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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.Emboss-module.html">Package Emboss</a> ::
Module Primer
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<h1 class="epydoc">Source Code for <a href="Bio.Emboss.Primer-module.html">Module Bio.Emboss.Primer</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-docstring">"""Code to interact with various Primer-related programs from EMBOSS.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"># standard library</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">import</tt> <tt class="py-name">string</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</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-keyword">import</tt> <tt class="py-name">handler</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-comment"># Martel</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">import</tt> <tt id="link-0" class="py-name" targets="Package Martel=Martel-module.html"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-0', 'Martel', 'link-0');">Martel</a></tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-1" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-1', 'Martel', 'link-0');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name" targets="Module Martel.RecordReader=Martel.RecordReader-module.html,Class Martel.RecordReader.RecordReader=Martel.RecordReader.RecordReader-class.html"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-2', 'RecordReader', 'link-2');">RecordReader</a></tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-comment"># biopython stuff</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">from</tt> <tt id="link-3" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-3', 'Bio', 'link-3');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Module Bio.ParserSupport=Bio.ParserSupport-module.html"><a title="Bio.ParserSupport" class="py-name" href="#" onclick="return doclink('link-4', 'ParserSupport', 'link-4');">ParserSupport</a></tt> <tt class="py-keyword">import</tt> <tt id="link-5" class="py-name" targets="Class Bio.ParserSupport.AbstractConsumer=Bio.ParserSupport.AbstractConsumer-class.html"><a title="Bio.ParserSupport.AbstractConsumer" class="py-name" href="#" onclick="return doclink('link-5', 'AbstractConsumer', 'link-5');">AbstractConsumer</a></tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-6" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-6', 'Bio', 'link-3');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-7" class="py-name"><a title="Bio.ParserSupport" class="py-name" href="#" onclick="return doclink('link-7', 'ParserSupport', 'link-4');">ParserSupport</a></tt> <tt class="py-keyword">import</tt> <tt id="link-8" class="py-name" targets="Class Bio.ParserSupport.EventGenerator=Bio.ParserSupport.EventGenerator-class.html"><a title="Bio.ParserSupport.EventGenerator" class="py-name" href="#" onclick="return doclink('link-8', 'EventGenerator', 'link-8');">EventGenerator</a></tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-9" class="py-name" targets="Module Bio.Emboss.primersearch_format=Bio.Emboss.primersearch_format-module.html"><a title="Bio.Emboss.primersearch_format" class="py-name" href="#" onclick="return doclink('link-9', 'primersearch_format', 'link-9');">primersearch_format</a></tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-10" class="py-name" targets="Module Bio.Emboss.primer3_format=Bio.Emboss.primer3_format-module.html"><a title="Bio.Emboss.primer3_format" class="py-name" href="#" onclick="return doclink('link-10', 'primer3_format', 'link-10');">primer3_format</a></tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-comment"># --- primersearch</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="PrimerSearchInputRecord"></a><div id="PrimerSearchInputRecord-def"><a name="L20"></a><tt class="py-lineno"> 20</tt> <a class="py-toggle" href="#" id="PrimerSearchInputRecord-toggle" onclick="return toggle('PrimerSearchInputRecord');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Emboss.Primer.PrimerSearchInputRecord-class.html">PrimerSearchInputRecord</a><tt class="py-op">:</tt> </tt>
</div><div id="PrimerSearchInputRecord-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="PrimerSearchInputRecord-expanded"><a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"> <tt class="py-docstring">"""Represent the input file into the primersearch program.</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring"> This makes it easy to add primer information and write it out to the</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring"> simple primer file format.</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="PrimerSearchInputRecord.__init__"></a><div id="PrimerSearchInputRecord.__init__-def"><a name="L26"></a><tt class="py-lineno"> 26</tt> <a class="py-toggle" href="#" id="PrimerSearchInputRecord.__init__-toggle" onclick="return toggle('PrimerSearchInputRecord.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer.PrimerSearchInputRecord-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PrimerSearchInputRecord.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PrimerSearchInputRecord.__init__-expanded"><a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">primer_info</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
</div><a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"> </tt>
<a name="PrimerSearchInputRecord.__str__"></a><div id="PrimerSearchInputRecord.__str__-def"><a name="L29"></a><tt class="py-lineno"> 29</tt> <a class="py-toggle" href="#" id="PrimerSearchInputRecord.__str__-toggle" onclick="return toggle('PrimerSearchInputRecord.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer.PrimerSearchInputRecord-class.html#__str__">__str__</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="PrimerSearchInputRecord.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PrimerSearchInputRecord.__str__-expanded"><a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-11" 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-11', 'name', 'link-11');">name</a></tt><tt class="py-op">,</tt> <tt class="py-name">primer1</tt><tt class="py-op">,</tt> <tt class="py-name">primer2</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">primer_info</tt><tt class="py-op">:</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-string">"%s %s %s\n"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-12" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-12', 'name', 'link-11');">name</a></tt><tt class="py-op">,</tt> <tt class="py-name">primer1</tt><tt class="py-op">,</tt> <tt class="py-name">primer2</tt><tt class="py-op">)</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">output</tt> </tt>
</div><a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"> </tt>
<a name="PrimerSearchInputRecord.add_primer_set"></a><div id="PrimerSearchInputRecord.add_primer_set-def"><a name="L35"></a><tt class="py-lineno"> 35</tt> <a class="py-toggle" href="#" id="PrimerSearchInputRecord.add_primer_set-toggle" onclick="return toggle('PrimerSearchInputRecord.add_primer_set');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer.PrimerSearchInputRecord-class.html#add_primer_set">add_primer_set</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">primer_name</tt><tt class="py-op">,</tt> <tt class="py-param">first_primer_seq</tt><tt class="py-op">,</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-param">second_primer_seq</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PrimerSearchInputRecord.add_primer_set-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PrimerSearchInputRecord.add_primer_set-expanded"><a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt class="py-docstring">"""Add primer information to the record.</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-docstring"> """</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">primer_info</tt><tt class="py-op">.</tt><tt id="link-13" 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-13', 'append', 'link-13');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-14" class="py-name" targets="Method Bio.Emboss.Primer._PrimerSearchRecordConsumer.primer_name()=Bio.Emboss.Primer._PrimerSearchRecordConsumer-class.html#primer_name,Variable Bio.Emboss.primersearch_format.primer_name=Bio.Emboss.primersearch_format-module.html#primer_name"><a title="Bio.Emboss.Primer._PrimerSearchRecordConsumer.primer_name
Bio.Emboss.primersearch_format.primer_name" class="py-name" href="#" onclick="return doclink('link-14', 'primer_name', 'link-14');">primer_name</a></tt><tt class="py-op">,</tt> <tt class="py-name">first_primer_seq</tt><tt class="py-op">,</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> <tt class="py-name">second_primer_seq</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> </tt>
<a name="PrimerSearchParser"></a><div id="PrimerSearchParser-def"><a name="L42"></a><tt class="py-lineno"> 42</tt> <a class="py-toggle" href="#" id="PrimerSearchParser-toggle" onclick="return toggle('PrimerSearchParser');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Emboss.Primer.PrimerSearchParser-class.html">PrimerSearchParser</a><tt class="py-op">:</tt> </tt>
</div><div id="PrimerSearchParser-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="PrimerSearchParser-expanded"><a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt class="py-docstring">"""Parse primersearch output into a PrimerSearchOutputRecord.</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="PrimerSearchParser.__init__"></a><div id="PrimerSearchParser.__init__-def"><a name="L45"></a><tt class="py-lineno"> 45</tt> <a class="py-toggle" href="#" id="PrimerSearchParser.__init__-toggle" onclick="return toggle('PrimerSearchParser.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer.PrimerSearchParser-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_level</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="PrimerSearchParser.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PrimerSearchParser.__init__-expanded"><a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_scanner</tt> <tt class="py-op">=</tt> <tt id="link-15" class="py-name" targets="Class Bio.Emboss.Primer._PrimerSearchScanner=Bio.Emboss.Primer._PrimerSearchScanner-class.html"><a title="Bio.Emboss.Primer._PrimerSearchScanner" class="py-name" href="#" onclick="return doclink('link-15', '_PrimerSearchScanner', 'link-15');">_PrimerSearchScanner</a></tt><tt class="py-op">(</tt><tt class="py-name">debug_level</tt><tt class="py-op">)</tt> </tt>
</div><a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> </tt>
