ResidueDepth'.ResidueDepth.__init__
Bio.PDB.Structure.Structure.__init__
Bio.PDB.StructureAlignment'.StructureAlignment.__init__
Bio.PDB.StructureBuilder.StructureBuilder.__init__
Bio.PDB.Superimposer'.Superimposer.__init__
Bio.PDB.Vector'.Vector.__init__
Bio.ParserSupport.EventGenerator.__init__
Bio.ParserSupport.SGMLStrippingConsumer.__init__
Bio.ParserSupport.TaggingConsumer.__init__
Bio.Parsers.spark.GenericASTBuilder.__init__
Bio.Parsers.spark.GenericASTMatcher.__init__
Bio.Parsers.spark.GenericASTTraversal.__init__
Bio.Parsers.spark.GenericParser.__init__
Bio.Parsers.spark.GenericScanner.__init__
Bio.Pathway.Network.__init__
Bio.Pathway.Reaction.__init__
Bio.Pathway.Rep.Graph.Graph.__init__
Bio.Pathway.Rep.HashSet.HashSet.__init__
Bio.Pathway.Rep.MultiGraph.MultiGraph.__init__
Bio.Pathway.System.__init__
Bio.PopGen.Async.Async.__init__
Bio.PopGen.Async.DirectoryRetriever.__init__
Bio.PopGen.Async.FileRetriever.__init__
Bio.PopGen.Async.Local.Local.__init__
Bio.PopGen.FDist.Async.FDistAsync.__init__
Bio.PopGen.FDist.Async.SplitFDist.__init__
Bio.PopGen.FDist.Controller.FDistController.__init__
Bio.PopGen.FDist.Record.__init__
Bio.PopGen.FDist.RecordParser.__init__
Bio.PopGen.FDist._RecordConsumer.__init__
Bio.PopGen.GenePop.Record.__init__
Bio.PopGen.GenePop.RecordParser.__init__
Bio.PopGen.GenePop._RecordConsumer.__init__
Bio.PopGen.SimCoal.Async.SimCoalCache.__init__
Bio.PopGen.SimCoal.Cache.SimCoalCache.__init__
Bio.PopGen.SimCoal.Controller.SimCoalController.__init__
Bio.PropertyManager.PropertyManager.__init__
Bio.Prosite.Dictionary.__init__
Bio.Prosite.ExPASyDictionary.__init__
Bio.Prosite.Iterator.__init__
Bio.Prosite.Pattern.Prosite.__init__
Bio.Prosite.Pattern.PrositeMatch.__init__
Bio.Prosite.Pattern.PrositeTerm.__init__
Bio.Prosite.PatternHit.__init__
Bio.Prosite.Prodoc.Dictionary.__init__
Bio.Prosite.Prodoc.ExPASyDictionary.__init__
Bio.Prosite.Prodoc.Iterator.__init__
Bio.Prosite.Prodoc.Record.__init__
Bio.Prosite.Prodoc.RecordParser.__init__
Bio.Prosite.Prodoc.Reference.__init__
Bio.Prosite.Prodoc._RecordConsumer.__init__
Bio.Prosite.Record.__init__
Bio.Prosite.RecordParser.__init__
Bio.Prosite._RecordConsumer.__init__
Bio.PubMed.Dictionary.__init__
Bio.Rebase.Dictionary.__init__
Bio.Rebase.Iterator.__init__
Bio.Rebase.Record.__init__
Bio.Rebase.RecordParser.__init__
Bio.Rebase._RecordConsumer.__init__
Bio.Restriction.PrintFormat.PrintFormat.__init__
Bio.Restriction.Restriction.Analysis.__init__
Bio.Restriction.Restriction.FormattedSeq.__init__
Bio.Restriction.Restriction.RestrictionBatch.__init__
Bio.Restriction.Restriction.RestrictionType.__init__
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.__init__
Bio.Restriction._Update.RestrictionCompiler.TypeCompiler.__init__
Bio.Restriction._Update.RestrictionCompiler.newenzyme.__init__
Bio.Restriction._Update.Update.ConnectionError.__init__
Bio.Restriction._Update.Update.FtpNameError.__init__
Bio.Restriction._Update.Update.FtpPasswordError.__init__
Bio.Restriction._Update.Update.RebaseUpdate.__init__
Bio.SCOP.Astral.__init__
Bio.SCOP.Cla.Index.__init__
Bio.SCOP.Cla.Iterator.__init__
Bio.SCOP.Cla.Parser.__init__
Bio.SCOP.Cla.Record.__init__
Bio.SCOP.Des.Iterator.__init__
Bio.SCOP.Des.Parser.__init__
Bio.SCOP.Des.Record.__init__
Bio.SCOP.Dom.Iterator.__init__
Bio.SCOP.Dom.Record.__init__
Bio.SCOP.Domain.__init__
Bio.SCOP.FileIndex.FileIndex.__init__
Bio.SCOP.FileIndex.defaultdict.__init__
Bio.SCOP.Hie.Iterator.__init__
Bio.SCOP.Hie.Parser.__init__
Bio.SCOP.Hie.Record.__init__
Bio.SCOP.Node.__init__
Bio.SCOP.Raf.Iterator.__init__
Bio.SCOP.Raf.Parser.__init__
Bio.SCOP.Raf.Res.__init__
Bio.SCOP.Raf.SeqMap.__init__
Bio.SCOP.Raf.SeqMapIndex.__init__
Bio.SCOP.Residues'.Residues.__init__
Bio.SCOP.Scop.__init__
Bio.SGMLExtractor.SGMLExtractor.LocalParser.__init__
Bio.SGMLExtractor.SGMLExtractor.__init__
Bio.SGMLExtractor.SGMLExtractorHandle.__init__
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__
Bio.Saf.Iterator.__init__
Bio.Saf.Record.Record.__init__
Bio.Saf.RecordParser.__init__
Bio.Saf._RecordConsumer.__init__
Bio.Saf._Scanner.__init__
Bio.Search.Algorithm.__init__
Bio.Search.Database.__init__
Bio.Search.HSP.__init__
Bio.Search.HSPSeq.__init__
Bio.Search.Hit.__init__
Bio.Search.HomologySeq.__init__
Bio.Search.Query.__init__
Bio.Search.Search.__init__
Bio.Search.TableInfo.__init__
Bio.Search._SeqLength.__init__
Bio.Seq.MutableSeq.__init__
Bio.Seq.Seq.__init__
Bio.SeqFeature.AbstractPosition.__init__
Bio.SeqFeature.AfterPosition.__init__
Bio.SeqFeature.BeforePosition.__init__
Bio.SeqFeature.BetweenPosition.__init__
Bio.SeqFeature.ExactPosition.__init__
Bio.SeqFeature.FeatureLocation.__init__
Bio.SeqFeature.OneOfPosition.__init__
Bio.SeqFeature.PositionGap.__init__
Bio.SeqFeature.Reference.__init__
Bio.SeqFeature.SeqFeature.__init__
Bio.SeqFeature.WithinPosition.__init__
Bio.SeqIO.ClustalIO.ClustalWriter.__init__
Bio.SeqIO.FastaIO.FastaWriter.__init__
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceWriter.__init__
Bio.SeqIO.Interfaces.SequentialSequenceWriter.__init__
Bio.SeqIO.PhylipIO.PhylipWriter.__init__
Bio.SeqIO.StockholmIO.StockholmIterator.__init__
Bio.SeqIO.StockholmIO.StockholmWriter.__init__
Bio.SeqRecord.SeqRecord.__init__
Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.__init__
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__
Bio.SeqUtils.MissingTable.__init__
Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__
Bio.Sequencing.Ace.ACEFileRecord.__init__
Bio.Sequencing.Ace.ACEParser.__init__
Bio.Sequencing.Ace.Contig.__init__
Bio.Sequencing.Ace.Iterator.__init__
Bio.Sequencing.Ace.Reads.__init__
Bio.Sequencing.Ace.RecordParser.__init__
Bio.Sequencing.Ace._RecordConsumer.__init__
Bio.Sequencing.Ace.af.__init__
Bio.Sequencing.Ace.bs.__init__
Bio.Sequencing.Ace.ct.__init__
Bio.Sequencing.Ace.ds.__init__
Bio.Sequencing.Ace.qa.__init__
Bio.Sequencing.Ace.rd.__init__
Bio.Sequencing.Ace.rt.__init__
Bio.Sequencing.Ace.wa.__init__
Bio.Sequencing.Ace.wr.__init__
Bio.Sequencing.Phd.Iterator.__init__
Bio.Sequencing.Phd.Record.__init__
Bio.Sequencing.Phd.RecordParser.__init__
Bio.Sequencing.Phd._RecordConsumer.__init__
Bio.Std.StdTerm.__init__
Bio.StdHandler.ConvertDispatchHandler.__init__
Bio.StdHandler.ConvertHandler.__init__
Bio.StdHandler.Feature.__init__
Bio.StdHandler.Handle_dbxref.__init__
Bio.StdHandler.Handle_feature_location.__init__
Bio.StdHandler.Handle_feature_qualifier.__init__
Bio.StdHandler.Handle_features.__init__
Bio.StdHandler.Handle_hsp.__init__
Bio.StdHandler.RecognizeHandler.__init__
Bio.SubsMat.FreqTable.FreqTable.__init__
Bio.SubsMat.SeqMat.__init__
Bio.SwissProt.KeyWList.ListParser.__init__
Bio.SwissProt.KeyWList.Record.__init__
Bio.SwissProt.KeyWList._ListConsumer.__init__
Bio.SwissProt.KeyWList._Scanner.__init__
Bio.SwissProt.SProt.Dictionary.__init__
Bio.SwissProt.SProt.ExPASyDictionary.__init__
Bio.SwissProt.SProt.Iterator.__init__
Bio.SwissProt.SProt.Record.__init__
Bio.SwissProt.SProt.RecordParser.__init__
Bio.SwissProt.SProt.Reference.__init__
Bio.SwissProt.SProt.SequenceParser.__init__
Bio.SwissProt.SProt._RecordConsumer.__init__
Bio.SwissProt.SProt._SequenceConsumer.__init__
Bio.Transcribe.Transcribe.__init__
Bio.Translate.Translator.__init__
Bio.UniGene.Iterator.__init__
Bio.UniGene.RecordParser.__init__
Bio.UniGene.UnigeneProtsimRecord.__init__
Bio.UniGene.UnigeneRecord.__init__
Bio.UniGene.UnigeneSTSRecord.__init__
Bio.UniGene.UnigeneSequenceRecord.__init__
Bio.UniGene._RecordConsumer.__init__
Bio.WWW.RequestLimiter.__init__
Bio.Wise.dnal.Statistics.__init__
Bio.Wise.psw.AlignmentColumn.__init__
Bio.Wise.psw.ColumnUnit.__init__
Bio.Writer.Writer.__init__
Bio.biblio.Biblio.__init__
Bio.biblio.BiblioCollection.__init__
Bio.builders.Search.search.BuildSearch.__init__
Bio.builders.SeqRecord.sequence.BuildSeqRecord.__init__
Bio.config.DBRegistry.BioCorbaDB.__init__
Bio.config.DBRegistry.BioSQLDB.__init__
Bio.config.DBRegistry.CGIDB.__init__
Bio.config.DBRegistry.DBGroup.__init__
Bio.config.DBRegistry.DBObject.__init__
Bio.config.DBRegistry.DBRegistry.__init__
Bio.config.DBRegistry.EUtilsDB.__init__
Bio.config.DBRegistry.IndexedFileDB.__init__
Bio.config.FormatRegistry.FormatGroup.__init__
Bio.config.FormatRegistry.FormatObject.__init__
Bio.config.FormatRegistry.FormatRegistry.__init__
Bio.config.Registry.RegisterableGroup.__init__
Bio.config.Registry.RegisterableObject.__init__
Bio.config.Registry.Registry.__init__
Bio.config.SeqDBRegistry.SeqDBRegistry.__init__
Bio.config._stanzaformat.Stanza.__init__
Bio.config._stanzaformat.StanzaFormat.__init__
Bio.config._support.make_cached_expression.__init__
Bio.config._support.make_rate_limited_function.__init__
Bio.kNN.kNN.__init__
Bio.pairwise2.affine_penalty.__init__
Bio.pairwise2.dictionary_match.__init__
Bio.pairwise2.identity_match.__init__
Bio.writers.SeqRecord.embl.WriteEmbl.__init__
Bio.writers.SeqRecord.fasta.WriteFasta.__init__
BioSQL.BioSeq.DBSeq.__init__
BioSQL.BioSeq.DBSeqRecord.__init__
BioSQL.BioSeqDatabase.Adaptor.__init__
BioSQL.BioSeqDatabase.BioSeqDatabase.__init__
BioSQL.BioSeqDatabase.DBServer.__init__
BioSQL.DBUtils.Generic_dbutils.__init__
BioSQL.Loader.DatabaseLoader.__init__
BioSQL.Loader.DatabaseRemover.__init__
Martel.Dispatch.Callback.__init__
Martel.Dispatch.DispatchHandler.__init__
Martel.Dispatch.Dispatcher.__init__
Martel.Dispatch.Multicall.__init__
Martel.Dispatch.RemapEnd.__init__
Martel.Dispatch.RemapStart.__init__
Martel.Expression.Alt.__init__
Martel.Expression.Any.__init__
Martel.Expression.Assert.__init__
Martel.Expression.Debug.__init__
Martel.Expression.FastFeature.__init__
Martel.Expression.Group.__init__
Martel.Expression.GroupRef.__init__
Martel.Expression.HeaderFooter.__init__
Martel.Expression.Literal.__init__
Martel.Expression.MaxRepeat.__init__
Martel.Expression.NullOp.__init__
Martel.Expression.ParseRecords.__init__
Martel.Expression.PassThrough.__init__
Martel.Expression.Seq.__init__
Martel.Expression.Str.__init__
Martel.Generate.CheckAssert.__init__
Martel.Generate.CheckAssertNot.__init__
Martel.Generate.CheckGroupRef.__init__
Martel.Generate.GeneratorState.__init__
Martel.Generate.HandleRepeatCount.__init__
Martel.Generate.SetGroupValue.__init__
Martel.Generate._call_call.__init__
Martel.Generate._call_calltag.__init__
Martel.Generate.print_debug.__init__
Martel.Generate.print_info.__init__
Martel.IterParser.IterHeaderFooter.__init__
Martel.IterParser.IterRecords.__init__
Martel.Iterator.EventStream.__init__
Martel.Iterator.HeaderFooterEventStream.__init__
Martel.Iterator.Iterate.__init__
Martel.Iterator.Iterator.__init__
Martel.Iterator.IteratorHeaderFooter.__init__
Martel.Iterator.IteratorRecords.__init__
Martel.Iterator.RecordEventStream.__init__
Martel.Iterator.StoreEvents.__init__
Martel.LAX.ElementInfo.__init__
Martel.LAX.LAX.__init__
Martel.Parser.HeaderFooterParser.__init__
Martel.Parser.Parser.__init__
Martel.Parser.ParserIncompleteException.__init__
Martel.Parser.ParserPositionException.__init__
Martel.Parser.RecordParser.__init__
Martel.RecordReader.CountLines.__init__
Martel.RecordReader.EndsWith.__init__
Martel.RecordReader.Everything.__init__
Martel.RecordReader.Nothing.__init__
Martel.RecordReader.RecordReader.__init__
Martel.RecordReader.StartsWith.__init__
Martel.RecordReader.Until.__init__
Martel.convert_re.GroupNames.__init__
Martel.msre_parse.Pattern.__init__
Martel.msre_parse.SubPattern.__init__
Martel.msre_parse.Tokenizer.__init__
Martel.test.support.CheckGood.__init__
Martel.test.support.Dump.__init__
Martel.test.support.Storage.__init__
Martel.test.test_Parser.CountErrors.__init__
Martel.test.test_Parser.CountRecords.__init__
Martel.test.test_delimiter.CatchFields.__init__
Martel.test.test_optimize.GetErrorPos.__init__" class="py-name" href="#" onclick="return doclink('link-14', '__init__', 'link-14');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">debug</tt><tt class="py-op">)</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parser</tt> <tt class="py-op">=</tt> <tt class="py-name">xml</tt><tt class="py-op">.</tt><tt class="py-name">sax</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name" targets="Method Bio.config.FormatRegistry.FormatObject.make_parser()=Bio.config.FormatRegistry.FormatObject-class.html#make_parser,Method Bio.config._support.make_cached_expression.make_parser()=Bio.config._support.make_cached_expression-class.html#make_parser,Method Martel.Expression.Expression.make_parser()=Martel.Expression.Expression-class.html#make_parser,Method Martel.Expression.HeaderFooter.make_parser()=Martel.Expression.HeaderFooter-class.html#make_parser,Method Martel.Expression.ParseRecords.make_parser()=Martel.Expression.ParseRecords-class.html#make_parser"><a title="Bio.config.FormatRegistry.FormatObject.make_parser
Bio.config._support.make_cached_expression.make_parser
Martel.Expression.Expression.make_parser
Martel.Expression.HeaderFooter.make_parser
Martel.Expression.ParseRecords.make_parser" class="py-name" href="#" onclick="return doclink('link-15', 'make_parser', 'link-15');">make_parser</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parser</tt><tt class="py-op">.</tt><tt class="py-name">setContentHandler</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-comment"># To avoid ValueError: unknown url type: NCBI_BlastOutput.dtd</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parser</tt><tt class="py-op">.</tt><tt class="py-name">setFeature</tt><tt class="py-op">(</tt><tt class="py-name">xml</tt><tt class="py-op">.</tt><tt class="py-name">sax</tt><tt class="py-op">.</tt><tt class="py-name">handler</tt><tt class="py-op">.</tt><tt class="py-name">feature_validation</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parser</tt><tt class="py-op">.</tt><tt class="py-name">setFeature</tt><tt class="py-op">(</tt><tt class="py-name">xml</tt><tt class="py-op">.</tt><tt class="py-name">sax</tt><tt class="py-op">.</tt><tt class="py-name">handler</tt><tt class="py-op">.</tt><tt class="py-name">feature_namespaces</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parser</tt><tt class="py-op">.</tt><tt class="py-name">setFeature</tt><tt class="py-op">(</tt><tt class="py-name">xml</tt><tt class="py-op">.</tt><tt class="py-name">sax</tt><tt class="py-op">.</tt><tt class="py-name">handler</tt><tt class="py-op">.</tt><tt class="py-name">feature_external_pes</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parser</tt><tt class="py-op">.</tt><tt class="py-name">setFeature</tt><tt class="py-op">(</tt><tt class="py-name">xml</tt><tt class="py-op">.</tt><tt class="py-name">sax</tt><tt class="py-op">.</tt><tt class="py-name">handler</tt><tt class="py-op">.</tt><tt class="py-name">feature_external_ges</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-16" class="py-name" targets="Method Bio.Blast.NCBIXML.BlastParser.reset()=Bio.Blast.NCBIXML.BlastParser-class.html#reset,Method Bio.InterPro.InterProParser.reset()=Bio.InterPro.InterProParser-class.html#reset,Method Bio.LocusLink.web_parse.LocusLinkParser.reset()=Bio.LocusLink.web_parse.LocusLinkParser-class.html#reset,Method Bio.Ndb.NdbParser.reset()=Bio.Ndb.NdbParser-class.html#reset,Method Bio.NetCatch.ExtractUrls.reset()=Bio.NetCatch.ExtractUrls-class.html#reset"><a title="Bio.Blast.NCBIXML.BlastParser.reset
Bio.InterPro.InterProParser.reset
Bio.LocusLink.web_parse.LocusLinkParser.reset
Bio.Ndb.NdbParser.reset
Bio.NetCatch.ExtractUrls.reset" class="py-name" href="#" onclick="return doclink('link-16', 'reset', 'link-16');">reset</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> </tt>
<a name="BlastParser.reset"></a><div id="BlastParser.reset-def"><a name="L138"></a><tt class="py-lineno">138</tt> <a class="py-toggle" href="#" id="BlastParser.reset-toggle" onclick="return toggle('BlastParser.reset');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#reset">reset</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.reset-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser.reset-expanded"><a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-docstring">"""Reset all the data allowing reuse of the BlastParser() object"""</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_records</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_header</tt> <tt class="py-op">=</tt> <tt id="link-17" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-17', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-18" class="py-name" targets="Class Bio.Blast.Record.Header=Bio.Blast.Record.Header-class.html"><a title="Bio.Blast.Record.Header" class="py-name" href="#" onclick="return doclink('link-18', 'Header', 'link-18');">Header</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parameters</tt> <tt class="py-op">=</tt> <tt id="link-19" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-19', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-20" class="py-name" targets="Class Bio.Blast.Record.Parameters=Bio.Blast.Record.Parameters-class.html"><a title="Bio.Blast.Record.Parameters" class="py-name" href="#" onclick="return doclink('link-20', 'Parameters', 'link-20');">Parameters</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parameters</tt><tt class="py-op">.</tt><tt id="link-21" 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-21', 'filter', 'link-21');">filter</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> <tt class="py-comment">#Maybe I should update the class?</tt> </tt>
</div><a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> </tt>
<a name="BlastParser.parse"></a><div id="BlastParser.parse-def"><a name="L145"></a><tt class="py-lineno">145</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.NCBIXML.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">handler</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="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt class="py-docstring">"""Parses the XML data</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"><tt class="py-docstring"> handler -- file handler or StringIO</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"><tt class="py-docstring"> This method returns a list of Blast record objects.</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">warnings</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-name">warnings</tt><tt class="py-op">.</tt><tt class="py-name">warn</tt><tt class="py-op">(</tt><tt class="py-string">"Bio.Blast.NCBIXML.BlastParser.parse has been deprecated; please use Bio.Blast.NCBIXML.parse instead"</tt><tt class="py-op">,</tt> <tt class="py-name">DeprecationWarning</tt><tt class="py-op">)</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name"><a title="Bio.Blast.NCBIXML.BlastParser.reset
Bio.InterPro.InterProParser.reset
Bio.LocusLink.web_parse.LocusLinkParser.reset
Bio.Ndb.NdbParser.reset
Bio.NetCatch.ExtractUrls.reset" class="py-name" href="#" onclick="return doclink('link-22', 'reset', 'link-16');">reset</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parser</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name" targets="Method Bio.Affy.CelFile.CelParser.parse()=Bio.Affy.CelFile.CelParser-class.html#parse,Method Bio.AlignAce.Parser.AlignAceParser.parse()=Bio.AlignAce.Parser.AlignAceParser-class.html#parse,Method Bio.AlignAce.Parser.CompareAceParser.parse()=Bio.AlignAce.Parser.CompareAceParser-class.html#parse,Function Bio.AlignIO.parse()=Bio.AlignIO-module.html#parse,Method Bio.Blast.NCBIStandalone.BlastErrorParser.parse()=Bio.Blast.NCBIStandalone.BlastErrorParser-class.html#parse,Method Bio.Blast.NCBIStandalone.BlastParser.parse()=Bio.Blast.NCBIStandalone.BlastParser-class.html#parse,Method Bio.Blast.NCBIStandalone.PSIBlastParser.parse()=Bio.Blast.NCBIStandalone.PSIBlastParser-class.html#parse,Method Bio.Blast.NCBIWWW.BlastParser.parse()=Bio.Blast.NCBIWWW.BlastParser-class.html#parse,Method Bio.Blast.NCBIXML.BlastParser.parse()=Bio.Blast.NCBIXML.BlastParser-class.html#parse,Function Bio.Blast.NCBIXML.parse()=Bio.Blast.NCBIXML-module.html#parse,Method Bio.CDD.RecordParser.parse()=Bio.CDD.RecordParser-class.html#parse,Method Bio.Compass.RecordParser.parse()=Bio.Compass.RecordParser-class.html#parse,Function Bio.Decode.parse()=Bio.Decode-module.html#parse,Method Bio.ECell.RecordParser.parse()=Bio.ECell.RecordParser-class.html#parse,Method Bio.EUtils.POM.POMDocument.parse()=Bio.EUtils.POM.POMDocument-class.html#parse,Module Bio.EUtils.parse=Bio.EUtils.parse-module.html,Method Bio.Emboss.Primer.Primer3Parser.parse()=Bio.Emboss.Primer.Primer3Parser-class.html#parse,Method Bio.Emboss.Primer.PrimerSearchParser.parse()=Bio.Emboss.Primer.PrimerSearchParser-class.html#parse,Method Bio.Enzyme.RecordParser.parse()=Bio.Enzyme.RecordParser-class.html#parse,Method Bio.Fasta.RecordParser.parse()=Bio.Fasta.RecordParser-class.html#parse,Method Bio.Fasta.SequenceParser.parse()=Bio.Fasta.SequenceParser-class.html#parse,Method Bio.GenBank.FeatureParser.parse()=Bio.GenBank.FeatureParser-class.html#parse,Function Bio.GenBank.LocationParser.parse()=Bio.GenBank.LocationParser-module.html#parse,Method Bio.GenBank.RecordParser.parse()=Bio.GenBank.RecordParser-class.html#parse,Method Bio.GenBank.Scanner.InsdcScanner.parse()=Bio.GenBank.Scanner.InsdcScanner-class.html#parse,Function Bio.Geo.parse()=Bio.Geo-module.html#parse,Method Bio.Gobase.RecordParser.parse()=Bio.Gobase.RecordParser-class.html#parse,Method Bio.IntelliGenetics.RecordParser.parse()=Bio.IntelliGenetics.RecordParser-class.html#parse,Method Bio.InterPro.InterProParser.parse()=Bio.InterPro.InterProParser-class.html#parse,Function Bio.KEGG.Compound.parse()=Bio.KEGG.Compound-module.html#parse,Function Bio.KEGG.Enzyme.parse()=Bio.KEGG.Enzyme-module.html#parse,Function Bio.KEGG.Map.parse()=Bio.KEGG.Map-module.html#parse,Method Bio.LocusLink.RecordParser.parse()=Bio.LocusLink.RecordParser-class.html#parse,Method Bio.LocusLink.web_parse.LocusLinkParser.parse()=Bio.LocusLink.web_parse.LocusLinkParser-class.html#parse,Method Bio.MEME.Parser.MASTParser.parse()=Bio.MEME.Parser.MASTParser-class.html#parse,Method Bio.MEME.Parser.MEMEParser.parse()=Bio.MEME.Parser.MEMEParser-class.html#parse,Method Bio.Medline.RecordParser.parse()=Bio.Medline.RecordParser-class.html#parse,Method Bio.MetaTool.RecordParser.parse()=Bio.MetaTool.RecordParser-class.html#parse,Method Bio.NBRF.RecordParser.parse()=Bio.NBRF.RecordParser-class.html#parse,Method Bio.Ndb.NdbParser.parse()=Bio.Ndb.NdbParser-class.html#parse,Method Bio.ParserSupport.AbstractParser.parse()=Bio.ParserSupport.AbstractParser-class.html#parse,Method Bio.Parsers.spark.GenericParser.parse()=Bio.Parsers.spark.GenericParser-class.html#parse,Method Bio.PopGen.FDist.RecordParser.parse()=Bio.PopGen.FDist.RecordParser-class.html#parse,Method Bio.PopGen.GenePop.RecordParser.parse()=Bio.PopGen.GenePop.RecordParser-class.html#parse,Function Bio.PopGen.GenePop.parse()=Bio.PopGen.GenePop-module.html#parse,Method Bio.Prosite.Prodoc.RecordParser.parse()=Bio.Prosite.Prodoc.RecordParser-class.html#parse,Function Bio.Prosite.Prodoc.parse()=Bio.Prosite.Prodoc-module.html#parse,Method Bio.Prosite.RecordParser.parse()=Bio.Prosite.RecordParser-class.html#parse,Function Bio.Prosite.parse()=Bio.Prosite-module.html#parse,Method Bio.Rebase.RecordParser.parse()=Bio.Rebase.RecordParser-class.html#parse,Method Bio.SCOP.Cla.Parser.parse()=Bio.SCOP.Cla.Parser-class.html#parse,Function Bio.SCOP.Cla.parse()=Bio.SCOP.Cla-module.html#parse,Method Bio.SCOP.Des.Parser.parse()=Bio.SCOP.Des.Parser-class.html#parse,Function Bio.SCOP.Des.parse()=Bio.SCOP.Des-module.html#parse,Method Bio.SCOP.Dom.Parser.parse()=Bio.SCOP.Dom.Parser-class.html#parse,Function Bio.SCOP.Dom.parse()=Bio.SCOP.Dom-module.html#parse,Method Bio.SCOP.Hie.Parser.parse()=Bio.SCOP.Hie.Parser-class.html#parse,Function Bio.SCOP.Hie.parse()=Bio.SCOP.Hie-module.html#parse,Method Bio.SCOP.Raf.Parser.parse()=Bio.SCOP.Raf.Parser-class.html#parse,Function Bio.SCOP.Raf.parse()=Bio.SCOP.Raf-module.html#parse,Method Bio.Saf.RecordParser.parse()=Bio.Saf.RecordParser-class.html#parse,Function Bio.SeqIO.parse()=Bio.SeqIO-module.html#parse,Method Bio.Sequencing.Ace.ACEParser.parse()=Bio.Sequencing.Ace.ACEParser-class.html#parse,Method Bio.Sequencing.Ace.RecordParser.parse()=Bio.Sequencing.Ace.RecordParser-class.html#parse,Method Bio.Sequencing.Phd.RecordParser.parse()=Bio.Sequencing.Phd.RecordParser-class.html#parse,Method Bio.SwissProt.KeyWList.ListParser.parse()=Bio.SwissProt.KeyWList.ListParser-class.html#parse,Function Bio.SwissProt.KeyWList.parse()=Bio.SwissProt.KeyWList-module.html#parse,Method Bio.SwissProt.SProt.RecordParser.parse()=Bio.SwissProt.SProt.RecordParser-class.html#parse,Method Bio.SwissProt.SProt.SequenceParser.parse()=Bio.SwissProt.SProt.SequenceParser-class.html#parse,Function Bio.SwissProt.parse()=Bio.SwissProt-module.html#parse,Method Bio.UniGene.RecordParser.parse()=Bio.UniGene.RecordParser-class.html#parse,Function Bio.Wise.psw.parse()=Bio.Wise.psw-module.html#parse,Method Martel.Parser.HeaderFooterParser.parse()=Martel.Parser.HeaderFooterParser-class.html#parse,Method Martel.Parser.Parser.parse()=Martel.Parser.Parser-class.html#parse,Method Martel.Parser.RecordParser.parse()=Martel.Parser.RecordParser-class.html#parse,Function Martel.msre_parse.parse()=Martel.msre_parse-module.html#parse"><a title="Bio.Affy.CelFile.CelParser.parse
Bio.AlignAce.Parser.AlignAceParser.parse
Bio.AlignAce.Parser.CompareAceParser.parse
Bio.AlignIO.parse
Bio.Blast.NCBIStandalone.BlastErrorParser.parse
Bio.Blast.NCBIStandalone.BlastParser.parse
Bio.Blast.NCBIStandalone.PSIBlastParser.parse
Bio.Blast.NCBIWWW.BlastParser.parse
Bio.Blast.NCBIXML.BlastParser.parse
Bio.Blast.NCBIXML.parse
Bio.CDD.RecordParser.parse
Bio.Compass.RecordParser.parse
Bio.Decode.parse
Bio.ECell.RecordParser.parse
Bio.EUtils.POM.POMDocument.parse
Bio.EUtils.parse
Bio.Emboss.Primer.Primer3Parser.parse
Bio.Emboss.Primer.PrimerSearchParser.parse
Bio.Enzyme.RecordParser.parse
Bio.Fasta.RecordParser.parse
Bio.Fasta.SequenceParser.parse
Bio.GenBank.FeatureParser.parse
Bio.GenBank.LocationParser.parse
Bio.GenBank.RecordParser.parse
Bio.GenBank.Scanner.InsdcScanner.parse
Bio.Geo.parse
Bio.Gobase.RecordParser.parse
Bio.IntelliGenetics.RecordParser.parse
Bio.InterPro.InterProParser.parse
Bio.KEGG.Compound.parse
Bio.KEGG.Enzyme.parse
Bio.KEGG.Map.parse
Bio.LocusLink.RecordParser.parse
Bio.LocusLink.web_parse.LocusLinkParser.parse
Bio.MEME.Parser.MASTParser.parse
Bio.MEME.Parser.MEMEParser.parse
Bio.Medline.RecordParser.parse
Bio.MetaTool.RecordParser.parse
Bio.NBRF.RecordParser.parse
Bio.Ndb.NdbParser.parse
Bio.ParserSupport.AbstractParser.parse
Bio.Parsers.spark.GenericParser.parse
Bio.PopGen.FDist.RecordParser.parse
Bio.PopGen.GenePop.RecordParser.parse
Bio.PopGen.GenePop.parse
Bio.Prosite.Prodoc.RecordParser.parse
Bio.Prosite.Prodoc.parse
Bio.Prosite.RecordParser.parse
Bio.Prosite.parse
Bio.Rebase.RecordParser.parse
Bio.SCOP.Cla.Parser.parse
Bio.SCOP.Cla.parse
Bio.SCOP.Des.Parser.parse
Bio.SCOP.Des.parse
Bio.SCOP.Dom.Parser.parse
Bio.SCOP.Dom.parse
Bio.SCOP.Hie.Parser.parse
Bio.SCOP.Hie.parse
Bio.SCOP.Raf.Parser.parse
Bio.SCOP.Raf.parse
Bio.Saf.RecordParser.parse
Bio.SeqIO.parse
Bio.Sequencing.Ace.ACEParser.parse
Bio.Sequencing.Ace.RecordParser.parse
Bio.Sequencing.Phd.RecordParser.parse
Bio.SwissProt.KeyWList.ListParser.parse
Bio.SwissProt.KeyWList.parse
Bio.SwissProt.SProt.RecordParser.parse
Bio.SwissProt.SProt.SequenceParser.parse
Bio.SwissProt.parse
Bio.UniGene.RecordParser.parse
Bio.Wise.psw.parse
Martel.Parser.HeaderFooterParser.parse
Martel.Parser.Parser.parse
Martel.Parser.RecordParser.parse
Martel.msre_parse.parse" class="py-name" href="#" onclick="return doclink('link-23', 'parse', 'link-23');">parse</a></tt><tt class="py-op">(</tt><tt class="py-name">handler</tt><tt class="py-op">)</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</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">_records</tt> </tt>
</div><a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> </tt>
<a name="BlastParser._start_Iteration"></a><div id="BlastParser._start_Iteration-def"><a name="L158"></a><tt class="py-lineno">158</tt> <a class="py-toggle" href="#" id="BlastParser._start_Iteration-toggle" onclick="return toggle('BlastParser._start_Iteration');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_start_Iteration">_start_Iteration</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._start_Iteration-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._start_Iteration-expanded"><a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_blast</tt> <tt class="py-op">=</tt> <tt id="link-24" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-24', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-25" class="py-name"><a title="Bio.Blast
Bio.Blast.Record.Blast" class="py-name" href="#" onclick="return doclink('link-25', 'Blast', 'link-1');">Blast</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
</div><a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> </tt>
<a name="BlastParser._end_Iteration"></a><div id="BlastParser._end_Iteration-def"><a name="L162"></a><tt class="py-lineno">162</tt> <a class="py-toggle" href="#" id="BlastParser._end_Iteration-toggle" onclick="return toggle('BlastParser._end_Iteration');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_Iteration">_end_Iteration</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._end_Iteration-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_Iteration-expanded"><a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt class="py-comment"># We stored a lot of generic "top level" information</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># in self._header (an object of type Record.Header)</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_blast</tt><tt class="py-op">.</tt><tt id="link-26" 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-26', 'reference', 'link-26');">reference</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_header</tt><tt class="py-op">.</tt><tt id="link-27" class="py-name"><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-27', 'reference', 'link-26');">reference</a></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 class="py-name">_blast</tt><tt class="py-op">.</tt><tt id="link-28" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.date()=Bio.GenBank._FeatureConsumer-class.html#date,Method Bio.GenBank._RecordConsumer.date()=Bio.GenBank._RecordConsumer-class.html#date,Method Bio.Prosite._RecordConsumer.date()=Bio.Prosite._RecordConsumer-class.html#date,Method Bio.SwissProt.SProt._RecordConsumer.date()=Bio.SwissProt.SProt._RecordConsumer-class.html#date,Method Bio.SwissProt.SProt._SequenceConsumer.date()=Bio.SwissProt.SProt._SequenceConsumer-class.html#date,Variable Bio.expressions.embl.embl65.date=Bio.expressions.embl.embl65-module.html#date,Variable Bio.expressions.genbank.date=Bio.expressions.genbank-module.html#date"><a title="Bio.GenBank._FeatureConsumer.date
Bio.GenBank._RecordConsumer.date
Bio.Prosite._RecordConsumer.date
Bio.SwissProt.SProt._RecordConsumer.date
Bio.SwissProt.SProt._SequenceConsumer.date
Bio.expressions.embl.embl65.date
Bio.expressions.genbank.date" class="py-name" href="#" onclick="return doclink('link-28', 'date', 'link-28');">date</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_header</tt><tt class="py-op">.</tt><tt id="link-29" class="py-name"><a title="Bio.GenBank._FeatureConsumer.date
Bio.GenBank._RecordConsumer.date
Bio.Prosite._RecordConsumer.date
Bio.SwissProt.SProt._RecordConsumer.date
Bio.SwissProt.SProt._SequenceConsumer.date
Bio.expressions.embl.embl65.date
Bio.expressions.genbank.date" class="py-name" href="#" onclick="return doclink('link-29', 'date', 'link-28');">date</a></tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_blast</tt><tt class="py-op">.</tt><tt id="link-30" 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-30', 'version', 'link-30');">version</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_header</tt><tt class="py-op">.</tt><tt id="link-31" class="py-name"><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-30');">version</a></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 class="py-name">_blast</tt><tt class="py-op">.</tt><tt id="link-32" 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-32', 'database', 'link-32');">database</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_header</tt><tt class="py-op">.</tt><tt id="link-33" class="py-name"><a title="Bio.Blast.NCBIStandalone._DatabaseReportConsumer.database" class="py-name" href="#" onclick="return doclink('link-33', 'database', 'link-32');">database</a></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 class="py-name">_blast</tt><tt class="py-op">.</tt><tt class="py-name">application</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_header</tt><tt class="py-op">.</tt><tt class="py-name">application</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-comment"># These are required for "old" pre 2.2.14 files</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># where only <BlastOutput_query-ID>, <BlastOutput_query-def></tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># and <BlastOutput_query-len> were used. Now they</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># are suplemented/replaced by <Iteration_query-ID>,</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <Iteration_query-def> and <Iteration_query-len></tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">hasattr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_blast</tt><tt class="py-op">,</tt> <tt class="py-string">"query"</tt><tt class="py-op">)</tt> \ </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-keyword">or</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_blast</tt><tt class="py-op">.</tt><tt id="link-34" 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-34', 'query', 'link-34');">query</a></tt> <tt class="py-op">:</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_blast</tt><tt class="py-op">.</tt><tt id="link-35" 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-35', 'query', 'link-34');">query</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_header</tt><tt class="py-op">.</tt><tt id="link-36" 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-36', 'query', 'link-34');">query</a></tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">hasattr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_blast</tt><tt class="py-op">,</tt> <tt class="py-string">"query_id"</tt><tt class="py-op">)</tt> \ </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-keyword">or</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_blast</tt><tt class="py-op">.</tt><tt class="py-name">query_id</tt> <tt class="py-op">:</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_blast</tt><tt class="py-op">.</tt><tt class="py-name">query_id</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_header</tt><tt class="py-op">.</tt><tt class="py-name">query_id</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">hasattr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_blast</tt><tt class="py-op">,</tt> <tt class="py-string">"query_letters"</tt><tt class="py-op">)</tt> \ </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> <tt class="py-keyword">or</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_blast</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.query_letters=Bio.expressions.blast.ncbiblast-module.html#query_letters"><a title="Bio.expressions.blast.ncbiblast.query_letters" class="py-name" href="#" onclick="return doclink('link-37', 'query_letters', 'link-37');">query_letters</a></tt> <tt class="py-op">:</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_blast</tt><tt class="py-op">.</tt><tt id="link-38" class="py-name"><a title="Bio.expressions.blast.ncbiblast.query_letters" class="py-name" href="#" onclick="return doclink('link-38', 'query_letters', 'link-37');">query_letters</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_header</tt><tt class="py-op">.</tt><tt id="link-39" class="py-name"><a title="Bio.expressions.blast.ncbiblast.query_letters" class="py-name" href="#" onclick="return doclink('link-39', 'query_letters', 'link-37');">query_letters</a></tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> <tt class="py-comment"># Apply the "top level" parameter information</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_blast</tt><tt class="py-op">.</tt><tt id="link-40" 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-40', 'matrix', 'link-40');">matrix</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parameters</tt><tt class="py-op">.</tt><tt id="link-41" class="py-name"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.matrix
Bio.MetaTool.metatool_format.matrix
Bio.Prosite._RecordConsumer.matrix" class="py-name" href="#" onclick="return doclink('link-41', 'matrix', 'link-40');">matrix</a></tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_blast</tt><tt class="py-op">.</tt><tt id="link-42" 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-42', 'num_seqs_better_e', 'link-42');">num_seqs_better_e</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parameters</tt><tt class="py-op">.</tt><tt id="link-43" class="py-name"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.num_seqs_better_e" class="py-name" href="#" onclick="return doclink('link-43', 'num_seqs_better_e', 'link-42');">num_seqs_better_e</a></tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_blast</tt><tt class="py-op">.</tt><tt id="link-44" 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-44', 'gap_penalties', 'link-44');">gap_penalties</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parameters</tt><tt class="py-op">.</tt><tt id="link-45" class="py-name"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.gap_penalties" class="py-name" href="#" onclick="return doclink('link-45', 'gap_penalties', 'link-44');">gap_penalties</a></tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_blast</tt><tt class="py-op">.</tt><tt id="link-46" class="py-name"><a title="Bio.FSSP.FSSPTools.filter
Bio.FilteredReader.FilteredReader.filter
Bio.expressions.swissprot.filter" class="py-name" href="#" onclick="return doclink('link-46', 'filter', 'link-21');">filter</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parameters</tt><tt class="py-op">.</tt><tt id="link-47" class="py-name"><a title="Bio.FSSP.FSSPTools.filter
Bio.FilteredReader.FilteredReader.filter