<a name="PrimerSearchParser.parse"></a><div id="PrimerSearchParser.parse-def"><a name="L48"></a><tt class="py-lineno"> 48</tt> <a class="py-toggle" href="#" id="PrimerSearchParser.parse-toggle" onclick="return toggle('PrimerSearchParser.parse');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer.PrimerSearchParser-class.html#parse">parse</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">handle</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PrimerSearchParser.parse-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PrimerSearchParser.parse-expanded"><a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_consumer</tt> <tt class="py-op">=</tt> <tt id="link-16" class="py-name" targets="Class Bio.Emboss.Primer._PrimerSearchRecordConsumer=Bio.Emboss.Primer._PrimerSearchRecordConsumer-class.html"><a title="Bio.Emboss.Primer._PrimerSearchRecordConsumer" class="py-name" href="#" onclick="return doclink('link-16', '_PrimerSearchRecordConsumer', 'link-16');">_PrimerSearchRecordConsumer</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_scanner</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name" targets="Method Bio.Affy.CelFile.CelScanner.feed()=Bio.Affy.CelFile.CelScanner-class.html#feed,Method Bio.AlignAce.Scanner.AlignAceScanner.feed()=Bio.AlignAce.Scanner.AlignAceScanner-class.html#feed,Method Bio.AlignAce.Scanner.CompareAceScanner.feed()=Bio.AlignAce.Scanner.CompareAceScanner-class.html#feed,Method Bio.Blast.NCBIStandalone._Scanner.feed()=Bio.Blast.NCBIStandalone._Scanner-class.html#feed,Method Bio.Blast.NCBIWWW._Scanner.feed()=Bio.Blast.NCBIWWW._Scanner-class.html#feed,Method Bio.CDD._Scanner.feed()=Bio.CDD._Scanner-class.html#feed,Method Bio.Compass._Scanner.feed()=Bio.Compass._Scanner-class.html#feed,Method Bio.ECell._Scanner.feed()=Bio.ECell._Scanner-class.html#feed,Method Bio.Emboss.Primer._Primer3Scanner.feed()=Bio.Emboss.Primer._Primer3Scanner-class.html#feed,Method Bio.Emboss.Primer._PrimerSearchScanner.feed()=Bio.Emboss.Primer._PrimerSearchScanner-class.html#feed,Method Bio.Enzyme._Scanner.feed()=Bio.Enzyme._Scanner-class.html#feed,Method Bio.GenBank.Scanner.InsdcScanner.feed()=Bio.GenBank.Scanner.InsdcScanner-class.html#feed,Method Bio.Gobase._Scanner.feed()=Bio.Gobase._Scanner-class.html#feed,Method Bio.IntelliGenetics._Scanner.feed()=Bio.IntelliGenetics._Scanner-class.html#feed,Method Bio.InterPro.InterProParser.feed()=Bio.InterPro.InterProParser-class.html#feed,Method Bio.LocusLink._Scanner.feed()=Bio.LocusLink._Scanner-class.html#feed,Method Bio.LocusLink.web_parse.LocusLinkParser.feed()=Bio.LocusLink.web_parse.LocusLinkParser-class.html#feed,Method Bio.MEME.Parser._MASTScanner.feed()=Bio.MEME.Parser._MASTScanner-class.html#feed,Method Bio.MEME.Parser._MEMEScanner.feed()=Bio.MEME.Parser._MEMEScanner-class.html#feed,Method Bio.Medline._Scanner.feed()=Bio.Medline._Scanner-class.html#feed,Method Bio.MetaTool._Scanner.feed()=Bio.MetaTool._Scanner-class.html#feed,Method Bio.NBRF._Scanner.feed()=Bio.NBRF._Scanner-class.html#feed,Method Bio.Ndb.NdbParser.feed()=Bio.Ndb.NdbParser-class.html#feed,Method Bio.NetCatch.ExtractUrls.feed()=Bio.NetCatch.ExtractUrls-class.html#feed,Method Bio.PopGen.FDist._Scanner.feed()=Bio.PopGen.FDist._Scanner-class.html#feed,Method Bio.PopGen.GenePop._Scanner.feed()=Bio.PopGen.GenePop._Scanner-class.html#feed,Method Bio.Prosite.Prodoc._Scanner.feed()=Bio.Prosite.Prodoc._Scanner-class.html#feed,Method Bio.Prosite._Scanner.feed()=Bio.Prosite._Scanner-class.html#feed,Method Bio.Rebase._Scanner.feed()=Bio.Rebase._Scanner-class.html#feed,Method Bio.Saf._Scanner.feed()=Bio.Saf._Scanner-class.html#feed,Method Bio.Sequencing.Ace._Scanner.feed()=Bio.Sequencing.Ace._Scanner-class.html#feed,Method Bio.Sequencing.Phd._Scanner.feed()=Bio.Sequencing.Phd._Scanner-class.html#feed,Method Bio.SwissProt.KeyWList._Scanner.feed()=Bio.SwissProt.KeyWList._Scanner-class.html#feed,Method Bio.SwissProt.SProt._Scanner.feed()=Bio.SwissProt.SProt._Scanner-class.html#feed,Method Bio.UniGene._Scanner.feed()=Bio.UniGene._Scanner-class.html#feed"><a title="Bio.Affy.CelFile.CelScanner.feed
Bio.AlignAce.Scanner.AlignAceScanner.feed
Bio.AlignAce.Scanner.CompareAceScanner.feed
Bio.Blast.NCBIStandalone._Scanner.feed
Bio.Blast.NCBIWWW._Scanner.feed
Bio.CDD._Scanner.feed
Bio.Compass._Scanner.feed
Bio.ECell._Scanner.feed
Bio.Emboss.Primer._Primer3Scanner.feed
Bio.Emboss.Primer._PrimerSearchScanner.feed
Bio.Enzyme._Scanner.feed
Bio.GenBank.Scanner.InsdcScanner.feed
Bio.Gobase._Scanner.feed
Bio.IntelliGenetics._Scanner.feed
Bio.InterPro.InterProParser.feed
Bio.LocusLink._Scanner.feed
Bio.LocusLink.web_parse.LocusLinkParser.feed
Bio.MEME.Parser._MASTScanner.feed
Bio.MEME.Parser._MEMEScanner.feed
Bio.Medline._Scanner.feed
Bio.MetaTool._Scanner.feed
Bio.NBRF._Scanner.feed
Bio.Ndb.NdbParser.feed
Bio.NetCatch.ExtractUrls.feed
Bio.PopGen.FDist._Scanner.feed
Bio.PopGen.GenePop._Scanner.feed
Bio.Prosite.Prodoc._Scanner.feed
Bio.Prosite._Scanner.feed
Bio.Rebase._Scanner.feed
Bio.Saf._Scanner.feed
Bio.Sequencing.Ace._Scanner.feed
Bio.Sequencing.Phd._Scanner.feed
Bio.SwissProt.KeyWList._Scanner.feed
Bio.SwissProt.SProt._Scanner.feed
Bio.UniGene._Scanner.feed" class="py-name" href="#" onclick="return doclink('link-17', 'feed', 'link-17');">feed</a></tt><tt class="py-op">(</tt><tt id="link-18" 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-18', 'handle', 'link-18');">handle</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_consumer</tt><tt class="py-op">)</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_consumer</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name" targets="Variable BioSQL.BioSeq.DBSeq.data=BioSQL.BioSeq.DBSeq-class.html#data"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-19', 'data', 'link-19');">data</a></tt> </tt>
</div></div><a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> </tt>
<a name="PrimerSearchOutputRecord"></a><div id="PrimerSearchOutputRecord-def"><a name="L53"></a><tt class="py-lineno"> 53</tt> <a class="py-toggle" href="#" id="PrimerSearchOutputRecord-toggle" onclick="return toggle('PrimerSearchOutputRecord');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Emboss.Primer.PrimerSearchOutputRecord-class.html">PrimerSearchOutputRecord</a><tt class="py-op">:</tt> </tt>
</div><div id="PrimerSearchOutputRecord-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="PrimerSearchOutputRecord-expanded"><a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-docstring">"""Represent the information from a primersearch job.</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"> amplifiers is a dictionary where the keys are the primer names and</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"><tt class="py-docstring"> the values are a list of PrimerSearchAmplifier objects.</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="PrimerSearchOutputRecord.__init__"></a><div id="PrimerSearchOutputRecord.__init__-def"><a name="L59"></a><tt class="py-lineno"> 59</tt> <a class="py-toggle" href="#" id="PrimerSearchOutputRecord.__init__-toggle" onclick="return toggle('PrimerSearchOutputRecord.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer.PrimerSearchOutputRecord-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PrimerSearchOutputRecord.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PrimerSearchOutputRecord.__init__-expanded"><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">amplifiers</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
</div></div><a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> </tt>
<a name="PrimerSearchAmplifier"></a><div id="PrimerSearchAmplifier-def"><a name="L62"></a><tt class="py-lineno"> 62</tt> <a class="py-toggle" href="#" id="PrimerSearchAmplifier-toggle" onclick="return toggle('PrimerSearchAmplifier');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Emboss.Primer.PrimerSearchAmplifier-class.html">PrimerSearchAmplifier</a><tt class="py-op">:</tt> </tt>
</div><div id="PrimerSearchAmplifier-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="PrimerSearchAmplifier-expanded"><a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-docstring">"""Represent a single amplification from a primer.</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="PrimerSearchAmplifier.__init__"></a><div id="PrimerSearchAmplifier.__init__-def"><a name="L65"></a><tt class="py-lineno"> 65</tt> <a class="py-toggle" href="#" id="PrimerSearchAmplifier.__init__-toggle" onclick="return toggle('PrimerSearchAmplifier.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer.PrimerSearchAmplifier-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PrimerSearchAmplifier.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PrimerSearchAmplifier.__init__-expanded"><a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">hit_info</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-20" 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-20', 'length', 'link-20');">length</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
</div></div><a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> </tt>
<a name="_PrimerSearchRecordConsumer"></a><div id="_PrimerSearchRecordConsumer-def"><a name="L69"></a><tt class="py-lineno"> 69</tt> <a class="py-toggle" href="#" id="_PrimerSearchRecordConsumer-toggle" onclick="return toggle('_PrimerSearchRecordConsumer');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Emboss.Primer._PrimerSearchRecordConsumer-class.html">_PrimerSearchRecordConsumer</a><tt class="py-op">(</tt><tt class="py-base-class">AbstractConsumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_PrimerSearchRecordConsumer-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_PrimerSearchRecordConsumer-expanded"><a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-docstring">"""Get output from primersearch into a PrimerSearchOutputRecord</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="_PrimerSearchRecordConsumer.__init__"></a><div id="_PrimerSearchRecordConsumer.__init__-def"><a name="L72"></a><tt class="py-lineno"> 72</tt> <a class="py-toggle" href="#" id="_PrimerSearchRecordConsumer.__init__-toggle" onclick="return toggle('_PrimerSearchRecordConsumer.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer._PrimerSearchRecordConsumer-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_PrimerSearchRecordConsumer.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_PrimerSearchRecordConsumer.__init__-expanded"><a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-21" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-21', 'data', 'link-19');">data</a></tt> <tt class="py-op">=</tt> <tt id="link-22" class="py-name" targets="Class Bio.Emboss.Primer.PrimerSearchOutputRecord=Bio.Emboss.Primer.PrimerSearchOutputRecord-class.html"><a title="Bio.Emboss.Primer.PrimerSearchOutputRecord" class="py-name" href="#" onclick="return doclink('link-22', 'PrimerSearchOutputRecord', 'link-22');">PrimerSearchOutputRecord</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cur_primer</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cur_amplifier</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
</div><a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> </tt>
<a name="_PrimerSearchRecordConsumer._add_last_amplifier"></a><div id="_PrimerSearchRecordConsumer._add_last_amplifier-def"><a name="L77"></a><tt class="py-lineno"> 77</tt> <a class="py-toggle" href="#" id="_PrimerSearchRecordConsumer._add_last_amplifier-toggle" onclick="return toggle('_PrimerSearchRecordConsumer._add_last_amplifier');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer._PrimerSearchRecordConsumer-class.html#_add_last_amplifier">_add_last_amplifier</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="_PrimerSearchRecordConsumer._add_last_amplifier-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_PrimerSearchRecordConsumer._add_last_amplifier-expanded"><a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-comment"># add on the last amplifier</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cur_primer</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt> <tt class="py-keyword">and</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cur_amplifier</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-23', 'data', 'link-19');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">amplifiers</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cur_primer</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-24" 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-24', 'append', 'link-13');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cur_amplifier</tt><tt class="py-op">)</tt> </tt>