Bio.expressions.swissprot.filter" class="py-name" href="#" onclick="return doclink('link-47', 'filter', 'link-21');">filter</a></tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_blast</tt><tt class="py-op">.</tt><tt id="link-48" 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-48', 'expect', 'link-48');">expect</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parameters</tt><tt class="py-op">.</tt><tt id="link-49" class="py-name"><a title="Bio.expressions.blast.ncbiblast.expect" class="py-name" href="#" onclick="return doclink('link-49', 'expect', 'link-48');">expect</a></tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_blast</tt><tt class="py-op">.</tt><tt class="py-name">sc_match</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parameters</tt><tt class="py-op">.</tt><tt class="py-name">sc_match</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_blast</tt><tt class="py-op">.</tt><tt class="py-name">sc_mismatch</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parameters</tt><tt class="py-op">.</tt><tt class="py-name">sc_mismatch</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt class="py-comment">#Add to the list</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_records</tt><tt class="py-op">.</tt><tt id="link-50" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-50', 'append', 'link-4');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_blast</tt><tt class="py-op">)</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt class="py-comment">#Clear the object (a new empty one is create in _start_Iteration)</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_blast</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_debug</tt> <tt class="py-op">:</tt> <tt class="py-string">"NCBIXML: Added Blast record to results"</tt> </tt>
</div><a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt class="py-comment"># Header</tt> </tt>
<a name="BlastParser._end_BlastOutput_program"></a><div id="BlastParser._end_BlastOutput_program-def"><a name="L203"></a><tt class="py-lineno">203</tt> <a class="py-toggle" href="#" id="BlastParser._end_BlastOutput_program-toggle" onclick="return toggle('BlastParser._end_BlastOutput_program');">-</a><tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_BlastOutput_program">_end_BlastOutput_program</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._end_BlastOutput_program-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_BlastOutput_program-expanded"><a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-docstring">"""BLAST program, e.g., blastp, blastn, etc.</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"><tt class="py-docstring"> Save this to put on each blast record object</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_header</tt><tt class="py-op">.</tt><tt class="py-name">application</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt><tt class="py-op">.</tt><tt class="py-name">upper</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> </tt>
<a name="BlastParser._end_BlastOutput_version"></a><div id="BlastParser._end_BlastOutput_version-def"><a name="L210"></a><tt class="py-lineno">210</tt> <a class="py-toggle" href="#" id="BlastParser._end_BlastOutput_version-toggle" onclick="return toggle('BlastParser._end_BlastOutput_version');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_BlastOutput_version">_end_BlastOutput_version</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._end_BlastOutput_version-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_BlastOutput_version-expanded"><a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt class="py-docstring">"""version number and date of the BLAST engine.</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"><tt class="py-docstring"> e.g. "BLASTX 2.2.12 [Aug-07-2005]" but there can also be</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"><tt class="py-docstring"> variants like "BLASTP 2.2.18+" without the date.</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"><tt class="py-docstring"> Save this to put on each blast record object</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt class="py-name">parts</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt><tt class="py-op">.</tt><tt id="link-51" class="py-name" targets="Method Bio.Nexus.Trees.Tree.split()=Bio.Nexus.Trees.Tree-class.html#split,Method Bio.Restriction.Restriction.RestrictionBatch.split()=Bio.Restriction.Restriction.RestrictionBatch-class.html#split"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-51', 'split', 'link-51');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> <tt class="py-comment">#TODO - Check the first word starts with BLAST?</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-comment">#The version is the second word (field one)</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_header</tt><tt class="py-op">.</tt><tt id="link-52" class="py-name"><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-52', 'version', 'link-30');">version</a></tt> <tt class="py-op">=</tt> <tt class="py-name">parts</tt><tt class="py-op">[</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>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> <tt class="py-comment">#Check there is a third word (the date)</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">parts</tt><tt class="py-op">)</tt> <tt class="py-op">>=</tt> <tt class="py-number">3</tt> <tt class="py-op">:</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">parts</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"["</tt> <tt class="py-keyword">and</tt> <tt class="py-name">parts</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"]"</tt> <tt class="py-op">:</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_header</tt><tt class="py-op">.</tt><tt id="link-53" class="py-name"><a title="Bio.GenBank._FeatureConsumer.date
Bio.GenBank._RecordConsumer.date
Bio.Prosite._RecordConsumer.date
Bio.SwissProt.SProt._RecordConsumer.date
Bio.SwissProt.SProt._SequenceConsumer.date
Bio.expressions.embl.embl65.date
Bio.expressions.genbank.date" class="py-name" href="#" onclick="return doclink('link-53', 'date', 'link-28');">date</a></tt> <tt class="py-op">=</tt> <tt class="py-name">parts</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> <tt class="py-comment">#Assume this is still a date, but without the</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#square brackets</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_header</tt><tt class="py-op">.</tt><tt id="link-54" class="py-name"><a title="Bio.GenBank._FeatureConsumer.date
Bio.GenBank._RecordConsumer.date
Bio.Prosite._RecordConsumer.date
Bio.SwissProt.SProt._RecordConsumer.date
Bio.SwissProt.SProt._SequenceConsumer.date
Bio.expressions.embl.embl65.date
Bio.expressions.genbank.date" class="py-name" href="#" onclick="return doclink('link-54', 'date', 'link-28');">date</a></tt> <tt class="py-op">=</tt> <tt class="py-name">parts</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> </tt>
</div><a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> </tt>
<a name="BlastParser._end_BlastOutput_reference"></a><div id="BlastParser._end_BlastOutput_reference-def"><a name="L233"></a><tt class="py-lineno">233</tt> <a class="py-toggle" href="#" id="BlastParser._end_BlastOutput_reference-toggle" onclick="return toggle('BlastParser._end_BlastOutput_reference');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_BlastOutput_reference">_end_BlastOutput_reference</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._end_BlastOutput_reference-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_BlastOutput_reference-expanded"><a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"> <tt class="py-docstring">"""a reference to the article describing the algorithm</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"><tt class="py-docstring"> Save this to put on each blast record object</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_header</tt><tt class="py-op">.</tt><tt id="link-55" class="py-name"><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-55', 'reference', 'link-26');">reference</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt> </tt>
</div><a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> </tt>
<a name="BlastParser._end_BlastOutput_db"></a><div id="BlastParser._end_BlastOutput_db-def"><a name="L240"></a><tt class="py-lineno">240</tt> <a class="py-toggle" href="#" id="BlastParser._end_BlastOutput_db-toggle" onclick="return toggle('BlastParser._end_BlastOutput_db');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_BlastOutput_db">_end_BlastOutput_db</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._end_BlastOutput_db-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_BlastOutput_db-expanded"><a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt class="py-docstring">"""the database(s) searched</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"><tt class="py-docstring"> Save this to put on each blast record object</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_header</tt><tt class="py-op">.</tt><tt id="link-56" class="py-name"><a title="Bio.Blast.NCBIStandalone._DatabaseReportConsumer.database" class="py-name" href="#" onclick="return doclink('link-56', 'database', 'link-32');">database</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt> </tt>
</div><a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> </tt>
<a name="BlastParser._end_BlastOutput_query_ID"></a><div id="BlastParser._end_BlastOutput_query_ID-def"><a name="L247"></a><tt class="py-lineno">247</tt> <a class="py-toggle" href="#" id="BlastParser._end_BlastOutput_query_ID-toggle" onclick="return toggle('BlastParser._end_BlastOutput_query_ID');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_BlastOutput_query_ID">_end_BlastOutput_query_ID</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._end_BlastOutput_query_ID-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_BlastOutput_query_ID-expanded"><a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> <tt class="py-docstring">"""the identifier of the query</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"><tt class="py-docstring"> Important in old pre 2.2.14 BLAST, for recent versions</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"><tt class="py-docstring"> <Iteration_query-ID> is enough</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_header</tt><tt class="py-op">.</tt><tt class="py-name">query_id</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt> </tt>
</div><a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"> </tt>
<a name="BlastParser._end_BlastOutput_query_def"></a><div id="BlastParser._end_BlastOutput_query_def-def"><a name="L255"></a><tt class="py-lineno">255</tt> <a class="py-toggle" href="#" id="BlastParser._end_BlastOutput_query_def-toggle" onclick="return toggle('BlastParser._end_BlastOutput_query_def');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_BlastOutput_query_def">_end_BlastOutput_query_def</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._end_BlastOutput_query_def-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_BlastOutput_query_def-expanded"><a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> <tt class="py-docstring">"""the definition line of the query</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"><tt class="py-docstring"> Important in old pre 2.2.14 BLAST, for recent versions</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"><tt class="py-docstring"> <Iteration_query-def> is enough</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_header</tt><tt class="py-op">.</tt><tt id="link-57" 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-57', 'query', 'link-34');">query</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt> </tt>
</div><a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> </tt>
<a name="BlastParser._end_BlastOutput_query_len"></a><div id="BlastParser._end_BlastOutput_query_len-def"><a name="L263"></a><tt class="py-lineno">263</tt> <a class="py-toggle" href="#" id="BlastParser._end_BlastOutput_query_len-toggle" onclick="return toggle('BlastParser._end_BlastOutput_query_len');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_BlastOutput_query_len">_end_BlastOutput_query_len</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._end_BlastOutput_query_len-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_BlastOutput_query_len-expanded"><a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> <tt class="py-docstring">"""the length of the query</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"><tt class="py-docstring"> Important in old pre 2.2.14 BLAST, for recent versions</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"><tt class="py-docstring"> <Iteration_query-len> is enough</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_header</tt><tt class="py-op">.</tt><tt id="link-58" class="py-name"><a title="Bio.expressions.blast.ncbiblast.query_letters" class="py-name" href="#" onclick="return doclink('link-58', 'query_letters', 'link-37');">query_letters</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt><tt class="py-op">)</tt> </tt>
</div><a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"> </tt>
<a name="BlastParser._end_Iteration_query_ID"></a><div id="BlastParser._end_Iteration_query_ID-def"><a name="L271"></a><tt class="py-lineno">271</tt> <a class="py-toggle" href="#" id="BlastParser._end_Iteration_query_ID-toggle" onclick="return toggle('BlastParser._end_Iteration_query_ID');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_Iteration_query_ID">_end_Iteration_query_ID</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._end_Iteration_query_ID-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_Iteration_query_ID-expanded"><a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> <tt class="py-docstring">"""the identifier of the query</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_blast</tt><tt class="py-op">.</tt><tt class="py-name">query_id</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt> </tt>
</div><a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"> </tt>
<a name="BlastParser._end_Iteration_query_def"></a><div id="BlastParser._end_Iteration_query_def-def"><a name="L276"></a><tt class="py-lineno">276</tt> <a class="py-toggle" href="#" id="BlastParser._end_Iteration_query_def-toggle" onclick="return toggle('BlastParser._end_Iteration_query_def');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_Iteration_query_def">_end_Iteration_query_def</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._end_Iteration_query_def-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_Iteration_query_def-expanded"><a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"> <tt class="py-docstring">"""the definition line of the query</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_blast</tt><tt class="py-op">.</tt><tt id="link-59" 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-59', 'query', 'link-34');">query</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt> </tt>
</div><a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> </tt>
<a name="BlastParser._end_Iteration_query_len"></a><div id="BlastParser._end_Iteration_query_len-def"><a name="L281"></a><tt class="py-lineno">281</tt> <a class="py-toggle" href="#" id="BlastParser._end_Iteration_query_len-toggle" onclick="return toggle('BlastParser._end_Iteration_query_len');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_Iteration_query_len">_end_Iteration_query_len</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._end_Iteration_query_len-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_Iteration_query_len-expanded"><a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"> <tt class="py-docstring">"""the length of the query</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_blast</tt><tt class="py-op">.</tt><tt id="link-60" class="py-name"><a title="Bio.expressions.blast.ncbiblast.query_letters" class="py-name" href="#" onclick="return doclink('link-60', 'query_letters', 'link-37');">query_letters</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt><tt class="py-op">)</tt> </tt>
</div><a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"><tt class="py-comment">## def _end_BlastOutput_query_seq(self):</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">## """the query sequence</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">## """</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">## pass # XXX Missing in Record.Blast ?</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"><tt class="py-comment">## def _end_BlastOutput_iter_num(self):</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">## """the psi-blast iteration number</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">## """</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">## pass # XXX TODO PSI</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="BlastParser._end_BlastOutput_hits"></a><div id="BlastParser._end_BlastOutput_hits-def"><a name="L296"></a><tt class="py-lineno">296</tt> <a class="py-toggle" href="#" id="BlastParser._end_BlastOutput_hits-toggle" onclick="return toggle('BlastParser._end_BlastOutput_hits');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_BlastOutput_hits">_end_BlastOutput_hits</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._end_BlastOutput_hits-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_BlastOutput_hits-expanded"><a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"> <tt class="py-docstring">"""hits to the database sequences, one for every sequence</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_blast</tt><tt class="py-op">.</tt><tt id="link-61" 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-61', 'num_hits', 'link-61');">num_hits</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt><tt class="py-op">)</tt> </tt>
</div><a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"><tt class="py-comment">## def _end_BlastOutput_message(self):</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">## """error messages</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">## """</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">## pass # XXX What to do ?</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"> <tt class="py-comment"># Parameters</tt> </tt>
<a name="BlastParser._end_Parameters_matrix"></a><div id="BlastParser._end_Parameters_matrix-def"><a name="L307"></a><tt class="py-lineno">307</tt> <a class="py-toggle" href="#" id="BlastParser._end_Parameters_matrix-toggle" onclick="return toggle('BlastParser._end_Parameters_matrix');">-</a><tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_Parameters_matrix">_end_Parameters_matrix</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._end_Parameters_matrix-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_Parameters_matrix-expanded"><a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"> <tt class="py-docstring">"""matrix used (-M)</tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parameters</tt><tt class="py-op">.</tt><tt id="link-62" class="py-name"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.matrix
Bio.MetaTool.metatool_format.matrix
Bio.Prosite._RecordConsumer.matrix" class="py-name" href="#" onclick="return doclink('link-62', 'matrix', 'link-40');">matrix</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt> </tt>
</div><a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"> </tt>