</div><a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> </tt>
<a name="_PrimerSearchRecordConsumer.primer_name"></a><div id="_PrimerSearchRecordConsumer.primer_name-def"><a name="L82"></a><tt class="py-lineno"> 82</tt> <a class="py-toggle" href="#" id="_PrimerSearchRecordConsumer.primer_name-toggle" onclick="return toggle('_PrimerSearchRecordConsumer.primer_name');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer._PrimerSearchRecordConsumer-class.html#primer_name">primer_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="_PrimerSearchRecordConsumer.primer_name-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_PrimerSearchRecordConsumer.primer_name-expanded"><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 id="link-25" class="py-name" targets="Method Bio.Emboss.Primer._PrimerSearchRecordConsumer._add_last_amplifier()=Bio.Emboss.Primer._PrimerSearchRecordConsumer-class.html#_add_last_amplifier"><a title="Bio.Emboss.Primer._PrimerSearchRecordConsumer._add_last_amplifier" class="py-name" href="#" onclick="return doclink('link-25', '_add_last_amplifier', 'link-25');">_add_last_amplifier</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-26', 'data', 'link-19');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">amplifiers</tt><tt class="py-op">[</tt><tt id="link-27" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-27', 'name', 'link-11');">name</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cur_primer</tt> <tt class="py-op">=</tt> <tt id="link-28" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-28', 'name', 'link-11');">name</a></tt> </tt>
</div><a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> </tt>
<a name="_PrimerSearchRecordConsumer.amplifier"></a><div id="_PrimerSearchRecordConsumer.amplifier-def"><a name="L87"></a><tt class="py-lineno"> 87</tt> <a class="py-toggle" href="#" id="_PrimerSearchRecordConsumer.amplifier-toggle" onclick="return toggle('_PrimerSearchRecordConsumer.amplifier');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer._PrimerSearchRecordConsumer-class.html#amplifier">amplifier</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">amplifier_num</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_PrimerSearchRecordConsumer.amplifier-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_PrimerSearchRecordConsumer.amplifier-expanded"><a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-29" class="py-name"><a title="Bio.Emboss.Primer._PrimerSearchRecordConsumer._add_last_amplifier" class="py-name" href="#" onclick="return doclink('link-29', '_add_last_amplifier', 'link-25');">_add_last_amplifier</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cur_amplifier</tt> <tt class="py-op">=</tt> <tt id="link-30" class="py-name" targets="Class Bio.Emboss.Primer.PrimerSearchAmplifier=Bio.Emboss.Primer.PrimerSearchAmplifier-class.html"><a title="Bio.Emboss.Primer.PrimerSearchAmplifier" class="py-name" href="#" onclick="return doclink('link-30', 'PrimerSearchAmplifier', 'link-30');">PrimerSearchAmplifier</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> </tt>
<a name="_PrimerSearchRecordConsumer.amplifier_sequence"></a><div id="_PrimerSearchRecordConsumer.amplifier_sequence-def"><a name="L91"></a><tt class="py-lineno"> 91</tt> <a class="py-toggle" href="#" id="_PrimerSearchRecordConsumer.amplifier_sequence-toggle" onclick="return toggle('_PrimerSearchRecordConsumer.amplifier_sequence');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer._PrimerSearchRecordConsumer-class.html#amplifier_sequence">amplifier_sequence</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">sequence_info</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_PrimerSearchRecordConsumer.amplifier_sequence-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_PrimerSearchRecordConsumer.amplifier_sequence-expanded"><a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cur_amplifier</tt><tt class="py-op">.</tt><tt class="py-name">hit_info</tt> <tt class="py-op">=</tt> <tt id="link-31" class="py-name" targets="Variable Bio.Emboss.primersearch_format.sequence_info=Bio.Emboss.primersearch_format-module.html#sequence_info,Variable Bio.expressions.hmmpfam.sequence_info=Bio.expressions.hmmpfam-module.html#sequence_info"><a title="Bio.Emboss.primersearch_format.sequence_info
Bio.expressions.hmmpfam.sequence_info" class="py-name" href="#" onclick="return doclink('link-31', 'sequence_info', 'link-31');">sequence_info</a></tt> </tt>
</div><a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> </tt>
<a name="_PrimerSearchRecordConsumer.amplifier_length"></a><div id="_PrimerSearchRecordConsumer.amplifier_length-def"><a name="L94"></a><tt class="py-lineno"> 94</tt> <a class="py-toggle" href="#" id="_PrimerSearchRecordConsumer.amplifier_length-toggle" onclick="return toggle('_PrimerSearchRecordConsumer.amplifier_length');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer._PrimerSearchRecordConsumer-class.html#amplifier_length">amplifier_length</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">amplifier_info</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_PrimerSearchRecordConsumer.amplifier_length-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_PrimerSearchRecordConsumer.amplifier_length-expanded"><a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cur_amplifier</tt><tt class="py-op">.</tt><tt id="link-32" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-32', 'length', 'link-20');">length</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">amplifier_info</tt><tt class="py-op">)</tt> </tt>
</div><a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> </tt>
<a name="_PrimerSearchRecordConsumer.end_record"></a><div id="_PrimerSearchRecordConsumer.end_record-def"><a name="L97"></a><tt class="py-lineno"> 97</tt> <a class="py-toggle" href="#" id="_PrimerSearchRecordConsumer.end_record-toggle" onclick="return toggle('_PrimerSearchRecordConsumer.end_record');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer._PrimerSearchRecordConsumer-class.html#end_record">end_record</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="_PrimerSearchRecordConsumer.end_record-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_PrimerSearchRecordConsumer.end_record-expanded"><a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-33" class="py-name"><a title="Bio.Emboss.Primer._PrimerSearchRecordConsumer._add_last_amplifier" class="py-name" href="#" onclick="return doclink('link-33', '_add_last_amplifier', 'link-25');">_add_last_amplifier</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> </tt>
<a name="_PrimerSearchScanner"></a><div id="_PrimerSearchScanner-def"><a name="L100"></a><tt class="py-lineno">100</tt> <a class="py-toggle" href="#" id="_PrimerSearchScanner-toggle" onclick="return toggle('_PrimerSearchScanner');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Emboss.Primer._PrimerSearchScanner-class.html">_PrimerSearchScanner</a><tt class="py-op">:</tt> </tt>
</div><div id="_PrimerSearchScanner-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_PrimerSearchScanner-expanded"><a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-docstring">"""Scan output from the primersearch program.</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="_PrimerSearchScanner.__init__"></a><div id="_PrimerSearchScanner.__init__-def"><a name="L103"></a><tt class="py-lineno">103</tt> <a class="py-toggle" href="#" id="_PrimerSearchScanner.__init__-toggle" onclick="return toggle('_PrimerSearchScanner.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer._PrimerSearchScanner-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="_PrimerSearchScanner.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_PrimerSearchScanner.__init__-expanded"><a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">interest_tags</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-string">"primer_name"</tt><tt class="py-op">,</tt> <tt class="py-string">"amplifier"</tt><tt class="py-op">,</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-string">"amplifier_sequence"</tt><tt class="py-op">,</tt> <tt class="py-string">"amplifier_length"</tt><tt class="py-op">,</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-string">"end_record"</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-name">expression</tt> <tt class="py-op">=</tt> <tt id="link-34" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-34', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-35" class="py-name" targets="Function Martel.select_names()=Martel-module.html#select_names"><a title="Martel.select_names" class="py-name" href="#" onclick="return doclink('link-35', 'select_names', 'link-35');">select_names</a></tt><tt class="py-op">(</tt><tt id="link-36" class="py-name"><a title="Bio.Emboss.primersearch_format" class="py-name" href="#" onclick="return doclink('link-36', 'primersearch_format', 'link-9');">primersearch_format</a></tt><tt class="py-op">.</tt><tt id="link-37" 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-37', 'record', 'link-37');">record</a></tt><tt class="py-op">,</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">interest_tags</tt><tt class="py-op">)</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</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">expression</tt><tt class="py-op">.</tt><tt id="link-38" 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-38', 'make_parser', 'link-38');">make_parser</a></tt><tt class="py-op">(</tt><tt class="py-name">debug_level</tt> <tt class="py-op">=</tt> <tt class="py-name">debug</tt><tt class="py-op">)</tt> </tt>
</div><a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> </tt>
<a name="_PrimerSearchScanner.feed"></a><div id="_PrimerSearchScanner.feed-def"><a name="L112"></a><tt class="py-lineno">112</tt> <a class="py-toggle" href="#" id="_PrimerSearchScanner.feed-toggle" onclick="return toggle('_PrimerSearchScanner.feed');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer._PrimerSearchScanner-class.html#feed">feed</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">handle</tt><tt class="py-op">,</tt> <tt class="py-param">consumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_PrimerSearchScanner.feed-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_PrimerSearchScanner.feed-expanded"><a name="L113"></a><tt class="py-lineno">113</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 id="link-39" class="py-name"><a title="Bio.ParserSupport.EventGenerator" class="py-name" href="#" onclick="return doclink('link-39', 'EventGenerator', 'link-8');">EventGenerator</a></tt><tt class="py-op">(</tt><tt class="py-name">consumer</tt><tt class="py-op">,</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">interest_tags</tt><tt class="py-op">,</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt id="link-40" class="py-name" targets="Function Bio.Emboss.Primer._strip_and_combine()=Bio.Emboss.Primer-module.html#_strip_and_combine"><a title="Bio.Emboss.Primer._strip_and_combine" class="py-name" href="#" onclick="return doclink('link-40', '_strip_and_combine', 'link-40');">_strip_and_combine</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</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">setErrorHandler</tt><tt class="py-op">(</tt><tt class="py-name">handler</tt><tt class="py-op">.</tt><tt class="py-name">ErrorHandler</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</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-41" class="py-name" targets="Method Bio.EUtils.POM.POMDocument.parseFile()=Bio.EUtils.POM.POMDocument-class.html#parseFile,Method Martel.Parser.HeaderFooterParser.parseFile()=Martel.Parser.HeaderFooterParser-class.html#parseFile,Method Martel.Parser.Parser.parseFile()=Martel.Parser.Parser-class.html#parseFile,Method Martel.Parser.RecordParser.parseFile()=Martel.Parser.RecordParser-class.html#parseFile"><a title="Bio.EUtils.POM.POMDocument.parseFile
Martel.Parser.HeaderFooterParser.parseFile
Martel.Parser.Parser.parseFile
Martel.Parser.RecordParser.parseFile" class="py-name" href="#" onclick="return doclink('link-41', 'parseFile', 'link-41');">parseFile</a></tt><tt class="py-op">(</tt><tt id="link-42" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-42', 'handle', 'link-18');">handle</a></tt><tt class="py-op">)</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-43" class="py-name" targets="Method Bio.Emboss.Primer._Primer3RecordConsumer.end_record()=Bio.Emboss.Primer._Primer3RecordConsumer-class.html#end_record,Method Bio.Emboss.Primer._PrimerSearchRecordConsumer.end_record()=Bio.Emboss.Primer._PrimerSearchRecordConsumer-class.html#end_record,Method Bio.Medline._RecordConsumer.end_record()=Bio.Medline._RecordConsumer-class.html#end_record,Method Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder.end_record()=Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder-class.html#end_record,Method Bio.PopGen.FDist._RecordConsumer.end_record()=Bio.PopGen.FDist._RecordConsumer-class.html#end_record,Method Bio.PopGen.GenePop._RecordConsumer.end_record()=Bio.PopGen.GenePop._RecordConsumer-class.html#end_record,Method Bio.Prosite.Prodoc._RecordConsumer.end_record()=Bio.Prosite.Prodoc._RecordConsumer-class.html#end_record,Method Bio.Prosite._RecordConsumer.end_record()=Bio.Prosite._RecordConsumer-class.html#end_record,Method Bio.SwissProt.SProt._RecordConsumer.end_record()=Bio.SwissProt.SProt._RecordConsumer-class.html#end_record,Method Bio.SwissProt.SProt._SequenceConsumer.end_record()=Bio.SwissProt.SProt._SequenceConsumer-class.html#end_record,Method Bio.builders.SeqRecord.sequence.BuildSeqRecord.end_record()=Bio.builders.SeqRecord.sequence.BuildSeqRecord-class.html#end_record"><a title="Bio.Emboss.Primer._Primer3RecordConsumer.end_record
Bio.Emboss.Primer._PrimerSearchRecordConsumer.end_record
Bio.Medline._RecordConsumer.end_record
Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder.end_record
Bio.PopGen.FDist._RecordConsumer.end_record
Bio.PopGen.GenePop._RecordConsumer.end_record
Bio.Prosite.Prodoc._RecordConsumer.end_record
Bio.Prosite._RecordConsumer.end_record
Bio.SwissProt.SProt._RecordConsumer.end_record
Bio.SwissProt.SProt._SequenceConsumer.end_record
Bio.builders.SeqRecord.sequence.BuildSeqRecord.end_record" class="py-name" href="#" onclick="return doclink('link-43', 'end_record', 'link-43');">end_record</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"><tt class="py-comment"># --- primer3</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="Primer3Record"></a><div id="Primer3Record-def"><a name="L123"></a><tt class="py-lineno">123</tt> <a class="py-toggle" href="#" id="Primer3Record-toggle" onclick="return toggle('Primer3Record');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Emboss.Primer.Primer3Record-class.html">Primer3Record</a><tt class="py-op">:</tt> </tt>
</div><div id="Primer3Record-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Primer3Record-expanded"><a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-docstring">"""Represent information from a primer3 run finding primers.</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"><tt class="py-docstring"> Members:</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"><tt class="py-docstring"> primers A list of primers that are generated (usually 5)</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="Primer3Record.__init__"></a><div id="Primer3Record.__init__-def"><a name="L130"></a><tt class="py-lineno">130</tt> <a class="py-toggle" href="#" id="Primer3Record.__init__-toggle" onclick="return toggle('Primer3Record.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer.Primer3Record-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Primer3Record.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Primer3Record.__init__-expanded"><a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-44" class="py-name" targets="Method Bio.Emboss.Primer._Primer3RecordConsumer.comments()=Bio.Emboss.Primer._Primer3RecordConsumer-class.html#comments,Variable Bio.Emboss.primer3_format.comments=Bio.Emboss.primer3_format-module.html#comments,Method Bio.Medline._RecordConsumer.comments()=Bio.Medline._RecordConsumer-class.html#comments"><a title="Bio.Emboss.Primer._Primer3RecordConsumer.comments
Bio.Emboss.primer3_format.comments
Bio.Medline._RecordConsumer.comments" class="py-name" href="#" onclick="return doclink('link-44', 'comments', 'link-44');">comments</a></tt> <tt class="py-op">=</tt> <tt class="py-string">""</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">primers</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
</div></div><a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> </tt>
<a name="Primer3Primers"></a><div id="Primer3Primers-def"><a name="L134"></a><tt class="py-lineno">134</tt> <a class="py-toggle" href="#" id="Primer3Primers-toggle" onclick="return toggle('Primer3Primers');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Emboss.Primer.Primer3Primers-class.html">Primer3Primers</a><tt class="py-op">:</tt> </tt>
</div><div id="Primer3Primers-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Primer3Primers-expanded"><a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt class="py-docstring">"""A primer set designed by Primer3.</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"><tt class="py-docstring"> Members:</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"><tt class="py-docstring"> size</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"><tt class="py-docstring"> forward_seq</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"><tt class="py-docstring"> forward_start</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"><tt class="py-docstring"> forward_length</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"><tt class="py-docstring"> forward_tm</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"><tt class="py-docstring"> forward_gc</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"><tt class="py-docstring"> reverse_seq</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"><tt class="py-docstring"> reverse_start</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"><tt class="py-docstring"> reverse_length</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"><tt class="py-docstring"> reverse_tm</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"><tt class="py-docstring"> reverse_gc</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="Primer3Primers.__init__"></a><div id="Primer3Primers.__init__-def"><a name="L151"></a><tt class="py-lineno">151</tt> <a class="py-toggle" href="#" id="Primer3Primers.__init__-toggle" onclick="return toggle('Primer3Primers.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer.Primer3Primers-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Primer3Primers.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Primer3Primers.__init__-expanded"><a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-45" class="py-name" targets="Method Bio.Affy.CelFile.CelRecord.size()=Bio.Affy.CelFile.CelRecord-class.html#size,Variable Bio.Alphabet.Alphabet.size=Bio.Alphabet.Alphabet-class.html#size,Variable Bio.Alphabet.Reduced.HPModel.size=Bio.Alphabet.Reduced.HPModel-class.html#size,Variable Bio.Alphabet.Reduced.Murphy10.size=Bio.Alphabet.Reduced.Murphy10-class.html#size,Variable Bio.Alphabet.Reduced.Murphy15.size=Bio.Alphabet.Reduced.Murphy15-class.html#size,Variable Bio.Alphabet.Reduced.Murphy4.size=Bio.Alphabet.Reduced.Murphy4-class.html#size,Variable Bio.Alphabet.Reduced.Murphy8.size=Bio.Alphabet.Reduced.Murphy8-class.html#size,Variable Bio.Alphabet.Reduced.PC5.size=Bio.Alphabet.Reduced.PC5-class.html#size,Variable Bio.Alphabet.SingleLetterAlphabet.size=Bio.Alphabet.SingleLetterAlphabet-class.html#size,Variable Bio.Alphabet.ThreeLetterProtein.size=Bio.Alphabet.ThreeLetterProtein-class.html#size,Method Bio.GenBank._FeatureConsumer.size()=Bio.GenBank._FeatureConsumer-class.html#size,Method Bio.GenBank._RecordConsumer.size()=Bio.GenBank._RecordConsumer-class.html#size,Variable Bio.expressions.genbank.size=Bio.expressions.genbank-module.html#size"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-45', 'size', 'link-45');">size</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-46" class="py-name" targets="Method Bio.Emboss.Primer._Primer3RecordConsumer.forward_seq()=Bio.Emboss.Primer._Primer3RecordConsumer-class.html#forward_seq"><a title="Bio.Emboss.Primer._Primer3RecordConsumer.forward_seq" class="py-name" href="#" onclick="return doclink('link-46', 'forward_seq', 'link-46');">forward_seq</a></tt> <tt class="py-op">=</tt> <tt class="py-string">""</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-47" class="py-name" targets="Method Bio.Emboss.Primer._Primer3RecordConsumer.forward_start()=Bio.Emboss.Primer._Primer3RecordConsumer-class.html#forward_start"><a title="Bio.Emboss.Primer._Primer3RecordConsumer.forward_start" class="py-name" href="#" onclick="return doclink('link-47', 'forward_start', 'link-47');">forward_start</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</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 id="link-48" class="py-name" targets="Method Bio.Emboss.Primer._Primer3RecordConsumer.forward_length()=Bio.Emboss.Primer._Primer3RecordConsumer-class.html#forward_length"><a title="Bio.Emboss.Primer._Primer3RecordConsumer.forward_length" class="py-name" href="#" onclick="return doclink('link-48', 'forward_length', 'link-48');">forward_length</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-49" class="py-name" targets="Method Bio.Emboss.Primer._Primer3RecordConsumer.forward_tm()=Bio.Emboss.Primer._Primer3RecordConsumer-class.html#forward_tm"><a title="Bio.Emboss.Primer._Primer3RecordConsumer.forward_tm" class="py-name" href="#" onclick="return doclink('link-49', 'forward_tm', 'link-49');">forward_tm</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0.0</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-50" class="py-name" targets="Method Bio.Emboss.Primer._Primer3RecordConsumer.forward_gc()=Bio.Emboss.Primer._Primer3RecordConsumer-class.html#forward_gc"><a title="Bio.Emboss.Primer._Primer3RecordConsumer.forward_gc" class="py-name" href="#" onclick="return doclink('link-50', 'forward_gc', 