<a name="BlastParser._end_Parameters_expect"></a><div id="BlastParser._end_Parameters_expect-def"><a name="L312"></a><tt class="py-lineno">312</tt> <a class="py-toggle" href="#" id="BlastParser._end_Parameters_expect-toggle" onclick="return toggle('BlastParser._end_Parameters_expect');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_Parameters_expect">_end_Parameters_expect</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._end_Parameters_expect-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_Parameters_expect-expanded"><a name="L313"></a><tt class="py-lineno">313</tt> <tt class="py-line"> <tt class="py-docstring">"""expect values cutoff (-e)</tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"> <tt class="py-comment"># NOTE: In old text output there was a line:</tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Number of sequences better than 1.0e-004: 1</tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># As far as I can see, parameters.num_seqs_better_e</tt> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># would take the value of 1, and the expectation</tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># value was not recorded.</tt> </tt>
<a name="L320"></a><tt class="py-lineno">320</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Anyway we should NOT record this against num_seqs_better_e</tt> </tt>
<a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parameters</tt><tt class="py-op">.</tt><tt id="link-63" class="py-name"><a title="Bio.expressions.blast.ncbiblast.expect" class="py-name" href="#" onclick="return doclink('link-63', 'expect', 'link-48');">expect</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt> </tt>
</div><a name="L323"></a><tt class="py-lineno">323</tt> <tt class="py-line"> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"><tt class="py-comment">## def _end_Parameters_include(self):</tt> </tt>
<a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## """inclusion threshold for a psi-blast iteration (-h)</tt> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## """</tt> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## pass # XXX TODO PSI</tt> </tt>
<a name="L328"></a><tt class="py-lineno">328</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="BlastParser._end_Parameters_sc_match"></a><div id="BlastParser._end_Parameters_sc_match-def"><a name="L329"></a><tt class="py-lineno">329</tt> <a class="py-toggle" href="#" id="BlastParser._end_Parameters_sc_match-toggle" onclick="return toggle('BlastParser._end_Parameters_sc_match');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_Parameters_sc_match">_end_Parameters_sc_match</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._end_Parameters_sc_match-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_Parameters_sc_match-expanded"><a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"> <tt class="py-docstring">"""match score for nucleotide-nucleotide comparaison (-r)</tt> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parameters</tt><tt class="py-op">.</tt><tt class="py-name">sc_match</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt><tt class="py-op">)</tt> </tt>
</div><a name="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"> </tt>
<a name="BlastParser._end_Parameters_sc_mismatch"></a><div id="BlastParser._end_Parameters_sc_mismatch-def"><a name="L334"></a><tt class="py-lineno">334</tt> <a class="py-toggle" href="#" id="BlastParser._end_Parameters_sc_mismatch-toggle" onclick="return toggle('BlastParser._end_Parameters_sc_mismatch');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_Parameters_sc_mismatch">_end_Parameters_sc_mismatch</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._end_Parameters_sc_mismatch-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_Parameters_sc_mismatch-expanded"><a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"> <tt class="py-docstring">"""mismatch penalty for nucleotide-nucleotide comparaison (-r)</tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parameters</tt><tt class="py-op">.</tt><tt class="py-name">sc_mismatch</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt><tt class="py-op">)</tt> </tt>
</div><a name="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"> </tt>
<a name="BlastParser._end_Parameters_gap_open"></a><div id="BlastParser._end_Parameters_gap_open-def"><a name="L339"></a><tt class="py-lineno">339</tt> <a class="py-toggle" href="#" id="BlastParser._end_Parameters_gap_open-toggle" onclick="return toggle('BlastParser._end_Parameters_gap_open');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_Parameters_gap_open">_end_Parameters_gap_open</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._end_Parameters_gap_open-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_Parameters_gap_open-expanded"><a name="L340"></a><tt class="py-lineno">340</tt> <tt class="py-line"> <tt class="py-docstring">"""gap existence cost (-G)</tt> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parameters</tt><tt class="py-op">.</tt><tt id="link-64" class="py-name"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.gap_penalties" class="py-name" href="#" onclick="return doclink('link-64', 'gap_penalties', 'link-44');">gap_penalties</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt><tt class="py-op">)</tt> </tt>
</div><a name="L343"></a><tt class="py-lineno">343</tt> <tt class="py-line"> </tt>
<a name="BlastParser._end_Parameters_gap_extend"></a><div id="BlastParser._end_Parameters_gap_extend-def"><a name="L344"></a><tt class="py-lineno">344</tt> <a class="py-toggle" href="#" id="BlastParser._end_Parameters_gap_extend-toggle" onclick="return toggle('BlastParser._end_Parameters_gap_extend');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_Parameters_gap_extend">_end_Parameters_gap_extend</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._end_Parameters_gap_extend-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_Parameters_gap_extend-expanded"><a name="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"> <tt class="py-docstring">"""gap extension cose (-E)</tt> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parameters</tt><tt class="py-op">.</tt><tt id="link-65" class="py-name"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.gap_penalties" class="py-name" href="#" onclick="return doclink('link-65', 'gap_penalties', 'link-44');">gap_penalties</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parameters</tt><tt class="py-op">.</tt><tt id="link-66" class="py-name"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.gap_penalties" class="py-name" href="#" onclick="return doclink('link-66', 'gap_penalties', 'link-44');">gap_penalties</a></tt><tt class="py-op">,</tt> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L349"></a><tt class="py-lineno">349</tt> <tt class="py-line"> </tt>
<a name="BlastParser._end_Parameters_filter"></a><div id="BlastParser._end_Parameters_filter-def"><a name="L350"></a><tt class="py-lineno">350</tt> <a class="py-toggle" href="#" id="BlastParser._end_Parameters_filter-toggle" onclick="return toggle('BlastParser._end_Parameters_filter');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_Parameters_filter">_end_Parameters_filter</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._end_Parameters_filter-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_Parameters_filter-expanded"><a name="L351"></a><tt class="py-lineno">351</tt> <tt class="py-line"> <tt class="py-docstring">"""filtering options (-F)</tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parameters</tt><tt class="py-op">.</tt><tt id="link-67" class="py-name"><a title="Bio.FSSP.FSSPTools.filter
Bio.FilteredReader.FilteredReader.filter
Bio.expressions.swissprot.filter" class="py-name" href="#" onclick="return doclink('link-67', 'filter', 'link-21');">filter</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt> </tt>
</div><a name="L354"></a><tt class="py-lineno">354</tt> <tt class="py-line"> </tt>
<a name="L355"></a><tt class="py-lineno">355</tt> <tt class="py-line"><tt class="py-comment">## def _end_Parameters_pattern(self):</tt> </tt>
<a name="L356"></a><tt class="py-lineno">356</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## """pattern used for phi-blast search</tt> </tt>
<a name="L357"></a><tt class="py-lineno">357</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## """</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">## pass # XXX TODO PSI</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt> <tt class="py-line"><tt class="py-comment">## def _end_Parameters_entrez_query(self):</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">## """entrez query used to limit search</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">## """</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">## pass # XXX TODO PSI</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-comment"># Hits</tt> </tt>
<a name="BlastParser._start_Hit"></a><div id="BlastParser._start_Hit-def"><a name="L366"></a><tt class="py-lineno">366</tt> <a class="py-toggle" href="#" id="BlastParser._start_Hit-toggle" onclick="return toggle('BlastParser._start_Hit');">-</a><tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_start_Hit">_start_Hit</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._start_Hit-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._start_Hit-expanded"><a name="L367"></a><tt class="py-lineno">367</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_blast</tt><tt class="py-op">.</tt><tt class="py-name">alignments</tt><tt class="py-op">.</tt><tt id="link-68" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-68', 'append', 'link-4');">append</a></tt><tt class="py-op">(</tt><tt id="link-69" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-69', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-70" class="py-name" targets="Class Bio.Align.Generic.Alignment=Bio.Align.Generic.Alignment-class.html,Class Bio.Blast.Record.Alignment=Bio.Blast.Record.Alignment-class.html,Class Bio.Wise.psw.Alignment=Bio.Wise.psw.Alignment-class.html"><a title="Bio.Align.Generic.Alignment
Bio.Blast.Record.Alignment
Bio.Wise.psw.Alignment" class="py-name" href="#" onclick="return doclink('link-70', 'Alignment', 'link-70');">Alignment</a></tt><tt class="py-op">(</tt><tt class="py-op">)</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 class="py-name">_blast</tt><tt class="py-op">.</tt><tt class="py-name">descriptions</tt><tt class="py-op">.</tt><tt id="link-71" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-71', 'append', 'link-4');">append</a></tt><tt class="py-op">(</tt><tt id="link-72" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-72', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-73" class="py-name" targets="Class Bio.Blast.Record.Description=Bio.Blast.Record.Description-class.html"><a title="Bio.Blast.Record.Description" class="py-name" href="#" onclick="return doclink('link-73', 'Description', 'link-73');">Description</a></tt><tt class="py-op">(</tt><tt class="py-op">)</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">self</tt><tt class="py-op">.</tt><tt class="py-name">_blast</tt><tt class="py-op">.</tt><tt class="py-name">multiple_alignment</tt> <tt class="py-op">=</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">self</tt><tt class="py-op">.</tt><tt class="py-name">_hit</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_blast</tt><tt class="py-op">.</tt><tt class="py-name">alignments</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L371"></a><tt class="py-lineno">371</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_descr</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_blast</tt><tt class="py-op">.</tt><tt class="py-name">descriptions</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L372"></a><tt class="py-lineno">372</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_descr</tt><tt class="py-op">.</tt><tt class="py-name">num_alignments</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
</div><a name="L373"></a><tt class="py-lineno">373</tt> <tt class="py-line"> </tt>
<a name="BlastParser._end_Hit"></a><div id="BlastParser._end_Hit-def"><a name="L374"></a><tt class="py-lineno">374</tt> <a class="py-toggle" href="#" id="BlastParser._end_Hit-toggle" onclick="return toggle('BlastParser._end_Hit');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_Hit">_end_Hit</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._end_Hit-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_Hit-expanded"><a name="L375"></a><tt class="py-lineno">375</tt> <tt class="py-line"> <tt class="py-comment">#Cleanup</tt> </tt>
<a name="L376"></a><tt class="py-lineno">376</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_blast</tt><tt class="py-op">.</tt><tt class="py-name">multiple_alignment</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L377"></a><tt class="py-lineno">377</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_hit</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L378"></a><tt class="py-lineno">378</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_descr</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
</div><a name="L379"></a><tt class="py-lineno">379</tt> <tt class="py-line"> </tt>
<a name="BlastParser._end_Hit_id"></a><div id="BlastParser._end_Hit_id-def"><a name="L380"></a><tt class="py-lineno">380</tt> <a class="py-toggle" href="#" id="BlastParser._end_Hit_id-toggle" onclick="return toggle('BlastParser._end_Hit_id');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_Hit_id">_end_Hit_id</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._end_Hit_id-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_Hit_id-expanded"><a name="L381"></a><tt class="py-lineno">381</tt> <tt class="py-line"> <tt class="py-docstring">"""identifier of the database sequence</tt> </tt>
<a name="L382"></a><tt class="py-lineno">382</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L383"></a><tt class="py-lineno">383</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_hit</tt><tt class="py-op">.</tt><tt class="py-name">hit_id</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_hit</tt><tt class="py-op">.</tt><tt id="link-74" 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-74', 'title', 'link-74');">title</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt> <tt class="py-op">+</tt> <tt class="py-string">' '</tt> </tt>
</div><a name="L385"></a><tt class="py-lineno">385</tt> <tt class="py-line"> </tt>
<a name="BlastParser._end_Hit_def"></a><div id="BlastParser._end_Hit_def-def"><a name="L386"></a><tt class="py-lineno">386</tt> <a class="py-toggle" href="#" id="BlastParser._end_Hit_def-toggle" onclick="return toggle('BlastParser._end_Hit_def');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_Hit_def">_end_Hit_def</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._end_Hit_def-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_Hit_def-expanded"><a name="L387"></a><tt class="py-lineno">387</tt> <tt class="py-line"> <tt class="py-docstring">"""definition line of the database sequence</tt> </tt>
<a name="L388"></a><tt class="py-lineno">388</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L389"></a><tt class="py-lineno">389</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_hit</tt><tt class="py-op">.</tt><tt class="py-name">hit_def</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt> </tt>
<a name="L390"></a><tt class="py-lineno">390</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_hit</tt><tt class="py-op">.</tt><tt id="link-75" class="py-name"><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-75', 'title', 'link-74');">title</a></tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt> </tt>
<a name="L391"></a><tt class="py-lineno">391</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_descr</tt><tt class="py-op">.</tt><tt id="link-76" class="py-name"><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-76', 'title', 'link-74');">title</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_hit</tt><tt class="py-op">.</tt><tt id="link-77" class="py-name"><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-77', 'title', 'link-74');">title</a></tt> </tt>
</div><a name="L392"></a><tt class="py-lineno">392</tt> <tt class="py-line"> </tt>
<a name="BlastParser._end_Hit_accession"></a><div id="BlastParser._end_Hit_accession-def"><a name="L393"></a><tt class="py-lineno">393</tt> <a class="py-toggle" href="#" id="BlastParser._end_Hit_accession-toggle" onclick="return toggle('BlastParser._end_Hit_accession');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_Hit_accession">_end_Hit_accession</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._end_Hit_accession-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_Hit_accession-expanded"><a name="L394"></a><tt class="py-lineno">394</tt> <tt class="py-line"> <tt class="py-docstring">"""accession of the database sequence</tt> </tt>
<a name="L395"></a><tt class="py-lineno">395</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L396"></a><tt class="py-lineno">396</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_hit</tt><tt class="py-op">.</tt><tt id="link-78" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.accession()=Bio.GenBank._FeatureConsumer-class.html#accession,Method Bio.GenBank._RecordConsumer.accession()=Bio.GenBank._RecordConsumer-class.html#accession,Method Bio.Prosite.Prodoc._RecordConsumer.accession()=Bio.Prosite.Prodoc._RecordConsumer-class.html#accession,Method Bio.Prosite._RecordConsumer.accession()=Bio.Prosite._RecordConsumer-class.html#accession,Method Bio.SwissProt.SProt._RecordConsumer.accession()=Bio.SwissProt.SProt._RecordConsumer-class.html#accession,Method Bio.SwissProt.SProt._SequenceConsumer.accession()=Bio.SwissProt.SProt._SequenceConsumer-class.html#accession,Variable Bio.expressions.embl.embl65.accession=Bio.expressions.embl.embl65-module.html#accession,Variable Bio.expressions.genbank.accession=Bio.expressions.genbank-module.html#accession"><a title="Bio.GenBank._FeatureConsumer.accession
Bio.GenBank._RecordConsumer.accession
Bio.Prosite.Prodoc._RecordConsumer.accession
Bio.Prosite._RecordConsumer.accession
Bio.SwissProt.SProt._RecordConsumer.accession
Bio.SwissProt.SProt._SequenceConsumer.accession
Bio.expressions.embl.embl65.accession
Bio.expressions.genbank.accession" class="py-name" href="#" onclick="return doclink('link-78', 'accession', 'link-78');">accession</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt> </tt>
<a name="L397"></a><tt class="py-lineno">397</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_descr</tt><tt class="py-op">.</tt><tt id="link-79" class="py-name"><a title="Bio.GenBank._FeatureConsumer.accession
Bio.GenBank._RecordConsumer.accession
Bio.Prosite.Prodoc._RecordConsumer.accession
Bio.Prosite._RecordConsumer.accession
Bio.SwissProt.SProt._RecordConsumer.accession
Bio.SwissProt.SProt._SequenceConsumer.accession
Bio.expressions.embl.embl65.accession
Bio.expressions.genbank.accession" class="py-name" href="#" onclick="return doclink('link-79', 'accession', 'link-78');">accession</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt> </tt>
</div><a name="L398"></a><tt class="py-lineno">398</tt> <tt class="py-line"> </tt>