'link-50');">forward_gc</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0.0</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-51" class="py-name" targets="Method Bio.Emboss.Primer._Primer3RecordConsumer.reverse_seq()=Bio.Emboss.Primer._Primer3RecordConsumer-class.html#reverse_seq"><a title="Bio.Emboss.Primer._Primer3RecordConsumer.reverse_seq" class="py-name" href="#" onclick="return doclink('link-51', 'reverse_seq', 'link-51');">reverse_seq</a></tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<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 id="link-52" class="py-name" targets="Method Bio.Emboss.Primer._Primer3RecordConsumer.reverse_start()=Bio.Emboss.Primer._Primer3RecordConsumer-class.html#reverse_start"><a title="Bio.Emboss.Primer._Primer3RecordConsumer.reverse_start" class="py-name" href="#" onclick="return doclink('link-52', 'reverse_start', 'link-52');">reverse_start</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-53" class="py-name" targets="Method Bio.Emboss.Primer._Primer3RecordConsumer.reverse_length()=Bio.Emboss.Primer._Primer3RecordConsumer-class.html#reverse_length"><a title="Bio.Emboss.Primer._Primer3RecordConsumer.reverse_length" class="py-name" href="#" onclick="return doclink('link-53', 'reverse_length', 'link-53');">reverse_length</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-54" class="py-name" targets="Method Bio.Emboss.Primer._Primer3RecordConsumer.reverse_tm()=Bio.Emboss.Primer._Primer3RecordConsumer-class.html#reverse_tm"><a title="Bio.Emboss.Primer._Primer3RecordConsumer.reverse_tm" class="py-name" href="#" onclick="return doclink('link-54', 'reverse_tm', 'link-54');">reverse_tm</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0.0</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-55" class="py-name" targets="Method Bio.Emboss.Primer._Primer3RecordConsumer.reverse_gc()=Bio.Emboss.Primer._Primer3RecordConsumer-class.html#reverse_gc"><a title="Bio.Emboss.Primer._Primer3RecordConsumer.reverse_gc" class="py-name" href="#" onclick="return doclink('link-55', 'reverse_gc', 'link-55');">reverse_gc</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0.0</tt> </tt>
</div></div><a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> </tt>
<a name="Primer3Parser"></a><div id="Primer3Parser-def"><a name="L164"></a><tt class="py-lineno">164</tt> <a class="py-toggle" href="#" id="Primer3Parser-toggle" onclick="return toggle('Primer3Parser');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Emboss.Primer.Primer3Parser-class.html">Primer3Parser</a><tt class="py-op">:</tt> </tt>
</div><div id="Primer3Parser-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Primer3Parser-expanded"><a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-docstring">"""Parse primer3 output into a Primer3Record.</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="Primer3Parser.__init__"></a><div id="Primer3Parser.__init__-def"><a name="L167"></a><tt class="py-lineno">167</tt> <a class="py-toggle" href="#" id="Primer3Parser.__init__-toggle" onclick="return toggle('Primer3Parser.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer.Primer3Parser-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_level</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="Primer3Parser.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Primer3Parser.__init__-expanded"><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">_scanner</tt> <tt class="py-op">=</tt> <tt id="link-56" class="py-name" targets="Class Bio.Emboss.Primer._Primer3Scanner=Bio.Emboss.Primer._Primer3Scanner-class.html"><a title="Bio.Emboss.Primer._Primer3Scanner" class="py-name" href="#" onclick="return doclink('link-56', '_Primer3Scanner', 'link-56');">_Primer3Scanner</a></tt><tt class="py-op">(</tt><tt class="py-name">debug_level</tt><tt class="py-op">)</tt> </tt>
</div><a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> </tt>
<a name="Primer3Parser.parse"></a><div id="Primer3Parser.parse-def"><a name="L170"></a><tt class="py-lineno">170</tt> <a class="py-toggle" href="#" id="Primer3Parser.parse-toggle" onclick="return toggle('Primer3Parser.parse');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer.Primer3Parser-class.html#parse">parse</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">handle</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Primer3Parser.parse-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Primer3Parser.parse-expanded"><a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_consumer</tt> <tt class="py-op">=</tt> <tt id="link-57" class="py-name" targets="Class Bio.Emboss.Primer._Primer3RecordConsumer=Bio.Emboss.Primer._Primer3RecordConsumer-class.html"><a title="Bio.Emboss.Primer._Primer3RecordConsumer" class="py-name" href="#" onclick="return doclink('link-57', '_Primer3RecordConsumer', 'link-57');">_Primer3RecordConsumer</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_scanner</tt><tt class="py-op">.</tt><tt id="link-58" class="py-name"><a title="Bio.Affy.CelFile.CelScanner.feed
Bio.AlignAce.Scanner.AlignAceScanner.feed
Bio.AlignAce.Scanner.CompareAceScanner.feed
Bio.Blast.NCBIStandalone._Scanner.feed
Bio.Blast.NCBIWWW._Scanner.feed
Bio.CDD._Scanner.feed
Bio.Compass._Scanner.feed
Bio.ECell._Scanner.feed
Bio.Emboss.Primer._Primer3Scanner.feed
Bio.Emboss.Primer._PrimerSearchScanner.feed
Bio.Enzyme._Scanner.feed
Bio.GenBank.Scanner.InsdcScanner.feed
Bio.Gobase._Scanner.feed
Bio.IntelliGenetics._Scanner.feed
Bio.InterPro.InterProParser.feed
Bio.LocusLink._Scanner.feed
Bio.LocusLink.web_parse.LocusLinkParser.feed
Bio.MEME.Parser._MASTScanner.feed
Bio.MEME.Parser._MEMEScanner.feed
Bio.Medline._Scanner.feed
Bio.MetaTool._Scanner.feed
Bio.NBRF._Scanner.feed
Bio.Ndb.NdbParser.feed
Bio.NetCatch.ExtractUrls.feed
Bio.PopGen.FDist._Scanner.feed
Bio.PopGen.GenePop._Scanner.feed
Bio.Prosite.Prodoc._Scanner.feed
Bio.Prosite._Scanner.feed
Bio.Rebase._Scanner.feed
Bio.Saf._Scanner.feed
Bio.Sequencing.Ace._Scanner.feed
Bio.Sequencing.Phd._Scanner.feed
Bio.SwissProt.KeyWList._Scanner.feed
Bio.SwissProt.SProt._Scanner.feed
Bio.UniGene._Scanner.feed" class="py-name" href="#" onclick="return doclink('link-58', 'feed', 'link-17');">feed</a></tt><tt class="py-op">(</tt><tt id="link-59" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-59', 'handle', 'link-18');">handle</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_consumer</tt><tt class="py-op">)</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_consumer</tt><tt class="py-op">.</tt><tt id="link-60" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-60', 'data', 'link-19');">data</a></tt> </tt>
</div></div><a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> </tt>
<a name="_Primer3RecordConsumer"></a><div id="_Primer3RecordConsumer-def"><a name="L175"></a><tt class="py-lineno">175</tt> <a class="py-toggle" href="#" id="_Primer3RecordConsumer-toggle" onclick="return toggle('_Primer3RecordConsumer');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Emboss.Primer._Primer3RecordConsumer-class.html">_Primer3RecordConsumer</a><tt class="py-op">(</tt><tt class="py-base-class">AbstractConsumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Primer3RecordConsumer-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_Primer3RecordConsumer-expanded"><a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt class="py-docstring">"""Get output from prime3 into a Primer3Record</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="_Primer3RecordConsumer.__init__"></a><div id="_Primer3RecordConsumer.__init__-def"><a name="L178"></a><tt class="py-lineno">178</tt> <a class="py-toggle" href="#" id="_Primer3RecordConsumer.__init__-toggle" onclick="return toggle('_Primer3RecordConsumer.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer._Primer3RecordConsumer-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Primer3RecordConsumer.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Primer3RecordConsumer.__init__-expanded"><a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-61" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-61', 'data', 'link-19');">data</a></tt> <tt class="py-op">=</tt> <tt id="link-62" class="py-name" targets="Class Bio.Emboss.Primer.Primer3Record=Bio.Emboss.Primer.Primer3Record-class.html"><a title="Bio.Emboss.Primer.Primer3Record" class="py-name" href="#" onclick="return doclink('link-62', 'Primer3Record', 'link-62');">Primer3Record</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cur_primer</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
</div><a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> </tt>
<a name="_Primer3RecordConsumer._add_last_primer"></a><div id="_Primer3RecordConsumer._add_last_primer-def"><a name="L182"></a><tt class="py-lineno">182</tt> <a class="py-toggle" href="#" id="_Primer3RecordConsumer._add_last_primer-toggle" onclick="return toggle('_Primer3RecordConsumer._add_last_primer');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer._Primer3RecordConsumer-class.html#_add_last_primer">_add_last_primer</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="_Primer3RecordConsumer._add_last_primer-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Primer3RecordConsumer._add_last_primer-expanded"><a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> <tt class="py-comment"># add on the last amplifier</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cur_primer</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-63" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-63', 'data', 'link-19');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">primers</tt><tt class="py-op">.</tt><tt id="link-64" 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-64', 'append', 'link-13');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cur_primer</tt><tt class="py-op">)</tt> </tt>
</div><a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> </tt>
<a name="_Primer3RecordConsumer.comments"></a><div id="_Primer3RecordConsumer.comments-def"><a name="L187"></a><tt class="py-lineno">187</tt> <a class="py-toggle" href="#" id="_Primer3RecordConsumer.comments-toggle" onclick="return toggle('_Primer3RecordConsumer.comments');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer._Primer3RecordConsumer-class.html#comments">comments</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">comment</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Primer3RecordConsumer.comments-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Primer3RecordConsumer.comments-expanded"><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 id="link-65" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-65', 'data', 'link-19');">data</a></tt><tt class="py-op">.</tt><tt id="link-66" class="py-name"><a title="Bio.Emboss.Primer._Primer3RecordConsumer.comments
Bio.Emboss.primer3_format.comments
Bio.Medline._RecordConsumer.comments" class="py-name" href="#" onclick="return doclink('link-66', 'comments', 'link-44');">comments</a></tt> <tt class="py-op">=</tt> <tt id="link-67" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.comment()=Bio.EUtils.POM.ElementNode-class.html#comment,Method Bio.Enzyme._RecordConsumer.comment()=Bio.Enzyme._RecordConsumer-class.html#comment,Method Bio.GenBank._FeatureConsumer.comment()=Bio.GenBank._FeatureConsumer-class.html#comment,Method Bio.GenBank._RecordConsumer.comment()=Bio.GenBank._RecordConsumer-class.html#comment,Method Bio.IntelliGenetics._RecordConsumer.comment()=Bio.IntelliGenetics._RecordConsumer-class.html#comment,Method Bio.NBRF._RecordConsumer.comment()=Bio.NBRF._RecordConsumer-class.html#comment,Method Bio.PopGen.GenePop._RecordConsumer.comment()=Bio.PopGen.GenePop._RecordConsumer-class.html#comment,Method Bio.Prosite._RecordConsumer.comment()=Bio.Prosite._RecordConsumer-class.html#comment,Method Bio.SwissProt.SProt._RecordConsumer.comment()=Bio.SwissProt.SProt._RecordConsumer-class.html#comment,Method Bio.SwissProt.SProt._SequenceConsumer.comment()=Bio.SwissProt.SProt._SequenceConsumer-class.html#comment,Variable Bio.expressions.swissprot.sprot38.comment=Bio.expressions.swissprot.sprot38-module.html#comment,Variable Martel.test.test_swissprot38.comment=Martel.test.test_swissprot38-module.html#comment,Variable Martel.test.testformats.swissprot38.comment=Martel.test.testformats.swissprot38-module.html#comment"><a title="Bio.EUtils.POM.ElementNode.comment
Bio.Enzyme._RecordConsumer.comment
Bio.GenBank._FeatureConsumer.comment
Bio.GenBank._RecordConsumer.comment
Bio.IntelliGenetics._RecordConsumer.comment
Bio.NBRF._RecordConsumer.comment
Bio.PopGen.GenePop._RecordConsumer.comment
Bio.Prosite._RecordConsumer.comment
Bio.SwissProt.SProt._RecordConsumer.comment
Bio.SwissProt.SProt._SequenceConsumer.comment
Bio.expressions.swissprot.sprot38.comment
Martel.test.test_swissprot38.comment
Martel.test.testformats.swissprot38.comment" class="py-name" href="#" onclick="return doclink('link-67', 'comment', 'link-67');">comment</a></tt> </tt>
</div><a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> </tt>
<a name="_Primer3RecordConsumer.start_primer"></a><div id="_Primer3RecordConsumer.start_primer-def"><a name="L190"></a><tt class="py-lineno">190</tt> <a class="py-toggle" href="#" id="_Primer3RecordConsumer.start_primer-toggle" onclick="return toggle('_Primer3RecordConsumer.start_primer');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer._Primer3RecordConsumer-class.html#start_primer">start_primer</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">junk</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Primer3RecordConsumer.start_primer-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Primer3RecordConsumer.start_primer-expanded"><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 id="link-68" class="py-name" targets="Method Bio.Emboss.Primer._Primer3RecordConsumer._add_last_primer()=Bio.Emboss.Primer._Primer3RecordConsumer-class.html#_add_last_primer"><a title="Bio.Emboss.Primer._Primer3RecordConsumer._add_last_primer" class="py-name" href="#" onclick="return doclink('link-68', '_add_last_primer', 'link-68');">_add_last_primer</a></tt><tt class="py-op">(</tt><tt class="py-op">)</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">_cur_primer</tt> <tt class="py-op">=</tt> <tt id="link-69" class="py-name" targets="Class Bio.Emboss.Primer.Primer3Primers=Bio.Emboss.Primer.Primer3Primers-class.html"><a title="Bio.Emboss.Primer.Primer3Primers" class="py-name" href="#" onclick="return doclink('link-69', 'Primer3Primers', 'link-69');">Primer3Primers</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> </tt>
<a name="_Primer3RecordConsumer.single_primer_line"></a><div id="_Primer3RecordConsumer.single_primer_line-def"><a name="L194"></a><tt class="py-lineno">194</tt> <a class="py-toggle" href="#" id="_Primer3RecordConsumer.single_primer_line-toggle" onclick="return toggle('_Primer3RecordConsumer.single_primer_line');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer._Primer3RecordConsumer-class.html#single_primer_line">single_primer_line</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">junk</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Primer3RecordConsumer.single_primer_line-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Primer3RecordConsumer.single_primer_line-expanded"><a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-70" class="py-name" targets="Method Bio.Emboss.Primer._Primer3RecordConsumer.start_primer()=Bio.Emboss.Primer._Primer3RecordConsumer-class.html#start_primer,Variable Bio.Emboss.primer3_format.start_primer=Bio.Emboss.primer3_format-module.html#start_primer"><a title="Bio.Emboss.Primer._Primer3RecordConsumer.start_primer
Bio.Emboss.primer3_format.start_primer" class="py-name" href="#" onclick="return doclink('link-70', 'start_primer', 'link-70');">start_primer</a></tt><tt class="py-op">(</tt><tt class="py-name">junk</tt><tt class="py-op">)</tt> </tt>
</div><a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> </tt>
<a name="_Primer3RecordConsumer.product_size"></a><div id="_Primer3RecordConsumer.product_size-def"><a name="L197"></a><tt class="py-lineno">197</tt> <a class="py-toggle" href="#" id="_Primer3RecordConsumer.product_size-toggle" onclick="return toggle('_Primer3RecordConsumer.product_size');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer._Primer3RecordConsumer-class.html#product_size">product_size</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">size</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Primer3RecordConsumer.product_size-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Primer3RecordConsumer.product_size-expanded"><a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cur_primer</tt><tt class="py-op">.</tt><tt id="link-71" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-71', 'size', 'link-45');">size</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-72" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-72', 'size', 'link-45');">size</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> </tt>
<a name="_Primer3RecordConsumer.forward_start"></a><div id="_Primer3RecordConsumer.forward_start-def"><a name="L200"></a><tt class="py-lineno">200</tt> <a class="py-toggle" href="#" id="_Primer3RecordConsumer.forward_start-toggle" onclick="return toggle('_Primer3RecordConsumer.forward_start');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer._Primer3RecordConsumer-class.html#forward_start">forward_start</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">start</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Primer3RecordConsumer.forward_start-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Primer3RecordConsumer.forward_start-expanded"><a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cur_primer</tt><tt class="py-op">.</tt><tt id="link-73" class="py-name"><a title="Bio.Emboss.Primer._Primer3RecordConsumer.forward_start" class="py-name" href="#" onclick="return doclink('link-73', 'forward_start', 'link-47');">forward_start</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-74" class="py-name" targets="Method Bio.GFF.easy.Location.start()=Bio.GFF.easy.Location-class.html#start,Method Bio.Prosite.Pattern.PrositeMatch.start()=Bio.Prosite.Pattern.PrositeMatch-class.html#start,Variable Bio.Restriction._Update.RestrictionCompiler.start=Bio.Restriction._Update.RestrictionCompiler-module.html#start,Method Martel.LAX.LAX.start()=Martel.LAX.LAX-class.html#start"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-74', 'start', 'link-74');">start</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> </tt>
<a name="_Primer3RecordConsumer.forward_length"></a><div id="_Primer3RecordConsumer.forward_length-def"><a name="L203"></a><tt class="py-lineno">203</tt> <a class="py-toggle" href="#" id="_Primer3RecordConsumer.forward_length-toggle" onclick="return toggle('_Primer3RecordConsumer.forward_length');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer._Primer3RecordConsumer-class.html#forward_length">forward_length</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">length</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Primer3RecordConsumer.forward_length-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Primer3RecordConsumer.forward_length-expanded"><a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cur_primer</tt><tt class="py-op">.</tt><tt id="link-75" class="py-name"><a title="Bio.Emboss.Primer._Primer3RecordConsumer.forward_length" class="py-name" href="#" onclick="return doclink('link-75', 'forward_length', 'link-48');">forward_length</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-76" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-76', 'length', 'link-20');">length</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> </tt>
<a name="_Primer3RecordConsumer.forward_tm"></a><div id="_Primer3RecordConsumer.forward_tm-def"><a name="L206"></a><tt class="py-lineno">206</tt> <a class="py-toggle" href="#" id="_Primer3RecordConsumer.forward_tm-toggle" onclick="return toggle('_Primer3RecordConsumer.forward_tm');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer._Primer3RecordConsumer-class.html#forward_tm">forward_tm</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">tm</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Primer3RecordConsumer.forward_tm-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Primer3RecordConsumer.forward_tm-expanded"><a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cur_primer</tt><tt class="py-op">.</tt><tt id="link-77" class="py-name"><a title="Bio.Emboss.Primer._Primer3RecordConsumer.forward_tm" class="py-name" href="#" onclick="return doclink('link-77', 'forward_tm', 'link-49');">forward_tm</a></tt> <tt class="py-op">=</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">tm</tt><tt class="py-op">)</tt> </tt>
</div><a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> </tt>
<a name="_Primer3RecordConsumer.forward_gc"></a><div id="_Primer3RecordConsumer.forward_gc-def"><a name="L209"></a><tt class="py-lineno">209</tt> <a class="py-toggle" href="#" id="_Primer3RecordConsumer.forward_gc-toggle" onclick="return toggle('_Primer3RecordConsumer.forward_gc');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer._Primer3RecordConsumer-class.html#forward_gc">forward_gc</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">gc</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Primer3RecordConsumer.forward_gc-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Primer3RecordConsumer.forward_gc-expanded"><a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cur_primer</tt><tt class="py-op">.</tt><tt id="link-78" class="py-name"><a title="Bio.Emboss.Primer._Primer3RecordConsumer.forward_gc" class="py-name" href="#" onclick="return doclink('link-78', 'forward_gc', 'link-50');">forward_gc</a></tt> <tt class="py-op">=</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">gc</tt><tt class="py-op">)</tt> </tt>
</div><a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> </tt>
<a name="_Primer3RecordConsumer.forward_seq"></a><div id="_Primer3RecordConsumer.forward_seq-def"><a name="L212"></a><tt class="py-lineno">212</tt> <a class="py-toggle" href="#" id="_Primer3RecordConsumer.forward_seq-toggle" onclick="return toggle('_Primer3RecordConsumer.forward_seq');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer._Primer3RecordConsumer-class.html#forward_seq">forward_seq</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">seq</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Primer3RecordConsumer.forward_seq-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Primer3RecordConsumer.forward_seq-expanded"><a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cur_primer</tt><tt class="py-op">.</tt><tt id="link-79" class="py-name"><a title="Bio.Emboss.Primer._Primer3RecordConsumer.forward_seq" class="py-name" href="#" onclick="return doclink('link-79', 'forward_seq', 'link-46');">forward_seq</a></tt> <tt class="py-op">=</tt> <tt id="link-80" class="py-name" targets="Method Bio.GFF.Feature.seq()=Bio.GFF.Feature-class.html#seq,Method Bio.GFF.FeatureAggregate.seq()=Bio.GFF.FeatureAggregate-class.html#seq,Variable BioSQL.BioSeq.DBSeqRecord.seq=BioSQL.BioSeq.DBSeqRecord-class.html#seq"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-80', 'seq', 'link-80');">seq</a></tt> </tt>