<a name="BlastParser._end_Hit_len"></a><div id="BlastParser._end_Hit_len-def"><a name="L399"></a><tt class="py-lineno">399</tt> <a class="py-toggle" href="#" id="BlastParser._end_Hit_len-toggle" onclick="return toggle('BlastParser._end_Hit_len');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_Hit_len">_end_Hit_len</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._end_Hit_len-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_Hit_len-expanded"><a name="L400"></a><tt class="py-lineno">400</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_hit</tt><tt class="py-op">.</tt><tt id="link-80" 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-80', 'length', 'link-80');">length</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt><tt class="py-op">)</tt> </tt>
</div><a name="L401"></a><tt class="py-lineno">401</tt> <tt class="py-line"> </tt>
<a name="L402"></a><tt class="py-lineno">402</tt> <tt class="py-line"> <tt class="py-comment"># HSPs</tt> </tt>
<a name="BlastParser._start_Hsp"></a><div id="BlastParser._start_Hsp-def"><a name="L403"></a><tt class="py-lineno">403</tt> <a class="py-toggle" href="#" id="BlastParser._start_Hsp-toggle" onclick="return toggle('BlastParser._start_Hsp');">-</a><tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_start_Hsp">_start_Hsp</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._start_Hsp-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._start_Hsp-expanded"><a name="L404"></a><tt class="py-lineno">404</tt> <tt class="py-line"> <tt class="py-comment">#Note that self._start_Hit() should have been called</tt> </tt>
<a name="L405"></a><tt class="py-lineno">405</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#to setup things like self._blast.multiple_alignment</tt> </tt>
<a name="L406"></a><tt class="py-lineno">406</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_hit</tt><tt class="py-op">.</tt><tt class="py-name">hsps</tt><tt class="py-op">.</tt><tt id="link-81" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-81', 'append', 'link-4');">append</a></tt><tt class="py-op">(</tt><tt id="link-82" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-82', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-83" class="py-name" targets="Class Bio.Blast.Record.HSP=Bio.Blast.Record.HSP-class.html,Class Bio.Search.HSP=Bio.Search.HSP-class.html"><a title="Bio.Blast.Record.HSP
Bio.Search.HSP" class="py-name" href="#" onclick="return doclink('link-83', 'HSP', 'link-83');">HSP</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L407"></a><tt class="py-lineno">407</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_hsp</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_hit</tt><tt class="py-op">.</tt><tt class="py-name">hsps</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</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 class="py-name">_descr</tt><tt class="py-op">.</tt><tt class="py-name">num_alignments</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L409"></a><tt class="py-lineno">409</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_blast</tt><tt class="py-op">.</tt><tt class="py-name">multiple_alignment</tt><tt class="py-op">.</tt><tt id="link-84" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-84', 'append', 'link-4');">append</a></tt><tt class="py-op">(</tt><tt id="link-85" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-85', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-86" class="py-name" targets="Class Bio.Blast.Record.MultipleAlignment=Bio.Blast.Record.MultipleAlignment-class.html"><a title="Bio.Blast.Record.MultipleAlignment" class="py-name" href="#" onclick="return doclink('link-86', 'MultipleAlignment', 'link-86');">MultipleAlignment</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L410"></a><tt class="py-lineno">410</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_mult_al</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_blast</tt><tt class="py-op">.</tt><tt class="py-name">multiple_alignment</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</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="L412"></a><tt class="py-lineno">412</tt> <tt class="py-line"> <tt class="py-comment"># Hsp_num is useless</tt> </tt>
<a name="BlastParser._end_Hsp_score"></a><div id="BlastParser._end_Hsp_score-def"><a name="L413"></a><tt class="py-lineno">413</tt> <a class="py-toggle" href="#" id="BlastParser._end_Hsp_score-toggle" onclick="return toggle('BlastParser._end_Hsp_score');">-</a><tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_Hsp_score">_end_Hsp_score</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._end_Hsp_score-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_Hsp_score-expanded"><a name="L414"></a><tt class="py-lineno">414</tt> <tt class="py-line"> <tt class="py-docstring">"""raw score of HSP</tt> </tt>
<a name="L415"></a><tt class="py-lineno">415</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L416"></a><tt class="py-lineno">416</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_hsp</tt><tt class="py-op">.</tt><tt id="link-87" 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-87', 'score', 'link-87');">score</a></tt> <tt class="py-op">=</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt><tt class="py-op">)</tt> </tt>
<a name="L417"></a><tt class="py-lineno">417</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_descr</tt><tt class="py-op">.</tt><tt id="link-88" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-88', 'score', 'link-87');">score</a></tt> <tt class="py-op">==</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L418"></a><tt class="py-lineno">418</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_descr</tt><tt class="py-op">.</tt><tt id="link-89" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-89', 'score', 'link-87');">score</a></tt> <tt class="py-op">=</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt><tt class="py-op">)</tt> </tt>
</div><a name="L419"></a><tt class="py-lineno">419</tt> <tt class="py-line"> </tt>
<a name="BlastParser._end_Hsp_bit_score"></a><div id="BlastParser._end_Hsp_bit_score-def"><a name="L420"></a><tt class="py-lineno">420</tt> <a class="py-toggle" href="#" id="BlastParser._end_Hsp_bit_score-toggle" onclick="return toggle('BlastParser._end_Hsp_bit_score');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_Hsp_bit_score">_end_Hsp_bit_score</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._end_Hsp_bit_score-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_Hsp_bit_score-expanded"><a name="L421"></a><tt class="py-lineno">421</tt> <tt class="py-line"> <tt class="py-docstring">"""bit score of HSP</tt> </tt>
<a name="L422"></a><tt class="py-lineno">422</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L423"></a><tt class="py-lineno">423</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_hsp</tt><tt class="py-op">.</tt><tt class="py-name">bits</tt> <tt class="py-op">=</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt><tt class="py-op">)</tt> </tt>
<a name="L424"></a><tt class="py-lineno">424</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_descr</tt><tt class="py-op">.</tt><tt class="py-name">bits</tt> <tt class="py-op">==</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L425"></a><tt class="py-lineno">425</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_descr</tt><tt class="py-op">.</tt><tt class="py-name">bits</tt> <tt class="py-op">=</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt><tt class="py-op">)</tt> </tt>
</div><a name="L426"></a><tt class="py-lineno">426</tt> <tt class="py-line"> </tt>
<a name="BlastParser._end_Hsp_evalue"></a><div id="BlastParser._end_Hsp_evalue-def"><a name="L427"></a><tt class="py-lineno">427</tt> <a class="py-toggle" href="#" id="BlastParser._end_Hsp_evalue-toggle" onclick="return toggle('BlastParser._end_Hsp_evalue');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_Hsp_evalue">_end_Hsp_evalue</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._end_Hsp_evalue-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_Hsp_evalue-expanded"><a name="L428"></a><tt class="py-lineno">428</tt> <tt class="py-line"> <tt class="py-docstring">"""expect value value of the HSP</tt> </tt>
<a name="L429"></a><tt class="py-lineno">429</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L430"></a><tt class="py-lineno">430</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_hsp</tt><tt class="py-op">.</tt><tt id="link-90" class="py-name"><a title="Bio.expressions.blast.ncbiblast.expect" class="py-name" href="#" onclick="return doclink('link-90', 'expect', 'link-48');">expect</a></tt> <tt class="py-op">=</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt><tt class="py-op">)</tt> </tt>
<a name="L431"></a><tt class="py-lineno">431</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_descr</tt><tt class="py-op">.</tt><tt id="link-91" class="py-name" targets="Variable Bio.Affy.CelFile.e=Bio.Affy.CelFile-module.html#e,Variable Bio.LogisticRegression.e=Bio.LogisticRegression-module.html#e,Variable Bio.MarkovModel.e=Bio.MarkovModel-module.html#e,Variable Bio.MaxEntropy.e=Bio.MaxEntropy-module.html#e,Variable Bio.NaiveBayes.e=Bio.NaiveBayes-module.html#e,Variable Bio.Statistics.lowess.e=Bio.Statistics.lowess-module.html#e,Variable Bio.distance.e=Bio.distance-module.html#e,Variable Bio.kNN.e=Bio.kNN-module.html#e"><a title="Bio.Affy.CelFile.e
Bio.LogisticRegression.e
Bio.MarkovModel.e
Bio.MaxEntropy.e
Bio.NaiveBayes.e
Bio.Statistics.lowess.e
Bio.distance.e
Bio.kNN.e" class="py-name" href="#" onclick="return doclink('link-91', 'e', 'link-91');">e</a></tt> <tt class="py-op">==</tt> <tt class="py-name">None</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 class="py-name">_descr</tt><tt class="py-op">.</tt><tt id="link-92" class="py-name"><a title="Bio.Affy.CelFile.e
Bio.LogisticRegression.e
Bio.MarkovModel.e
Bio.MaxEntropy.e
Bio.NaiveBayes.e
Bio.Statistics.lowess.e
Bio.distance.e
Bio.kNN.e" class="py-name" href="#" onclick="return doclink('link-92', 'e', 'link-91');">e</a></tt> <tt class="py-op">=</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt><tt class="py-op">)</tt> </tt>
</div><a name="L433"></a><tt class="py-lineno">433</tt> <tt class="py-line"> </tt>
<a name="BlastParser._end_Hsp_query_from"></a><div id="BlastParser._end_Hsp_query_from-def"><a name="L434"></a><tt class="py-lineno">434</tt> <a class="py-toggle" href="#" id="BlastParser._end_Hsp_query_from-toggle" onclick="return toggle('BlastParser._end_Hsp_query_from');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_Hsp_query_from">_end_Hsp_query_from</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._end_Hsp_query_from-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_Hsp_query_from-expanded"><a name="L435"></a><tt class="py-lineno">435</tt> <tt class="py-line"> <tt class="py-docstring">"""offset of query at the start of the alignment (one-offset)</tt> </tt>
<a name="L436"></a><tt class="py-lineno">436</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L437"></a><tt class="py-lineno">437</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_hsp</tt><tt class="py-op">.</tt><tt class="py-name">query_start</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt><tt class="py-op">)</tt> </tt>
</div><a name="L438"></a><tt class="py-lineno">438</tt> <tt class="py-line"> </tt>
<a name="BlastParser._end_Hsp_query_to"></a><div id="BlastParser._end_Hsp_query_to-def"><a name="L439"></a><tt class="py-lineno">439</tt> <a class="py-toggle" href="#" id="BlastParser._end_Hsp_query_to-toggle" onclick="return toggle('BlastParser._end_Hsp_query_to');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_Hsp_query_to">_end_Hsp_query_to</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._end_Hsp_query_to-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_Hsp_query_to-expanded"><a name="L440"></a><tt class="py-lineno">440</tt> <tt class="py-line"> <tt class="py-docstring">"""offset of query at the end of the alignment (one-offset)</tt> </tt>
<a name="L441"></a><tt class="py-lineno">441</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L442"></a><tt class="py-lineno">442</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_hsp</tt><tt class="py-op">.</tt><tt class="py-name">query_end</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt><tt class="py-op">)</tt> </tt>
</div><a name="L443"></a><tt class="py-lineno">443</tt> <tt class="py-line"> </tt>
<a name="BlastParser._end_Hsp_hit_from"></a><div id="BlastParser._end_Hsp_hit_from-def"><a name="L444"></a><tt class="py-lineno">444</tt> <a class="py-toggle" href="#" id="BlastParser._end_Hsp_hit_from-toggle" onclick="return toggle('BlastParser._end_Hsp_hit_from');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_Hsp_hit_from">_end_Hsp_hit_from</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._end_Hsp_hit_from-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_Hsp_hit_from-expanded"><a name="L445"></a><tt class="py-lineno">445</tt> <tt class="py-line"> <tt class="py-docstring">"""offset of the database at the start of the alignment (one-offset)</tt> </tt>
<a name="L446"></a><tt class="py-lineno">446</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L447"></a><tt class="py-lineno">447</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_hsp</tt><tt class="py-op">.</tt><tt class="py-name">sbjct_start</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt><tt class="py-op">)</tt> </tt>
</div><a name="L448"></a><tt class="py-lineno">448</tt> <tt class="py-line"> </tt>
<a name="BlastParser._end_Hsp_hit_to"></a><div id="BlastParser._end_Hsp_hit_to-def"><a name="L449"></a><tt class="py-lineno">449</tt> <a class="py-toggle" href="#" id="BlastParser._end_Hsp_hit_to-toggle" onclick="return toggle('BlastParser._end_Hsp_hit_to');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_Hsp_hit_to">_end_Hsp_hit_to</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._end_Hsp_hit_to-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_Hsp_hit_to-expanded"><a name="L450"></a><tt class="py-lineno">450</tt> <tt class="py-line"> <tt class="py-docstring">"""offset of the database at the end of the alignment (one-offset)</tt> </tt>
<a name="L451"></a><tt class="py-lineno">451</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L452"></a><tt class="py-lineno">452</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_hsp</tt><tt class="py-op">.</tt><tt class="py-name">sbjct_end</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt><tt class="py-op">)</tt> </tt>
</div><a name="L453"></a><tt class="py-lineno">453</tt> <tt class="py-line"> </tt>
<a name="L454"></a><tt class="py-lineno">454</tt> <tt class="py-line"><tt class="py-comment">## def _end_Hsp_pattern_from(self):</tt> </tt>
<a name="L455"></a><tt class="py-lineno">455</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## """start of phi-blast pattern on the query (one-offset)</tt> </tt>
<a name="L456"></a><tt class="py-lineno">456</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## """</tt> </tt>
<a name="L457"></a><tt class="py-lineno">457</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## pass # XXX TODO PSI</tt> </tt>
<a name="L458"></a><tt class="py-lineno">458</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L459"></a><tt class="py-lineno">459</tt> <tt class="py-line"><tt class="py-comment">## def _end_Hsp_pattern_to(self):</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">## """end of phi-blast pattern on the query (one-offset)</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">## pass # XXX TODO PSI</tt> </tt>
<a name="L463"></a><tt class="py-lineno">463</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="BlastParser._end_Hsp_query_frame"></a><div id="BlastParser._end_Hsp_query_frame-def"><a name="L464"></a><tt class="py-lineno">464</tt> <a class="py-toggle" href="#" id="BlastParser._end_Hsp_query_frame-toggle" onclick="return toggle('BlastParser._end_Hsp_query_frame');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_Hsp_query_frame">_end_Hsp_query_frame</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._end_Hsp_query_frame-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_Hsp_query_frame-expanded"><a name="L465"></a><tt class="py-lineno">465</tt> <tt class="py-line"> <tt class="py-docstring">"""frame of the query if applicable</tt> </tt>
<a name="L466"></a><tt class="py-lineno">466</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L467"></a><tt class="py-lineno">467</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_hsp</tt><tt class="py-op">.</tt><tt id="link-93" 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-93', 'frame', 'link-93');">frame</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-op">)</tt> </tt>
</div><a name="L468"></a><tt class="py-lineno">468</tt> <tt class="py-line"> </tt>
<a name="BlastParser._end_Hsp_hit_frame"></a><div id="BlastParser._end_Hsp_hit_frame-def"><a name="L469"></a><tt class="py-lineno">469</tt> <a class="py-toggle" href="#" id="BlastParser._end_Hsp_hit_frame-toggle" onclick="return toggle('BlastParser._end_Hsp_hit_frame');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_Hsp_hit_frame">_end_Hsp_hit_frame</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._end_Hsp_hit_frame-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_Hsp_hit_frame-expanded"><a name="L470"></a><tt class="py-lineno">470</tt> <tt class="py-line"> <tt class="py-docstring">"""frame of the database sequence if applicable</tt> </tt>
<a name="L471"></a><tt class="py-lineno">471</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L472"></a><tt class="py-lineno">472</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_hsp</tt><tt class="py-op">.</tt><tt id="link-94" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.frame
Bio.expressions.blast.ncbiblast.frame" class="py-name" href="#" onclick="return doclink('link-94', 'frame', 'link-93');">frame</a></tt> <tt class="py-op">+=</tt> <tt class="py-op">(</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-op">)</tt> </tt>
</div><a name="L473"></a><tt class="py-lineno">473</tt> <tt class="py-line"> </tt>
<a name="BlastParser._end_Hsp_identity"></a><div id="BlastParser._end_Hsp_identity-def"><a name="L474"></a><tt class="py-lineno">474</tt> <a class="py-toggle" href="#" id="BlastParser._end_Hsp_identity-toggle" onclick="return toggle('BlastParser._end_Hsp_identity');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_Hsp_identity">_end_Hsp_identity</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._end_Hsp_identity-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_Hsp_identity-expanded"><a name="L475"></a><tt class="py-lineno">475</tt> <tt class="py-line"> <tt class="py-docstring">"""number of identities in the alignment</tt> </tt>
<a name="L476"></a><tt class="py-lineno">476</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L477"></a><tt class="py-lineno">477</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_hsp</tt><tt class="py-op">.</tt><tt id="link-95" 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-95', 'identities', 'link-95');">identities</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt><tt class="py-op">)</tt> </tt>