</div><a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> </tt>
<a name="_Primer3RecordConsumer.reverse_start"></a><div id="_Primer3RecordConsumer.reverse_start-def"><a name="L215"></a><tt class="py-lineno">215</tt> <a class="py-toggle" href="#" id="_Primer3RecordConsumer.reverse_start-toggle" onclick="return toggle('_Primer3RecordConsumer.reverse_start');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer._Primer3RecordConsumer-class.html#reverse_start">reverse_start</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">start</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Primer3RecordConsumer.reverse_start-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Primer3RecordConsumer.reverse_start-expanded"><a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cur_primer</tt><tt class="py-op">.</tt><tt id="link-81" class="py-name"><a title="Bio.Emboss.Primer._Primer3RecordConsumer.reverse_start" class="py-name" href="#" onclick="return doclink('link-81', 'reverse_start', 'link-52');">reverse_start</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-82" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-82', 'start', 'link-74');">start</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> </tt>
<a name="_Primer3RecordConsumer.reverse_length"></a><div id="_Primer3RecordConsumer.reverse_length-def"><a name="L218"></a><tt class="py-lineno">218</tt> <a class="py-toggle" href="#" id="_Primer3RecordConsumer.reverse_length-toggle" onclick="return toggle('_Primer3RecordConsumer.reverse_length');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer._Primer3RecordConsumer-class.html#reverse_length">reverse_length</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">length</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Primer3RecordConsumer.reverse_length-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Primer3RecordConsumer.reverse_length-expanded"><a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cur_primer</tt><tt class="py-op">.</tt><tt id="link-83" class="py-name"><a title="Bio.Emboss.Primer._Primer3RecordConsumer.reverse_length" class="py-name" href="#" onclick="return doclink('link-83', 'reverse_length', 'link-53');">reverse_length</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-84" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-84', 'length', 'link-20');">length</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> </tt>
<a name="_Primer3RecordConsumer.reverse_tm"></a><div id="_Primer3RecordConsumer.reverse_tm-def"><a name="L221"></a><tt class="py-lineno">221</tt> <a class="py-toggle" href="#" id="_Primer3RecordConsumer.reverse_tm-toggle" onclick="return toggle('_Primer3RecordConsumer.reverse_tm');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer._Primer3RecordConsumer-class.html#reverse_tm">reverse_tm</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">tm</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Primer3RecordConsumer.reverse_tm-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Primer3RecordConsumer.reverse_tm-expanded"><a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cur_primer</tt><tt class="py-op">.</tt><tt id="link-85" class="py-name"><a title="Bio.Emboss.Primer._Primer3RecordConsumer.reverse_tm" class="py-name" href="#" onclick="return doclink('link-85', 'reverse_tm', 'link-54');">reverse_tm</a></tt> <tt class="py-op">=</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">tm</tt><tt class="py-op">)</tt> </tt>
</div><a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> </tt>
<a name="_Primer3RecordConsumer.reverse_gc"></a><div id="_Primer3RecordConsumer.reverse_gc-def"><a name="L224"></a><tt class="py-lineno">224</tt> <a class="py-toggle" href="#" id="_Primer3RecordConsumer.reverse_gc-toggle" onclick="return toggle('_Primer3RecordConsumer.reverse_gc');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer._Primer3RecordConsumer-class.html#reverse_gc">reverse_gc</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">gc</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Primer3RecordConsumer.reverse_gc-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Primer3RecordConsumer.reverse_gc-expanded"><a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cur_primer</tt><tt class="py-op">.</tt><tt id="link-86" class="py-name"><a title="Bio.Emboss.Primer._Primer3RecordConsumer.reverse_gc" class="py-name" href="#" onclick="return doclink('link-86', 'reverse_gc', 'link-55');">reverse_gc</a></tt> <tt class="py-op">=</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">gc</tt><tt class="py-op">)</tt> </tt>
</div><a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> </tt>
<a name="_Primer3RecordConsumer.reverse_seq"></a><div id="_Primer3RecordConsumer.reverse_seq-def"><a name="L227"></a><tt class="py-lineno">227</tt> <a class="py-toggle" href="#" id="_Primer3RecordConsumer.reverse_seq-toggle" onclick="return toggle('_Primer3RecordConsumer.reverse_seq');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer._Primer3RecordConsumer-class.html#reverse_seq">reverse_seq</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">seq</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Primer3RecordConsumer.reverse_seq-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Primer3RecordConsumer.reverse_seq-expanded"><a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cur_primer</tt><tt class="py-op">.</tt><tt id="link-87" class="py-name"><a title="Bio.Emboss.Primer._Primer3RecordConsumer.reverse_seq" class="py-name" href="#" onclick="return doclink('link-87', 'reverse_seq', 'link-51');">reverse_seq</a></tt> <tt class="py-op">=</tt> <tt id="link-88" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-88', 'seq', 'link-80');">seq</a></tt> </tt>
</div><a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> </tt>
<a name="_Primer3RecordConsumer.internal_start"></a><div id="_Primer3RecordConsumer.internal_start-def"><a name="L230"></a><tt class="py-lineno">230</tt> <a class="py-toggle" href="#" id="_Primer3RecordConsumer.internal_start-toggle" onclick="return toggle('_Primer3RecordConsumer.internal_start');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer._Primer3RecordConsumer-class.html#internal_start">internal_start</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">start</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Primer3RecordConsumer.internal_start-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Primer3RecordConsumer.internal_start-expanded"><a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cur_primer</tt><tt class="py-op">.</tt><tt id="link-89" class="py-name" targets="Method Bio.Emboss.Primer._Primer3RecordConsumer.internal_start()=Bio.Emboss.Primer._Primer3RecordConsumer-class.html#internal_start"><a title="Bio.Emboss.Primer._Primer3RecordConsumer.internal_start" class="py-name" href="#" onclick="return doclink('link-89', 'internal_start', 'link-89');">internal_start</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-90" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-90', 'start', 'link-74');">start</a></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="_Primer3RecordConsumer.internal_length"></a><div id="_Primer3RecordConsumer.internal_length-def"><a name="L233"></a><tt class="py-lineno">233</tt> <a class="py-toggle" href="#" id="_Primer3RecordConsumer.internal_length-toggle" onclick="return toggle('_Primer3RecordConsumer.internal_length');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer._Primer3RecordConsumer-class.html#internal_length">internal_length</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">length</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Primer3RecordConsumer.internal_length-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Primer3RecordConsumer.internal_length-expanded"><a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cur_primer</tt><tt class="py-op">.</tt><tt id="link-91" class="py-name" targets="Method Bio.Emboss.Primer._Primer3RecordConsumer.internal_length()=Bio.Emboss.Primer._Primer3RecordConsumer-class.html#internal_length"><a title="Bio.Emboss.Primer._Primer3RecordConsumer.internal_length" class="py-name" href="#" onclick="return doclink('link-91', 'internal_length', 'link-91');">internal_length</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-92" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-92', 'length', 'link-20');">length</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> </tt>
<a name="_Primer3RecordConsumer.internal_tm"></a><div id="_Primer3RecordConsumer.internal_tm-def"><a name="L236"></a><tt class="py-lineno">236</tt> <a class="py-toggle" href="#" id="_Primer3RecordConsumer.internal_tm-toggle" onclick="return toggle('_Primer3RecordConsumer.internal_tm');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer._Primer3RecordConsumer-class.html#internal_tm">internal_tm</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">tm</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Primer3RecordConsumer.internal_tm-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Primer3RecordConsumer.internal_tm-expanded"><a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cur_primer</tt><tt class="py-op">.</tt><tt id="link-93" class="py-name" targets="Method Bio.Emboss.Primer._Primer3RecordConsumer.internal_tm()=Bio.Emboss.Primer._Primer3RecordConsumer-class.html#internal_tm"><a title="Bio.Emboss.Primer._Primer3RecordConsumer.internal_tm" class="py-name" href="#" onclick="return doclink('link-93', 'internal_tm', 'link-93');">internal_tm</a></tt> <tt class="py-op">=</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">tm</tt><tt class="py-op">)</tt> </tt>
</div><a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> </tt>
<a name="_Primer3RecordConsumer.internal_gc"></a><div id="_Primer3RecordConsumer.internal_gc-def"><a name="L239"></a><tt class="py-lineno">239</tt> <a class="py-toggle" href="#" id="_Primer3RecordConsumer.internal_gc-toggle" onclick="return toggle('_Primer3RecordConsumer.internal_gc');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer._Primer3RecordConsumer-class.html#internal_gc">internal_gc</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">gc</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Primer3RecordConsumer.internal_gc-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Primer3RecordConsumer.internal_gc-expanded"><a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cur_primer</tt><tt class="py-op">.</tt><tt id="link-94" class="py-name" targets="Method Bio.Emboss.Primer._Primer3RecordConsumer.internal_gc()=Bio.Emboss.Primer._Primer3RecordConsumer-class.html#internal_gc"><a title="Bio.Emboss.Primer._Primer3RecordConsumer.internal_gc" class="py-name" href="#" onclick="return doclink('link-94', 'internal_gc', 'link-94');">internal_gc</a></tt> <tt class="py-op">=</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">gc</tt><tt class="py-op">)</tt> </tt>
</div><a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> </tt>
<a name="_Primer3RecordConsumer.internal_seq"></a><div id="_Primer3RecordConsumer.internal_seq-def"><a name="L242"></a><tt class="py-lineno">242</tt> <a class="py-toggle" href="#" id="_Primer3RecordConsumer.internal_seq-toggle" onclick="return toggle('_Primer3RecordConsumer.internal_seq');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer._Primer3RecordConsumer-class.html#internal_seq">internal_seq</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">seq</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Primer3RecordConsumer.internal_seq-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Primer3RecordConsumer.internal_seq-expanded"><a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cur_primer</tt><tt class="py-op">.</tt><tt id="link-95" class="py-name" targets="Method Bio.Emboss.Primer._Primer3RecordConsumer.internal_seq()=Bio.Emboss.Primer._Primer3RecordConsumer-class.html#internal_seq"><a title="Bio.Emboss.Primer._Primer3RecordConsumer.internal_seq" class="py-name" href="#" onclick="return doclink('link-95', 'internal_seq', 'link-95');">internal_seq</a></tt> <tt class="py-op">=</tt> <tt id="link-96" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-96', 'seq', 'link-80');">seq</a></tt> </tt>
</div><a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> </tt>
<a name="_Primer3RecordConsumer.end_record"></a><div id="_Primer3RecordConsumer.end_record-def"><a name="L245"></a><tt class="py-lineno">245</tt> <a class="py-toggle" href="#" id="_Primer3RecordConsumer.end_record-toggle" onclick="return toggle('_Primer3RecordConsumer.end_record');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer._Primer3RecordConsumer-class.html#end_record">end_record</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="_Primer3RecordConsumer.end_record-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Primer3RecordConsumer.end_record-expanded"><a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-97" class="py-name"><a title="Bio.Emboss.Primer._Primer3RecordConsumer._add_last_primer" class="py-name" href="#" onclick="return doclink('link-97', '_add_last_primer', 'link-68');">_add_last_primer</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"> </tt>
<a name="_Primer3Scanner"></a><div id="_Primer3Scanner-def"><a name="L248"></a><tt class="py-lineno">248</tt> <a class="py-toggle" href="#" id="_Primer3Scanner-toggle" onclick="return toggle('_Primer3Scanner');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Emboss.Primer._Primer3Scanner-class.html">_Primer3Scanner</a><tt class="py-op">:</tt> </tt>
</div><div id="_Primer3Scanner-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_Primer3Scanner-expanded"><a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> <tt class="py-docstring">"""Scan output from the primer3 program.</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="_Primer3Scanner.__init__"></a><div id="_Primer3Scanner.__init__-def"><a name="L251"></a><tt class="py-lineno">251</tt> <a class="py-toggle" href="#" id="_Primer3Scanner.__init__-toggle" onclick="return toggle('_Primer3Scanner.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer._Primer3Scanner-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="_Primer3Scanner.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Primer3Scanner.__init__-expanded"><a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">interest_tags</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-string">"comments"</tt><tt class="py-op">,</tt> <tt class="py-string">"single_primer_line"</tt><tt class="py-op">,</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> <tt class="py-string">"start_primer"</tt><tt class="py-op">,</tt> <tt class="py-string">"product_size"</tt><tt class="py-op">,</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"> <tt class="py-string">"forward_start"</tt><tt class="py-op">,</tt> <tt class="py-string">"forward_length"</tt><tt class="py-op">,</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"> <tt class="py-string">"forward_tm"</tt><tt class="py-op">,</tt> <tt class="py-string">"forward_gc"</tt><tt class="py-op">,</tt> <tt class="py-string">"forward_seq"</tt><tt class="py-op">,</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> <tt class="py-string">"reverse_start"</tt><tt class="py-op">,</tt> <tt class="py-string">"reverse_length"</tt><tt class="py-op">,</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"> <tt class="py-string">"reverse_tm"</tt><tt class="py-op">,</tt> <tt class="py-string">"reverse_gc"</tt><tt class="py-op">,</tt> <tt class="py-string">"reverse_seq"</tt><tt class="py-op">,</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> <tt class="py-string">"internal_start"</tt><tt class="py-op">,</tt> <tt class="py-string">"internal_length"</tt><tt class="py-op">,</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> <tt class="py-string">"internal_tm"</tt><tt class="py-op">,</tt> <tt class="py-string">"internal_gc"</tt><tt class="py-op">,</tt> <tt class="py-string">"internal_seq"</tt><tt class="py-op">,</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"> <tt class="py-string">"end_record"</tt><tt class="py-op">]</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> <tt class="py-name">expression</tt> <tt class="py-op">=</tt> <tt id="link-98" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-98', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-99" class="py-name"><a title="Martel.select_names" class="py-name" href="#" onclick="return doclink('link-99', 'select_names', 'link-35');">select_names</a></tt><tt class="py-op">(</tt><tt id="link-100" class="py-name"><a title="Bio.Emboss.primer3_format" class="py-name" href="#" onclick="return doclink('link-100', 'primer3_format', 'link-10');">primer3_format</a></tt><tt class="py-op">.</tt><tt id="link-101" 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-101', 'record', 'link-37');">record</a></tt><tt class="py-op">,</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">interest_tags</tt><tt class="py-op">)</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</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">expression</tt><tt class="py-op">.</tt><tt id="link-102" class="py-name"><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-102', 'make_parser', 'link-38');">make_parser</a></tt><tt class="py-op">(</tt><tt class="py-name">debug_level</tt> <tt class="py-op">=</tt> <tt class="py-name">debug</tt><tt class="py-op">)</tt> </tt>
</div><a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"> </tt>
<a name="_Primer3Scanner.feed"></a><div id="_Primer3Scanner.feed-def"><a name="L266"></a><tt class="py-lineno">266</tt> <a class="py-toggle" href="#" id="_Primer3Scanner.feed-toggle" onclick="return toggle('_Primer3Scanner.feed');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer._Primer3Scanner-class.html#feed">feed</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">handle</tt><tt class="py-op">,</tt> <tt class="py-param">consumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Primer3Scanner.feed-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Primer3Scanner.feed-expanded"><a name="L267"></a><tt class="py-lineno">267</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 id="link-103" class="py-name"><a title="Bio.ParserSupport.EventGenerator" class="py-name" href="#" onclick="return doclink('link-103', 'EventGenerator', 'link-8');">EventGenerator</a></tt><tt class="py-op">(</tt><tt class="py-name">consumer</tt><tt class="py-op">,</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">interest_tags</tt><tt class="py-op">,</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"> <tt id="link-104" class="py-name"><a title="Bio.Emboss.Primer._strip_and_combine" class="py-name" href="#" onclick="return doclink('link-104', '_strip_and_combine', 'link-40');">_strip_and_combine</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</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">setErrorHandler</tt><tt class="py-op">(</tt><tt class="py-name">handler</tt><tt class="py-op">.</tt><tt class="py-name">ErrorHandler</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</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-105" class="py-name"><a title="Bio.EUtils.POM.POMDocument.parseFile
Martel.Parser.HeaderFooterParser.parseFile
Martel.Parser.Parser.parseFile
Martel.Parser.RecordParser.parseFile" class="py-name" href="#" onclick="return doclink('link-105', 'parseFile', 'link-41');">parseFile</a></tt><tt class="py-op">(</tt><tt id="link-106" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-106', 'handle', 'link-18');">handle</a></tt><tt class="py-op">)</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-107" class="py-name"><a title="Bio.Emboss.Primer._Primer3RecordConsumer.end_record
Bio.Emboss.Primer._PrimerSearchRecordConsumer.end_record
Bio.Medline._RecordConsumer.end_record
Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder.end_record
Bio.PopGen.FDist._RecordConsumer.end_record
Bio.PopGen.GenePop._RecordConsumer.end_record
Bio.Prosite.Prodoc._RecordConsumer.end_record
Bio.Prosite._RecordConsumer.end_record
Bio.SwissProt.SProt._RecordConsumer.end_record
Bio.SwissProt.SProt._SequenceConsumer.end_record
Bio.builders.SeqRecord.sequence.BuildSeqRecord.end_record" class="py-name" href="#" onclick="return doclink('link-107', 'end_record', 'link-43');">end_record</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> </tt>
<a name="_strip_and_combine"></a><div id="_strip_and_combine-def"><a name="L275"></a><tt class="py-lineno">275</tt> <a class="py-toggle" href="#" id="_strip_and_combine-toggle" onclick="return toggle('_strip_and_combine');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Emboss.Primer-module.html#_strip_and_combine">_strip_and_combine</a><tt class="py-op">(</tt><tt class="py-param">line_list</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_strip_and_combine-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_strip_and_combine-expanded"><a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"> <tt class="py-docstring">"""Combine multiple lines of content separated by spaces.</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> <tt class="py-comment"># first strip out extra whitespace</tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">stripped_line_list</tt> <tt class="py-op">=</tt> <tt id="link-108" class="py-name" targets="Method Bio.GFF.FeatureAggregate.map()=Bio.GFF.FeatureAggregate-class.html#map"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-108', 'map', 'link-108');">map</a></tt><tt class="py-op">(</tt><tt class="py-name">string</tt><tt class="py-op">.</tt><tt id="link-109" 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-109', 'strip', 'link-109');">strip</a></tt><tt class="py-op">,</tt> <tt class="py-name">line_list</tt><tt class="py-op">)</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> <tt class="py-comment"># now combine everything with spaces</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">stripped_line_list</tt><tt class="py-op">,</tt> <tt class="py-string">' '</tt><tt class="py-op">)</tt> </tt>
</div><a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"> </tt><script type="text/javascript">
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