</div><a name="L478"></a><tt class="py-lineno">478</tt> <tt class="py-line"> </tt>
<a name="BlastParser._end_Hsp_positive"></a><div id="BlastParser._end_Hsp_positive-def"><a name="L479"></a><tt class="py-lineno">479</tt> <a class="py-toggle" href="#" id="BlastParser._end_Hsp_positive-toggle" onclick="return toggle('BlastParser._end_Hsp_positive');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_Hsp_positive">_end_Hsp_positive</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._end_Hsp_positive-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_Hsp_positive-expanded"><a name="L480"></a><tt class="py-lineno">480</tt> <tt class="py-line"> <tt class="py-docstring">"""number of positive (conservative) substitutions in the alignment</tt> </tt>
<a name="L481"></a><tt class="py-lineno">481</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L482"></a><tt class="py-lineno">482</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_hsp</tt><tt class="py-op">.</tt><tt class="py-name">positives</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt><tt class="py-op">)</tt> </tt>
</div><a name="L483"></a><tt class="py-lineno">483</tt> <tt class="py-line"> </tt>
<a name="BlastParser._end_Hsp_gaps"></a><div id="BlastParser._end_Hsp_gaps-def"><a name="L484"></a><tt class="py-lineno">484</tt> <a class="py-toggle" href="#" id="BlastParser._end_Hsp_gaps-toggle" onclick="return toggle('BlastParser._end_Hsp_gaps');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_Hsp_gaps">_end_Hsp_gaps</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._end_Hsp_gaps-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_Hsp_gaps-expanded"><a name="L485"></a><tt class="py-lineno">485</tt> <tt class="py-line"> <tt class="py-docstring">"""number of gaps in the alignment</tt> </tt>
<a name="L486"></a><tt class="py-lineno">486</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L487"></a><tt class="py-lineno">487</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_hsp</tt><tt class="py-op">.</tt><tt class="py-name">gaps</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt><tt class="py-op">)</tt> </tt>
</div><a name="L488"></a><tt class="py-lineno">488</tt> <tt class="py-line"> </tt>
<a name="BlastParser._end_Hsp_align_len"></a><div id="BlastParser._end_Hsp_align_len-def"><a name="L489"></a><tt class="py-lineno">489</tt> <a class="py-toggle" href="#" id="BlastParser._end_Hsp_align_len-toggle" onclick="return toggle('BlastParser._end_Hsp_align_len');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_Hsp_align_len">_end_Hsp_align_len</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._end_Hsp_align_len-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_Hsp_align_len-expanded"><a name="L490"></a><tt class="py-lineno">490</tt> <tt class="py-line"> <tt class="py-docstring">"""length of the alignment</tt> </tt>
<a name="L491"></a><tt class="py-lineno">491</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L492"></a><tt class="py-lineno">492</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_hsp</tt><tt class="py-op">.</tt><tt class="py-name">align_length</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt><tt class="py-op">)</tt> </tt>
</div><a name="L493"></a><tt class="py-lineno">493</tt> <tt class="py-line"> </tt>
<a name="L494"></a><tt class="py-lineno">494</tt> <tt class="py-line"><tt class="py-comment">## def _en_Hsp_density(self):</tt> </tt>
<a name="L495"></a><tt class="py-lineno">495</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## """score density</tt> </tt>
<a name="L496"></a><tt class="py-lineno">496</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## """</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">## pass # XXX ???</tt> </tt>
<a name="L498"></a><tt class="py-lineno">498</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="BlastParser._end_Hsp_qseq"></a><div id="BlastParser._end_Hsp_qseq-def"><a name="L499"></a><tt class="py-lineno">499</tt> <a class="py-toggle" href="#" id="BlastParser._end_Hsp_qseq-toggle" onclick="return toggle('BlastParser._end_Hsp_qseq');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_Hsp_qseq">_end_Hsp_qseq</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._end_Hsp_qseq-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_Hsp_qseq-expanded"><a name="L500"></a><tt class="py-lineno">500</tt> <tt class="py-line"> <tt class="py-docstring">"""alignment string for the query</tt> </tt>
<a name="L501"></a><tt class="py-lineno">501</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L502"></a><tt class="py-lineno">502</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_hsp</tt><tt class="py-op">.</tt><tt id="link-96" 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-96', 'query', 'link-34');">query</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt> </tt>
</div><a name="L503"></a><tt class="py-lineno">503</tt> <tt class="py-line"> </tt>
<a name="BlastParser._end_Hsp_hseq"></a><div id="BlastParser._end_Hsp_hseq-def"><a name="L504"></a><tt class="py-lineno">504</tt> <a class="py-toggle" href="#" id="BlastParser._end_Hsp_hseq-toggle" onclick="return toggle('BlastParser._end_Hsp_hseq');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_Hsp_hseq">_end_Hsp_hseq</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._end_Hsp_hseq-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_Hsp_hseq-expanded"><a name="L505"></a><tt class="py-lineno">505</tt> <tt class="py-line"> <tt class="py-docstring">"""alignment string for the database</tt> </tt>
<a name="L506"></a><tt class="py-lineno">506</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L507"></a><tt class="py-lineno">507</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_hsp</tt><tt class="py-op">.</tt><tt id="link-97" 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-97', 'sbjct', 'link-97');">sbjct</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt> </tt>
</div><a name="L508"></a><tt class="py-lineno">508</tt> <tt class="py-line"> </tt>
<a name="BlastParser._end_Hsp_midline"></a><div id="BlastParser._end_Hsp_midline-def"><a name="L509"></a><tt class="py-lineno">509</tt> <a class="py-toggle" href="#" id="BlastParser._end_Hsp_midline-toggle" onclick="return toggle('BlastParser._end_Hsp_midline');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_Hsp_midline">_end_Hsp_midline</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._end_Hsp_midline-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_Hsp_midline-expanded"><a name="L510"></a><tt class="py-lineno">510</tt> <tt class="py-line"> <tt class="py-docstring">"""Formatting middle line as normally seen in BLAST report</tt> </tt>
<a name="L511"></a><tt class="py-lineno">511</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L512"></a><tt class="py-lineno">512</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_hsp</tt><tt class="py-op">.</tt><tt id="link-98" class="py-name" targets="Method Bio.Parsers.spark.GenericASTMatcher.match()=Bio.Parsers.spark.GenericASTMatcher-class.html#match,Method Bio.Prosite.Pattern.Prosite.match()=Bio.Prosite.Pattern.Prosite-class.html#match,Function Bio.triefind.match()=Bio.triefind-module.html#match,Method Martel.msre_parse.Tokenizer.match()=Martel.msre_parse.Tokenizer-class.html#match"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-98', 'match', 'link-98');">match</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt> </tt>
</div><a name="L513"></a><tt class="py-lineno">513</tt> <tt class="py-line"> </tt>
<a name="L514"></a><tt class="py-lineno">514</tt> <tt class="py-line"> <tt class="py-comment"># Statistics</tt> </tt>
<a name="BlastParser._end_Statistics_db_num"></a><div id="BlastParser._end_Statistics_db_num-def"><a name="L515"></a><tt class="py-lineno">515</tt> <a class="py-toggle" href="#" id="BlastParser._end_Statistics_db_num-toggle" onclick="return toggle('BlastParser._end_Statistics_db_num');">-</a><tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_Statistics_db_num">_end_Statistics_db_num</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._end_Statistics_db_num-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_Statistics_db_num-expanded"><a name="L516"></a><tt class="py-lineno">516</tt> <tt class="py-line"> <tt class="py-docstring">"""number of sequences in the database</tt> </tt>
<a name="L517"></a><tt class="py-lineno">517</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L518"></a><tt class="py-lineno">518</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_blast</tt><tt class="py-op">.</tt><tt id="link-99" 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-99', 'num_sequences_in_database', 'link-99');">num_sequences_in_database</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt><tt class="py-op">)</tt> </tt>
</div><a name="L519"></a><tt class="py-lineno">519</tt> <tt class="py-line"> </tt>
<a name="BlastParser._end_Statistics_db_len"></a><div id="BlastParser._end_Statistics_db_len-def"><a name="L520"></a><tt class="py-lineno">520</tt> <a class="py-toggle" href="#" id="BlastParser._end_Statistics_db_len-toggle" onclick="return toggle('BlastParser._end_Statistics_db_len');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_Statistics_db_len">_end_Statistics_db_len</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._end_Statistics_db_len-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_Statistics_db_len-expanded"><a name="L521"></a><tt class="py-lineno">521</tt> <tt class="py-line"> <tt class="py-docstring">"""number of letters in the database</tt> </tt>
<a name="L522"></a><tt class="py-lineno">522</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L523"></a><tt class="py-lineno">523</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_blast</tt><tt class="py-op">.</tt><tt id="link-100" 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-100', 'num_letters_in_database', 'link-100');">num_letters_in_database</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt><tt class="py-op">)</tt> </tt>
</div><a name="L524"></a><tt class="py-lineno">524</tt> <tt class="py-line"> </tt>
<a name="BlastParser._end_Statistics_hsp_len"></a><div id="BlastParser._end_Statistics_hsp_len-def"><a name="L525"></a><tt class="py-lineno">525</tt> <a class="py-toggle" href="#" id="BlastParser._end_Statistics_hsp_len-toggle" onclick="return toggle('BlastParser._end_Statistics_hsp_len');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_Statistics_hsp_len">_end_Statistics_hsp_len</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._end_Statistics_hsp_len-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_Statistics_hsp_len-expanded"><a name="L526"></a><tt class="py-lineno">526</tt> <tt class="py-line"> <tt class="py-docstring">"""the effective HSP length</tt> </tt>
<a name="L527"></a><tt class="py-lineno">527</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L528"></a><tt class="py-lineno">528</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_blast</tt><tt class="py-op">.</tt><tt id="link-101" 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-101', 'effective_hsp_length', 'link-101');">effective_hsp_length</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt><tt class="py-op">)</tt> </tt>
</div><a name="L529"></a><tt class="py-lineno">529</tt> <tt class="py-line"> </tt>
<a name="BlastParser._end_Statistics_eff_space"></a><div id="BlastParser._end_Statistics_eff_space-def"><a name="L530"></a><tt class="py-lineno">530</tt> <a class="py-toggle" href="#" id="BlastParser._end_Statistics_eff_space-toggle" onclick="return toggle('BlastParser._end_Statistics_eff_space');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_Statistics_eff_space">_end_Statistics_eff_space</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._end_Statistics_eff_space-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_Statistics_eff_space-expanded"><a name="L531"></a><tt class="py-lineno">531</tt> <tt class="py-line"> <tt class="py-docstring">"""the effective search space</tt> </tt>
<a name="L532"></a><tt class="py-lineno">532</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L533"></a><tt class="py-lineno">533</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_blast</tt><tt class="py-op">.</tt><tt id="link-102" 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-102', 'effective_search_space', 'link-102');">effective_search_space</a></tt> <tt class="py-op">=</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt><tt class="py-op">)</tt> </tt>
</div><a name="L534"></a><tt class="py-lineno">534</tt> <tt class="py-line"> </tt>
<a name="BlastParser._end_Statistics_kappa"></a><div id="BlastParser._end_Statistics_kappa-def"><a name="L535"></a><tt class="py-lineno">535</tt> <a class="py-toggle" href="#" id="BlastParser._end_Statistics_kappa-toggle" onclick="return toggle('BlastParser._end_Statistics_kappa');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_Statistics_kappa">_end_Statistics_kappa</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._end_Statistics_kappa-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_Statistics_kappa-expanded"><a name="L536"></a><tt class="py-lineno">536</tt> <tt class="py-line"> <tt class="py-docstring">"""Karlin-Altschul parameter K</tt> </tt>
<a name="L537"></a><tt class="py-lineno">537</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L538"></a><tt class="py-lineno">538</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_blast</tt><tt class="py-op">.</tt><tt id="link-103" 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-103', 'ka_params', 'link-103');">ka_params</a></tt> <tt class="py-op">=</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt><tt class="py-op">)</tt> </tt>
</div><a name="L539"></a><tt class="py-lineno">539</tt> <tt class="py-line"> </tt>
<a name="BlastParser._end_Statistics_lambda"></a><div id="BlastParser._end_Statistics_lambda-def"><a name="L540"></a><tt class="py-lineno">540</tt> <a class="py-toggle" href="#" id="BlastParser._end_Statistics_lambda-toggle" onclick="return toggle('BlastParser._end_Statistics_lambda');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_Statistics_lambda">_end_Statistics_lambda</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._end_Statistics_lambda-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_Statistics_lambda-expanded"><a name="L541"></a><tt class="py-lineno">541</tt> <tt class="py-line"> <tt class="py-docstring">"""Karlin-Altschul parameter Lambda</tt> </tt>
<a name="L542"></a><tt class="py-lineno">542</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L543"></a><tt class="py-lineno">543</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_blast</tt><tt class="py-op">.</tt><tt id="link-104" class="py-name"><a title="Bio.Blast.NCBIStandalone._DatabaseReportConsumer.ka_params" class="py-name" href="#" onclick="return doclink('link-104', 'ka_params', 'link-103');">ka_params</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L544"></a><tt class="py-lineno">544</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_blast</tt><tt class="py-op">.</tt><tt id="link-105" class="py-name"><a title="Bio.Blast.NCBIStandalone._DatabaseReportConsumer.ka_params" class="py-name" href="#" onclick="return doclink('link-105', 'ka_params', 'link-103');">ka_params</a></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="BlastParser._end_Statistics_entropy"></a><div id="BlastParser._end_Statistics_entropy-def"><a name="L546"></a><tt class="py-lineno">546</tt> <a class="py-toggle" href="#" id="BlastParser._end_Statistics_entropy-toggle" onclick="return toggle('BlastParser._end_Statistics_entropy');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_Statistics_entropy">_end_Statistics_entropy</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._end_Statistics_entropy-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BlastParser._end_Statistics_entropy-expanded"><a name="L547"></a><tt class="py-lineno">547</tt> <tt class="py-line"> <tt class="py-docstring">"""Karlin-Altschul parameter H</tt> </tt>
<a name="L548"></a><tt class="py-lineno">548</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L549"></a><tt class="py-lineno">549</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_blast</tt><tt class="py-op">.</tt><tt id="link-106" class="py-name"><a title="Bio.Blast.NCBIStandalone._DatabaseReportConsumer.ka_params" class="py-name" href="#" onclick="return doclink('link-106', 'ka_params', 'link-103');">ka_params</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_blast</tt><tt class="py-op">.</tt><tt id="link-107" class="py-name"><a title="Bio.Blast.NCBIStandalone._DatabaseReportConsumer.ka_params" class="py-name" href="#" onclick="return doclink('link-107', 'ka_params', 'link-103');">ka_params</a></tt> <tt class="py-op">+</tt> <tt class="py-op">(</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_value</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L550"></a><tt class="py-lineno">550</tt> <tt class="py-line"> </tt>
<a name="parse"></a><div id="parse-def"><a name="L551"></a><tt class="py-lineno">551</tt> <a class="py-toggle" href="#" id="parse-toggle" onclick="return toggle('parse');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.NCBIXML-module.html#parse">parse</a><tt class="py-op">(</tt><tt class="py-param">handle</tt><tt class="py-op">,</tt> <tt class="py-param">debug</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="parse-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="parse-expanded"><a name="L552"></a><tt class="py-lineno">552</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns an iterator a Blast record for each query.</tt> </tt>
<a name="L553"></a><tt class="py-lineno">553</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L554"></a><tt class="py-lineno">554</tt> <tt class="py-line"><tt class="py-docstring"> handle - file handle to and XML file to parse</tt> </tt>
<a name="L555"></a><tt class="py-lineno">555</tt> <tt class="py-line"><tt class="py-docstring"> debug - integer, amount of debug information to print</tt> </tt>
<a name="L556"></a><tt class="py-lineno">556</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L557"></a><tt class="py-lineno">557</tt> <tt class="py-line"><tt class="py-docstring"> This is a generator function that returns multiple Blast records</tt> </tt>
<a name="L558"></a><tt class="py-lineno">558</tt> <tt class="py-line"><tt class="py-docstring"> objects - one for each query sequence given to blast. The file</tt> </tt>
<a name="L559"></a><tt class="py-lineno">559</tt> <tt class="py-line"><tt class="py-docstring"> is read incrementally, returning complete records as they are read</tt> </tt>
<a name="L560"></a><tt class="py-lineno">560</tt> <tt class="py-line"><tt class="py-docstring"> in.</tt> </tt>
<a name="L561"></a><tt class="py-lineno">561</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L562"></a><tt class="py-lineno">562</tt> <tt class="py-line"><tt class="py-docstring"> Should cope with new BLAST 2.2.14+ which gives a single XML file</tt> </tt>
<a name="L563"></a><tt class="py-lineno">563</tt> <tt class="py-line"><tt class="py-docstring"> for mutliple query records.</tt> </tt>
<a name="L564"></a><tt class="py-lineno">564</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L565"></a><tt class="py-lineno">565</tt> <tt class="py-line"><tt class="py-docstring"> Should also cope with XML output from older versions BLAST which</tt> </tt>
<a name="L566"></a><tt class="py-lineno">566</tt> <tt class="py-line"><tt class="py-docstring"> gave multiple XML files concatenated together (giving a single file</tt> </tt>
<a name="L567"></a><tt class="py-lineno">567</tt> <tt class="py-line"><tt class="py-docstring"> which strictly speaking wasn't valid XML)."""</tt> </tt>
<a name="L568"></a><tt class="py-lineno">568</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt class="py-name">xml</tt><tt class="py-op">.</tt><tt class="py-name">parsers</tt> <tt class="py-keyword">import</tt> <tt class="py-name">expat</tt> </tt>
<a name="L569"></a><tt class="py-lineno">569</tt> <tt class="py-line"> <tt class="py-name">BLOCK</tt> <tt class="py-op">=</tt> <tt class="py-number">1024</tt> </tt>
<a name="L570"></a><tt class="py-lineno">570</tt> <tt class="py-line"> <tt class="py-name">MARGIN</tt> <tt class="py-op">=</tt> <tt class="py-number">10</tt> <tt class="py-comment"># must be at least length of newline + XML start</tt> </tt>
<a name="L571"></a><tt class="py-lineno">571</tt> <tt class="py-line"> <tt class="py-name">XML_START</tt> <tt class="py-op">=</tt> <tt class="py-string">"<?xml"</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 id="link-108" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.text()=Bio.EUtils.POM.ElementNode-class.html#text,Method Bio.Prosite.Prodoc._RecordConsumer.text()=Bio.Prosite.Prodoc._RecordConsumer-class.html#text,Variable Martel.test.test_Iterator.text=Martel.test.test_Iterator-module.html#text,Variable Martel.test.test_ParseRecords.text=Martel.test.test_ParseRecords-module.html#text"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-108', 'text', 'link-108');">text</a></tt> <tt class="py-op">=</tt> <tt id="link-109" 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-109', 'handle', 'link-109');">handle</a></tt><tt class="py-op">.</tt><tt id="link-110" 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-110', 'read', 'link-110');">read</a></tt><tt class="py-op">(</tt><tt class="py-name">BLOCK</tt><tt class="py-op">)</tt> </tt>
<a name="L574"></a><tt class="py-lineno">574</tt> <tt class="py-line"> <tt class="py-name">pending</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L575"></a><tt class="py-lineno">575</tt> <tt class="py-line"> </tt>
<a name="L576"></a><tt class="py-lineno">576</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-111" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-111', 'text', 'link-108');">text</a></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">#NO DATA FOUND!</tt> </tt>
<a name="L578"></a><tt class="py-lineno">578</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">"Your XML file was empty"</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-keyword">while</tt> <tt id="link-112" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-112', 'text', 'link-108');">text</a></tt> <tt class="py-op">:</tt> </tt>
<a name="L581"></a><tt class="py-lineno">581</tt> <tt class="py-line"> <tt class="py-comment">#We are now starting a new XML file</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 class="py-keyword">not</tt> <tt id="link-113" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-113', 'text', 'link-108');">text</a></tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-name">XML_START</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L583"></a><tt class="py-lineno">583</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">"Your XML file did not start with %s..."</tt> \ </tt>
<a name="L584"></a><tt class="py-lineno">584</tt> <tt class="py-line"> <tt class="py-op">%</tt> <tt class="py-name">XML_START</tt><tt class="py-op">)</tt> </tt>
<a name="L585"></a><tt class="py-lineno">585</tt> <tt class="py-line"> </tt>
<a name="L586"></a><tt class="py-lineno">586</tt> <tt class="py-line"> <tt class="py-name">expat_parser</tt> <tt class="py-op">=</tt> <tt class="py-name">expat</tt><tt class="py-op">.</tt><tt class="py-name">ParserCreate</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L587"></a><tt class="py-lineno">587</tt> <tt class="py-line"> <tt class="py-name">blast_parser</tt> <tt class="py-op">=</tt> <tt id="link-114" class="py-name" targets="Class Bio.Blast.NCBIStandalone.BlastParser=Bio.Blast.NCBIStandalone.BlastParser-class.html,Class Bio.Blast.NCBIWWW.BlastParser=Bio.Blast.NCBIWWW.BlastParser-class.html,Class Bio.Blast.NCBIXML.BlastParser=Bio.Blast.NCBIXML.BlastParser-class.html"><a title="Bio.Blast.NCBIStandalone.BlastParser
Bio.Blast.NCBIWWW.BlastParser
Bio.Blast.NCBIXML.BlastParser" class="py-name" href="#" onclick="return doclink('link-114', 'BlastParser', 'link-114');">BlastParser</a></tt><tt class="py-op">(</tt><tt class="py-name">debug</tt><tt class="py-op">)</tt> </tt>
<a name="L588"></a><tt class="py-lineno">588</tt> <tt class="py-line"> <tt class="py-name">expat_parser</tt><tt class="py-op">.</tt><tt class="py-name">StartElementHandler</tt> <tt class="py-op">=</tt> <tt class="py-name">blast_parser</tt><tt class="py-op">.</tt><tt id="link-115" class="py-name" targets="Method Bio.Blast.NCBIXML._XMLparser.startElement()=Bio.Blast.NCBIXML._XMLparser-class.html#startElement,Method Bio.EUtils.POM.ObjectParserHandler.startElement()=Bio.EUtils.POM.ObjectParserHandler-class.html#startElement,Method Bio.Entrez.Parser.DataHandler.startElement()=Bio.Entrez.Parser.DataHandler-class.html#startElement,Method Bio.Mindy.XPath.GrabXPathNodes.startElement()=Bio.Mindy.XPath.GrabXPathNodes-class.html#startElement,Method Bio.ParserSupport.EventGenerator.startElement()=Bio.ParserSupport.EventGenerator-class.html#startElement,Method Bio.StdHandler.ConvertHandler.startElement()=Bio.StdHandler.ConvertHandler-class.html#startElement,Method Martel.Dispatch.Dispatcher.startElement()=Martel.Dispatch.Dispatcher-class.html#startElement,Method Martel.Iterator.StoreEvents.startElement()=Martel.Iterator.StoreEvents-class.html#startElement,Method Martel.LAX.LAX.startElement()=Martel.LAX.LAX-class.html#startElement,Method Martel.test.support.Dump.startElement()=Martel.test.support.Dump-class.html#startElement,Method Martel.test.test_Parser.CountRecords.startElement()=Martel.test.test_Parser.CountRecords-class.html#startElement,Method Martel.test.test_attrs.GrabElements.startElement()=Martel.test.test_attrs.GrabElements-class.html#startElement,Method Martel.test.test_delimiter.CatchFields.startElement()=Martel.test.test_delimiter.CatchFields-class.html#startElement,Method Martel.test.test_macros.Capture.startElement()=Martel.test.test_macros.Capture-class.html#startElement"><a title="Bio.Blast.NCBIXML._XMLparser.startElement
Bio.EUtils.POM.ObjectParserHandler.startElement
Bio.Entrez.Parser.DataHandler.startElement
Bio.Mindy.XPath.GrabXPathNodes.startElement
Bio.ParserSupport.EventGenerator.startElement
Bio.StdHandler.ConvertHandler.startElement
Martel.Dispatch.Dispatcher.startElement
Martel.Iterator.StoreEvents.startElement
Martel.LAX.LAX.startElement
Martel.test.support.Dump.startElement
Martel.test.test_Parser.CountRecords.startElement
Martel.test.test_attrs.GrabElements.startElement
Martel.test.test_delimiter.CatchFields.startElement
Martel.test.test_macros.Capture.startElement" class="py-name" href="#" onclick="return doclink('link-115', 'startElement', 'link-115');">startElement</a></tt> </tt>
<a name="L589"></a><tt class="py-lineno">589</tt> <tt class="py-line"> <tt class="py-name">expat_parser</tt><tt class="py-op">.</tt><tt class="py-name">EndElementHandler</tt> <tt class="py-op">=</tt> <tt class="py-name">blast_parser</tt><tt class="py-op">.</tt><tt id="link-116" class="py-name" targets="Method Bio.Blast.NCBIXML._XMLparser.endElement()=Bio.Blast.NCBIXML._XMLparser-class.html#endElement,Method Bio.EUtils.POM.ObjectParserHandler.endElement()=Bio.EUtils.POM.ObjectParserHandler-class.html#endElement,Method Bio.Entrez.Parser.DataHandler.endElement()=Bio.Entrez.Parser.DataHandler-class.html#endElement,Method Bio.Mindy.XPath.GrabXPathNodes.endElement()=Bio.Mindy.XPath.GrabXPathNodes-class.html#endElement,Method Bio.ParserSupport.EventGenerator.endElement()=Bio.ParserSupport.EventGenerator-class.html#endElement,Method Bio.StdHandler.ConvertHandler.endElement()=Bio.StdHandler.ConvertHandler-class.html#endElement,Method Bio.StdHandler.RecognizeHandler.endElement()=Bio.StdHandler.RecognizeHandler-class.html#endElement,Method Martel.Dispatch.Dispatcher.endElement()=Martel.Dispatch.Dispatcher-class.html#endElement,Method Martel.Iterator.StoreEvents.endElement()=Martel.Iterator.StoreEvents-class.html#endElement,Method Martel.LAX.LAX.endElement()=Martel.LAX.LAX-class.html#endElement,Method Martel.test.support.Dump.endElement()=Martel.test.support.Dump-class.html#endElement,Method Martel.test.test_delimiter.CatchFields.endElement()=Martel.test.test_delimiter.CatchFields-class.html#endElement,Method Martel.test.test_macros.Capture.endElement()=Martel.test.test_macros.Capture-class.html#endElement"><a title="Bio.Blast.NCBIXML._XMLparser.endElement
Bio.EUtils.POM.ObjectParserHandler.endElement
Bio.Entrez.Parser.DataHandler.endElement
Bio.Mindy.XPath.GrabXPathNodes.endElement
Bio.ParserSupport.EventGenerator.endElement
Bio.StdHandler.ConvertHandler.endElement
Bio.StdHandler.RecognizeHandler.endElement
Martel.Dispatch.Dispatcher.endElement
Martel.Iterator.StoreEvents.endElement
Martel.LAX.LAX.endElement
Martel.test.support.Dump.endElement
Martel.test.test_delimiter.CatchFields.endElement
Martel.test.test_macros.Capture.endElement" class="py-name" href="#" onclick="return doclink('link-116', 'endElement', 'link-116');">endElement</a></tt> </tt>
<a name="L590"></a><tt class="py-lineno">590</tt> <tt class="py-line"> <tt class="py-name">expat_parser</tt><tt class="py-op">.</tt><tt class="py-name">CharacterDataHandler</tt> <tt class="py-op">=</tt> <tt class="py-name">blast_parser</tt><tt class="py-op">.</tt><tt id="link-117" class="py-name" targets="Method Bio.Blast.NCBIXML._XMLparser.characters()=Bio.Blast.NCBIXML._XMLparser-class.html#characters,Method Bio.EUtils.POM.ObjectParserHandler.characters()=Bio.EUtils.POM.ObjectParserHandler-class.html#characters,Method Bio.Entrez.Parser.DataHandler.characters()=Bio.Entrez.Parser.DataHandler-class.html#characters,Method Bio.Mindy.XPath.GrabXPathNodes.characters()=Bio.Mindy.XPath.GrabXPathNodes-class.html#characters,Method Bio.ParserSupport.EventGenerator.characters()=Bio.ParserSupport.EventGenerator-class.html#characters,Method Martel.Dispatch.Dispatcher.characters()=Martel.Dispatch.Dispatcher-class.html#characters,Method Martel.LAX.LAX.characters()=Martel.LAX.LAX-class.html#characters,Method Martel.test.support.Dump.characters()=Martel.test.support.Dump-class.html#characters,Method Martel.test.test_delimiter.CatchFields.characters()=Martel.test.test_delimiter.CatchFields-class.html#characters"><a title="Bio.Blast.NCBIXML._XMLparser.characters
Bio.EUtils.POM.ObjectParserHandler.characters
Bio.Entrez.Parser.DataHandler.characters
Bio.Mindy.XPath.GrabXPathNodes.characters
Bio.ParserSupport.EventGenerator.characters
Martel.Dispatch.Dispatcher.characters
Martel.LAX.LAX.characters
Martel.test.support.Dump.characters
Martel.test.test_delimiter.CatchFields.characters" class="py-name" href="#" onclick="return doclink('link-117', 'characters', 'link-117');">characters</a></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 class="py-name">expat_parser</tt><tt class="py-op">.</tt><tt class="py-name">Parse</tt><tt class="py-op">(</tt><tt id="link-118" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-118', 'text', 'link-108');">text</a></tt><tt class="py-op">,</tt> <tt id="link-119" class="py-name" targets="Variable Bio.EUtils.POM.False=Bio.EUtils.POM-module.html#False"><a title="Bio.EUtils.POM.False" class="py-name" href="#" onclick="return doclink('link-119', 'False', 'link-119');">False</a></tt><tt class="py-op">)</tt> </tt>
<a name="L593"></a><tt class="py-lineno">593</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-name">blast_parser</tt><tt class="py-op">.</tt><tt class="py-name">_records</tt><tt class="py-op">:</tt> </tt>
<a name="L594"></a><tt class="py-lineno">594</tt> <tt class="py-line"> <tt id="link-120" class="py-name" targets="Variable Bio.Emboss.primer3_format.record=Bio.Emboss.primer3_format-module.html#record,Variable Bio.Emboss.primersearch_format.record=Bio.Emboss.primersearch_format-module.html#record,Method Bio.GFF.Feature.record()=Bio.GFF.Feature-class.html#record,Variable Bio.LocusLink.web_parse.record=Bio.LocusLink.web_parse-module.html#record,Variable Bio.Ndb.record=Bio.Ndb-module.html#record,Function Bio.Std.record()=Bio.Std-module.html#record,Variable Bio.expressions.blocks.record=Bio.expressions.blocks-module.html#record,Variable Bio.expressions.embl.embl65.record=Bio.expressions.embl.embl65-module.html#record,Variable Bio.expressions.fasta.record=Bio.expressions.fasta-module.html#record,Variable Bio.expressions.genbank.record=Bio.expressions.genbank-module.html#record,Variable Bio.expressions.hmmpfam.record=Bio.expressions.hmmpfam-module.html#record,Variable Bio.expressions.swissprot.ipi.record=Bio.expressions.swissprot.ipi-module.html#record,Variable Bio.expressions.swissprot.speclist.record=Bio.expressions.swissprot.speclist-module.html#record,Variable Bio.expressions.swissprot.sprot38.record=Bio.expressions.swissprot.sprot38-module.html#record,Variable Bio.expressions.swissprot.sprot40.record=Bio.expressions.swissprot.sprot40-module.html#record,Variable Martel.test.test_swissprot38.record=Martel.test.test_swissprot38-module.html#record,Variable Martel.test.testformats.swissprot38.record=Martel.test.testformats.swissprot38-module.html#record"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-120', 'record', 'link-120');">record</a></tt> <tt class="py-op">=</tt> <tt class="py-name">blast_parser</tt><tt class="py-op">.</tt><tt class="py-name">_records</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L595"></a><tt class="py-lineno">595</tt> <tt class="py-line"> <tt class="py-name">blast_parser</tt><tt class="py-op">.</tt><tt class="py-name">_records</tt> <tt class="py-op">=</tt> <tt class="py-name">blast_parser</tt><tt class="py-op">.</tt><tt class="py-name">_records</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="L596"></a><tt class="py-lineno">596</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt id="link-121" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-121', 'record', 'link-120');">record</a></tt> </tt>
<a name="L597"></a><tt class="py-lineno">597</tt> <tt class="py-line"> </tt>
<a name="L598"></a><tt class="py-lineno">598</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt id="link-122" class="py-name" targets="Variable Bio.EUtils.POM.True=Bio.EUtils.POM-module.html#True"><a title="Bio.EUtils.POM.True" class="py-name" href="#" onclick="return doclink('link-122', 'True', 'link-122');">True</a></tt> <tt class="py-op">:</tt> </tt>
<a name="L599"></a><tt class="py-lineno">599</tt> <tt class="py-line"> <tt class="py-comment">#Read in another block of the file...</tt> </tt>
<a name="L600"></a><tt class="py-lineno">600</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-123" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-123', 'text', 'link-108');">text</a></tt><tt class="py-op">,</tt> <tt class="py-name">pending</tt> <tt class="py-op">=</tt> <tt class="py-name">pending</tt> <tt class="py-op">+</tt> <tt id="link-124" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-124', 'handle', 'link-109');">handle</a></tt><tt class="py-op">.</tt><tt id="link-125" 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-125', 'read', 'link-110');">read</a></tt><tt class="py-op">(</tt><tt class="py-name">BLOCK</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">""</tt> </tt>
<a name="L601"></a><tt class="py-lineno">601</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-126" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-126', 'text', 'link-108');">text</a></tt><tt class="py-op">:</tt> </tt>
<a name="L602"></a><tt class="py-lineno">602</tt> <tt class="py-line"> <tt class="py-comment">#End of the file!</tt> </tt>
<a name="L603"></a><tt class="py-lineno">603</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">expat_parser</tt><tt class="py-op">.</tt><tt class="py-name">Parse</tt><tt class="py-op">(</tt><tt class="py-string">""</tt><tt class="py-op">,</tt> <tt id="link-127" class="py-name"><a title="Bio.EUtils.POM.True" class="py-name" href="#" onclick="return doclink('link-127', 'True', 'link-122');">True</a></tt><tt class="py-op">)</tt> <tt class="py-comment"># End of XML record</tt> </tt>
<a name="L604"></a><tt class="py-lineno">604</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L605"></a><tt class="py-lineno">605</tt> <tt class="py-line"> </tt>
<a name="L606"></a><tt class="py-lineno">606</tt> <tt class="py-line"> <tt class="py-comment">#Now read a little bit more so we can check for the</tt> </tt>
<a name="L607"></a><tt class="py-lineno">607</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#start of another XML file...</tt> </tt>
<a name="L608"></a><tt class="py-lineno">608</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">pending</tt> <tt class="py-op">=</tt> <tt id="link-128" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-128', 'handle', 'link-109');">handle</a></tt><tt class="py-op">.</tt><tt id="link-129" 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-129', 'read', 'link-110');">read</a></tt><tt class="py-op">(</tt><tt class="py-name">MARGIN</tt><tt class="py-op">)</tt> </tt>
<a name="L609"></a><tt class="py-lineno">609</tt> <tt class="py-line"> </tt>
<a name="L610"></a><tt class="py-lineno">610</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt id="link-130" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-130', 'text', 'link-108');">text</a></tt><tt class="py-op">+</tt><tt class="py-name">pending</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-131" 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-131', 'find', 'link-131');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">"\n"</tt> <tt class="py-op">+</tt> <tt class="py-name">XML_START</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt> <tt class="py-op">:</tt> </tt>
<a name="L611"></a><tt class="py-lineno">611</tt> <tt class="py-line"> <tt class="py-comment"># Good - still dealing with the same XML file</tt> </tt>
<a name="L612"></a><tt class="py-lineno">612</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">expat_parser</tt><tt class="py-op">.</tt><tt class="py-name">Parse</tt><tt class="py-op">(</tt><tt id="link-132" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-132', 'text', 'link-108');">text</a></tt><tt class="py-op">,</tt> <tt id="link-133" class="py-name"><a title="Bio.EUtils.POM.False" class="py-name" href="#" onclick="return doclink('link-133', 'False', 'link-119');">False</a></tt><tt class="py-op">)</tt> </tt>
<a name="L613"></a><tt class="py-lineno">613</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-name">blast_parser</tt><tt class="py-op">.</tt><tt class="py-name">_records</tt><tt class="py-op">:</tt> </tt>
<a name="L614"></a><tt class="py-lineno">614</tt> <tt class="py-line"> <tt id="link-134" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-134', 'record', 'link-120');">record</a></tt> <tt class="py-op">=</tt> <tt class="py-name">blast_parser</tt><tt class="py-op">.</tt><tt class="py-name">_records</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L615"></a><tt class="py-lineno">615</tt> <tt class="py-line"> <tt class="py-name">blast_parser</tt><tt class="py-op">.</tt><tt class="py-name">_records</tt> <tt class="py-op">=</tt> <tt class="py-name">blast_parser</tt><tt class="py-op">.</tt><tt class="py-name">_records</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="L616"></a><tt class="py-lineno">616</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt id="link-135" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-135', 'record', 'link-120');">record</a></tt> </tt>
<a name="L617"></a><tt class="py-lineno">617</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L618"></a><tt class="py-lineno">618</tt> <tt class="py-line"> <tt class="py-comment"># This is output from pre 2.2.14 BLAST,</tt> </tt>
<a name="L619"></a><tt class="py-lineno">619</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># one XML file for each query!</tt> </tt>
<a name="L620"></a><tt class="py-lineno">620</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L621"></a><tt class="py-lineno">621</tt> <tt class="py-line"> <tt class="py-comment"># Finish the old file:</tt> </tt>
<a name="L622"></a><tt class="py-lineno">622</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-136" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-136', 'text', 'link-108');">text</a></tt><tt class="py-op">,</tt> <tt class="py-name">pending</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-137" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-137', 'text', 'link-108');">text</a></tt><tt class="py-op">+</tt><tt class="py-name">pending</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-138" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-138', 'split', 'link-51');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">"\n"</tt> <tt class="py-op">+</tt> <tt class="py-name">XML_START</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L623"></a><tt class="py-lineno">623</tt> <tt class="py-line"> <tt class="py-name">pending</tt> <tt class="py-op">=</tt> <tt class="py-name">XML_START</tt> <tt class="py-op">+</tt> <tt class="py-name">pending</tt> </tt>
<a name="L624"></a><tt class="py-lineno">624</tt> <tt class="py-line"> </tt>
<a name="L625"></a><tt class="py-lineno">625</tt> <tt class="py-line"> <tt class="py-name">expat_parser</tt><tt class="py-op">.</tt><tt class="py-name">Parse</tt><tt class="py-op">(</tt><tt id="link-139" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-139', 'text', 'link-108');">text</a></tt><tt class="py-op">,</tt> <tt id="link-140" class="py-name"><a title="Bio.EUtils.POM.True" class="py-name" href="#" onclick="return doclink('link-140', 'True', 'link-122');">True</a></tt><tt class="py-op">)</tt> <tt class="py-comment"># End of XML record</tt> </tt>
<a name="L626"></a><tt class="py-lineno">626</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-name">blast_parser</tt><tt class="py-op">.</tt><tt class="py-name">_records</tt><tt class="py-op">:</tt> </tt>
<a name="L627"></a><tt class="py-lineno">627</tt> <tt class="py-line"> <tt id="link-141" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-141', 'record', 'link-120');">record</a></tt> <tt class="py-op">=</tt> <tt class="py-name">blast_parser</tt><tt class="py-op">.</tt><tt class="py-name">_records</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L628"></a><tt class="py-lineno">628</tt> <tt class="py-line"> <tt class="py-name">blast_parser</tt><tt class="py-op">.</tt><tt class="py-name">_records</tt> <tt class="py-op">=</tt> <tt class="py-name">blast_parser</tt><tt class="py-op">.</tt><tt class="py-name">_records</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="L629"></a><tt class="py-lineno">629</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt id="link-142" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-142', 'record', 'link-120');">record</a></tt> </tt>
<a name="L630"></a><tt class="py-lineno">630</tt> <tt class="py-line"> </tt>
<a name="L631"></a><tt class="py-lineno">631</tt> <tt class="py-line"> <tt class="py-comment">#Now we are going to re-loop, reset the</tt> </tt>
<a name="L632"></a><tt class="py-lineno">632</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#parsers and start reading the next XML file</tt> </tt>
<a name="L633"></a><tt class="py-lineno">633</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-143" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-143', 'text', 'link-108');">text</a></tt><tt class="py-op">,</tt> <tt class="py-name">pending</tt> <tt class="py-op">=</tt> <tt class="py-name">pending</tt><tt class="py-op">,</tt> <tt class="py-string">""</tt> </tt>
<a name="L634"></a><tt class="py-lineno">634</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L635"></a><tt class="py-lineno">635</tt> <tt class="py-line"> </tt>
<a name="L636"></a><tt class="py-lineno">636</tt> <tt class="py-line"> <tt class="py-comment">#At this point we have finished the first XML record.</tt> </tt>
<a name="L637"></a><tt class="py-lineno">637</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#If the file is from an old version of blast, it may</tt> </tt>
<a name="L638"></a><tt class="py-lineno">638</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#contain more XML records (check if text=="").</tt> </tt>
<a name="L639"></a><tt class="py-lineno">639</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">assert</tt> <tt class="py-name">pending</tt><tt class="py-op">==</tt><tt class="py-string">""</tt> </tt>
<a name="L640"></a><tt class="py-lineno">640</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">blast_parser</tt><tt class="py-op">.</tt><tt class="py-name">_records</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt> </tt>
<a name="L641"></a><tt class="py-lineno">641</tt> <tt class="py-line"> </tt>
<a name="L642"></a><tt class="py-lineno">642</tt> <tt class="py-line"> <tt class="py-comment">#We should have finished the file!</tt> </tt>
<a name="L643"></a><tt class="py-lineno">643</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">assert</tt> <tt id="link-144" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-144', 'text', 'link-108');">text</a></tt><tt class="py-op">==</tt><tt class="py-string">""</tt> </tt>
<a name="L644"></a><tt class="py-lineno">644</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">pending</tt><tt class="py-op">==</tt><tt class="py-string">""</tt> </tt>
<a name="L645"></a><tt class="py-lineno">645</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">blast_parser</tt><tt class="py-op">.</tt><tt class="py-name">_records</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt> </tt>
</div><a name="L646"></a><tt class="py-lineno">646</tt> <tt class="py-line"> </tt>
<a name="L647"></a><tt class="py-lineno">647</tt> <tt class="py-line"><tt class="py-keyword">if</tt> <tt class="py-name">__name__</tt> <tt class="py-op">==</tt> <tt class="py-string">'__main__'</tt><tt class="py-op">:</tt> </tt>
<a name="L648"></a><tt class="py-lineno">648</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">sys</tt> </tt>
<a name="L649"></a><tt class="py-lineno">649</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">os</tt> </tt>
<a name="L650"></a><tt class="py-lineno">650</tt> <tt class="py-line"> <tt id="link-145" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-145', 'handle', 'link-109');">handle</a></tt> <tt class="py-op">=</tt> <tt id="link-146" class="py-name" targets="Function Bio.Mindy.FlatDB.open()=Bio.Mindy.FlatDB-module.html#open,Function Bio.Mindy.open()=Bio.Mindy-module.html#open"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-146', 'open', 'link-146');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</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="L651"></a><tt class="py-lineno">651</tt> <tt class="py-line"> <tt class="py-name">r_list</tt> <tt class="py-op">=</tt> <tt id="link-147" class="py-name"><a title="Bio.Affy.CelFile.CelParser.parse
Bio.AlignAce.Parser.AlignAceParser.parse
Bio.AlignAce.Parser.CompareAceParser.parse
Bio.AlignIO.parse
Bio.Blast.NCBIStandalone.BlastErrorParser.parse
Bio.Blast.NCBIStandalone.BlastParser.parse
Bio.Blast.NCBIStandalone.PSIBlastParser.parse
Bio.Blast.NCBIWWW.BlastParser.parse
Bio.Blast.NCBIXML.BlastParser.parse
Bio.Blast.NCBIXML.parse
Bio.CDD.RecordParser.parse
Bio.Compass.RecordParser.parse
Bio.Decode.parse
Bio.ECell.RecordParser.parse
Bio.EUtils.POM.POMDocument.parse
Bio.EUtils.parse
Bio.Emboss.Primer.Primer3Parser.parse
Bio.Emboss.Primer.PrimerSearchParser.parse
Bio.Enzyme.RecordParser.parse
Bio.Fasta.RecordParser.parse
Bio.Fasta.SequenceParser.parse
Bio.GenBank.FeatureParser.parse
Bio.GenBank.LocationParser.parse
Bio.GenBank.RecordParser.parse
Bio.GenBank.Scanner.InsdcScanner.parse
Bio.Geo.parse
Bio.Gobase.RecordParser.parse
Bio.IntelliGenetics.RecordParser.parse
Bio.InterPro.InterProParser.parse
Bio.KEGG.Compound.parse
Bio.KEGG.Enzyme.parse
Bio.KEGG.Map.parse
Bio.LocusLink.RecordParser.parse
Bio.LocusLink.web_parse.LocusLinkParser.parse
Bio.MEME.Parser.MASTParser.parse
Bio.MEME.Parser.MEMEParser.parse
Bio.Medline.RecordParser.parse
Bio.MetaTool.RecordParser.parse
Bio.NBRF.RecordParser.parse
Bio.Ndb.NdbParser.parse
Bio.ParserSupport.AbstractParser.parse
Bio.Parsers.spark.GenericParser.parse
Bio.PopGen.FDist.RecordParser.parse
Bio.PopGen.GenePop.RecordParser.parse
Bio.PopGen.GenePop.parse
Bio.Prosite.Prodoc.RecordParser.parse
Bio.Prosite.Prodoc.parse
Bio.Prosite.RecordParser.parse
Bio.Prosite.parse
Bio.Rebase.RecordParser.parse
Bio.SCOP.Cla.Parser.parse
Bio.SCOP.Cla.parse
Bio.SCOP.Des.Parser.parse
Bio.SCOP.Des.parse
Bio.SCOP.Dom.Parser.parse
Bio.SCOP.Dom.parse
Bio.SCOP.Hie.Parser.parse
Bio.SCOP.Hie.parse
Bio.SCOP.Raf.Parser.parse
Bio.SCOP.Raf.parse
Bio.Saf.RecordParser.parse
Bio.SeqIO.parse
Bio.Sequencing.Ace.ACEParser.parse
Bio.Sequencing.Ace.RecordParser.parse
Bio.Sequencing.Phd.RecordParser.parse
Bio.SwissProt.KeyWList.ListParser.parse
Bio.SwissProt.KeyWList.parse
Bio.SwissProt.SProt.RecordParser.parse
Bio.SwissProt.SProt.SequenceParser.parse
Bio.SwissProt.parse
Bio.UniGene.RecordParser.parse
Bio.Wise.psw.parse
Martel.Parser.HeaderFooterParser.parse
Martel.Parser.Parser.parse
Martel.Parser.RecordParser.parse
Martel.msre_parse.parse" class="py-name" href="#" onclick="return doclink('link-147', 'parse', 'link-23');">parse</a></tt><tt class="py-op">(</tt><tt id="link-148" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-148', 'handle', 'link-109');">handle</a></tt><tt class="py-op">)</tt> </tt>
<a name="L652"></a><tt class="py-lineno">652</tt> <tt class="py-line"> </tt>
<a name="L653"></a><tt class="py-lineno">653</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">r</tt> <tt class="py-keyword">in</tt> <tt class="py-name">r_list</tt> <tt class="py-op">:</tt> </tt>
<a name="L654"></a><tt class="py-lineno">654</tt> <tt class="py-line"> <tt class="py-comment"># Small test</tt> </tt>
<a name="L655"></a><tt class="py-lineno">655</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">print</tt> <tt class="py-string">'Blast of'</tt><tt class="py-op">,</tt> <tt class="py-name">r</tt><tt class="py-op">.</tt><tt id="link-149" 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-149', 'query', 'link-34');">query</a></tt> </tt>
<a name="L656"></a><tt class="py-lineno">656</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'Found %s alignments with a total of %s HSPs'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">r</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="L657"></a><tt class="py-lineno">657</tt> <tt class="py-line"> <tt class="py-name">reduce</tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt class="py-name">a</tt><tt class="py-op">,</tt><tt class="py-name">b</tt><tt class="py-op">:</tt> <tt class="py-name">a</tt><tt class="py-op">+</tt><tt class="py-name">b</tt><tt class="py-op">,</tt> </tt>
<a name="L658"></a><tt class="py-lineno">658</tt> <tt class="py-line"> <tt class="py-op">[</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">a</tt><tt class="py-op">.</tt><tt class="py-name">hsps</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">a</tt> <tt class="py-keyword">in</tt> <tt class="py-name">r</tt><tt class="py-op">.</tt><tt class="py-name">alignments</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L659"></a><tt class="py-lineno">659</tt> <tt class="py-line"> </tt>
<a name="L660"></a><tt class="py-lineno">660</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">al</tt> <tt class="py-keyword">in</tt> <tt class="py-name">r</tt><tt class="py-op">.</tt><tt class="py-name">alignments</tt><tt class="py-op">:</tt> </tt>
<a name="L661"></a><tt class="py-lineno">661</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">al</tt><tt class="py-op">.</tt><tt id="link-150" class="py-name"><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-150', 'title', 'link-74');">title</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">50</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">al</tt><tt class="py-op">.</tt><tt id="link-151" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-151', 'length', 'link-80');">length</a></tt><tt class="py-op">,</tt> <tt class="py-string">'bp'</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">al</tt><tt class="py-op">.</tt><tt class="py-name">hsps</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">'HSPs'</tt> </tt>
<a name="L662"></a><tt class="py-lineno">662</tt> <tt class="py-line"> </tt>
<a name="L663"></a><tt class="py-lineno">663</tt> <tt class="py-line"> <tt class="py-comment"># Cookbook example</tt> </tt>
<a name="L664"></a><tt class="py-lineno">664</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">E_VALUE_THRESH</tt> <tt class="py-op">=</tt> <tt class="py-number">0.04</tt> </tt>
<a name="L665"></a><tt class="py-lineno">665</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-152" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.alignment=Bio.expressions.blast.ncbiblast-module.html#alignment"><a title="Bio.expressions.blast.ncbiblast.alignment" class="py-name" href="#" onclick="return doclink('link-152', 'alignment', 'link-152');">alignment</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">r</tt><tt class="py-op">.</tt><tt class="py-name">alignments</tt><tt class="py-op">:</tt> </tt>
<a name="L666"></a><tt class="py-lineno">666</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-153" class="py-name" targets="Function Bio.Std.hsp()=Bio.Std-module.html#hsp,Variable Bio.expressions.blast.ncbiblast.hsp=Bio.expressions.blast.ncbiblast-module.html#hsp"><a title="Bio.Std.hsp
Bio.expressions.blast.ncbiblast.hsp" class="py-name" href="#" onclick="return doclink('link-153', 'hsp', 'link-153');">hsp</a></tt> <tt class="py-keyword">in</tt> <tt id="link-154" class="py-name"><a title="Bio.expressions.blast.ncbiblast.alignment" class="py-name" href="#" onclick="return doclink('link-154', 'alignment', 'link-152');">alignment</a></tt><tt class="py-op">.</tt><tt class="py-name">hsps</tt><tt class="py-op">:</tt> </tt>
<a name="L667"></a><tt class="py-lineno">667</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-155" class="py-name"><a title="Bio.Std.hsp
Bio.expressions.blast.ncbiblast.hsp" class="py-name" href="#" onclick="return doclink('link-155', 'hsp', 'link-153');">hsp</a></tt><tt class="py-op">.</tt><tt id="link-156" class="py-name"><a title="Bio.expressions.blast.ncbiblast.expect" class="py-name" href="#" onclick="return doclink('link-156', 'expect', 'link-48');">expect</a></tt> <tt class="py-op"><</tt> <tt class="py-name">E_VALUE_THRESH</tt><tt class="py-op">:</tt> </tt>
<a name="L668"></a><tt class="py-lineno">668</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'*****'</tt> </tt>
<a name="L669"></a><tt class="py-lineno">669</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'sequence'</tt><tt class="py-op">,</tt> <tt id="link-157" class="py-name"><a title="Bio.expressions.blast.ncbiblast.alignment" class="py-name" href="#" onclick="return doclink('link-157', 'alignment', 'link-152');">alignment</a></tt><tt class="py-op">.</tt><tt id="link-158" class="py-name"><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-158', 'title', 'link-74');">title</a></tt> </tt>
<a name="L670"></a><tt class="py-lineno">670</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'length'</tt><tt class="py-op">,</tt> <tt id="link-159" class="py-name"><a title="Bio.expressions.blast.ncbiblast.alignment" class="py-name" href="#" onclick="return doclink('link-159', 'alignment', 'link-152');">alignment</a></tt><tt class="py-op">.</tt><tt id="link-160" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-160', 'length', 'link-80');">length</a></tt> </tt>
<a name="L671"></a><tt class="py-lineno">671</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'e value'</tt><tt class="py-op">,</tt> <tt id="link-161" class="py-name"><a title="Bio.Std.hsp
Bio.expressions.blast.ncbiblast.hsp" class="py-name" href="#" onclick="return doclink('link-161', 'hsp', 'link-153');">hsp</a></tt><tt class="py-op">.</tt><tt id="link-162" class="py-name"><a title="Bio.expressions.blast.ncbiblast.expect" class="py-name" href="#" onclick="return doclink('link-162', 'expect', 'link-48');">expect</a></tt> </tt>
<a name="L672"></a><tt class="py-lineno">672</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt id="link-163" class="py-name"><a title="Bio.Std.hsp
Bio.expressions.blast.ncbiblast.hsp" class="py-name" href="#" onclick="return doclink('link-163', 'hsp', 'link-153');">hsp</a></tt><tt class="py-op">.</tt><tt id="link-164" 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-164', 'query', 'link-34');">query</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">75</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-string">'...'</tt> </tt>
<a name="L673"></a><tt class="py-lineno">673</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt id="link-165" class="py-name"><a title="Bio.Std.hsp
Bio.expressions.blast.ncbiblast.hsp" class="py-name" href="#" onclick="return doclink('link-165', 'hsp', 'link-153');">hsp</a></tt><tt class="py-op">.</tt><tt id="link-166" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-166', 'match', 'link-98');">match</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">75</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-string">'...'</tt> </tt>
<a name="L674"></a><tt class="py-lineno">674</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt id="link-167" class="py-name"><a title="Bio.Std.hsp
Bio.expressions.blast.ncbiblast.hsp" class="py-name" href="#" onclick="return doclink('link-167', 'hsp', 'link-153');">hsp</a></tt><tt class="py-op">.</tt><tt id="link-168" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.sbjct" class="py-name" href="#" onclick="return doclink('link-168', 'sbjct', 'link-97');">sbjct</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">75</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-string">'...'</tt> </tt>
<a name="L675"></a><tt class="py-lineno">675</tt> <tt class="py-line"> </tt><script type="text/javascript">
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