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<a href="Bio-module.html">Package Bio</a> ::
Module EZRetrieve
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<h1 class="epydoc">Source Code for <a href="Bio.EZRetrieve-module.html">Module Bio.EZRetrieve</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-docstring">"""This module contains code to access EZRetrieve.</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-docstring">Functions:</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-docstring">retrieve_single Retrieve a single sequence from EZRetrieve.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-docstring">parse_single Parse the results from EZRetrieve into FASTA format.</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"> </tt>
<a name="retrieve_single"></a><div id="retrieve_single-def"><a name="L9"></a><tt class="py-lineno"> 9</tt> <a class="py-toggle" href="#" id="retrieve_single-toggle" onclick="return toggle('retrieve_single');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EZRetrieve-module.html#retrieve_single">retrieve_single</a><tt class="py-op">(</tt><tt class="py-param">id</tt><tt class="py-op">,</tt> <tt class="py-param">from_</tt><tt class="py-op">,</tt> <tt class="py-param">to</tt><tt class="py-op">,</tt> <tt class="py-param">retrieve_by</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">organism</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"> <tt class="py-param">parse_results</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="retrieve_single-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="retrieve_single-expanded"><a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">urllib</tt> </tt>
<a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"> </tt>
<a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"> <tt class="py-name">CGI</tt> <tt class="py-op">=</tt> <tt class="py-string">"http://siriusb.umdnj.edu:18080/EZRetrieve/single_r_run.jsp"</tt> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"> <tt class="py-name">org2value</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">"Hs"</tt> <tt class="py-op">:</tt> <tt class="py-string">"0"</tt><tt class="py-op">,</tt> <tt class="py-string">"Mm"</tt> <tt class="py-op">:</tt> <tt class="py-string">"1"</tt><tt class="py-op">,</tt> <tt class="py-string">"Rn"</tt> <tt class="py-op">:</tt> <tt class="py-number">2</tt><tt class="py-op">}</tt> </tt>
<a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"> <tt id="link-0" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.organism()=Bio.GenBank._FeatureConsumer-class.html#organism,Method Bio.GenBank._RecordConsumer.organism()=Bio.GenBank._RecordConsumer-class.html#organism,Variable Bio.expressions.embl.embl65.organism=Bio.expressions.embl.embl65-module.html#organism,Variable Bio.expressions.genbank.organism=Bio.expressions.genbank-module.html#organism"><a title="Bio.GenBank._FeatureConsumer.organism
Bio.GenBank._RecordConsumer.organism
Bio.expressions.embl.embl65.organism
Bio.expressions.genbank.organism" class="py-name" href="#" onclick="return doclink('link-0', 'organism', 'link-0');">organism</a></tt> <tt class="py-op">=</tt> <tt id="link-1" class="py-name"><a title="Bio.GenBank._FeatureConsumer.organism
Bio.GenBank._RecordConsumer.organism
Bio.expressions.embl.embl65.organism
Bio.expressions.genbank.organism" class="py-name" href="#" onclick="return doclink('link-1', 'organism', 'link-0');">organism</a></tt> <tt class="py-keyword">or</tt> <tt class="py-string">"Hs"</tt> </tt>
<a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-2" class="py-name"><a title="Bio.GenBank._FeatureConsumer.organism
Bio.GenBank._RecordConsumer.organism
Bio.expressions.embl.embl65.organism
Bio.expressions.genbank.organism" class="py-name" href="#" onclick="return doclink('link-2', 'organism', 'link-0');">organism</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">org2value</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-name">acctype2value</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">"genbank"</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">"unigene"</tt><tt class="py-op">:</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-string">"locuslink"</tt><tt class="py-op">:</tt><tt class="py-number">2</tt><tt class="py-op">,</tt> <tt class="py-string">"image"</tt><tt class="py-op">:</tt><tt class="py-number">3</tt><tt class="py-op">}</tt> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"> <tt class="py-name">retrieve_by</tt> <tt class="py-op">=</tt> <tt class="py-name">retrieve_by</tt> <tt class="py-keyword">or</tt> <tt class="py-string">"GenBank"</tt> </tt>
<a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"> <tt class="py-name">retrieve_by</tt> <tt class="py-op">=</tt> <tt class="py-name">retrieve_by</tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">retrieve_by</tt> <tt class="py-keyword">in</tt> <tt class="py-name">acctype2value</tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"> <tt class="py-name">params</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"> <tt class="py-string">"input"</tt> <tt class="py-op">:</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-3" class="py-name" targets="Variable Bio.Data.CodonTable.id=Bio.Data.CodonTable-module.html#id,Variable Bio.Encodings.IUPACEncoding.id=Bio.Encodings.IUPACEncoding-module.html#id,Method Bio.GFF.Feature.id()=Bio.GFF.Feature-class.html#id"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-3', 'id', 'link-3');">id</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"> <tt class="py-string">"from"</tt> <tt class="py-op">:</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">from_</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"> <tt class="py-string">"to"</tt> <tt class="py-op">:</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">to</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"> <tt class="py-string">"org"</tt> <tt class="py-op">:</tt> <tt class="py-name">org2value</tt><tt class="py-op">[</tt><tt id="link-4" class="py-name"><a title="Bio.GenBank._FeatureConsumer.organism
Bio.GenBank._RecordConsumer.organism
Bio.expressions.embl.embl65.organism
Bio.expressions.genbank.organism" class="py-name" href="#" onclick="return doclink('link-4', 'organism', 'link-0');">organism</a></tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"> <tt class="py-string">"AccType"</tt> <tt class="py-op">:</tt> <tt class="py-name">acctype2value</tt><tt class="py-op">[</tt><tt class="py-name">retrieve_by</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"> <tt class="py-op">}</tt> </tt>
<a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"> <tt class="py-name">options</tt> <tt class="py-op">=</tt> <tt class="py-name">urllib</tt><tt class="py-op">.</tt><tt class="py-name">urlencode</tt><tt class="py-op">(</tt><tt class="py-name">params</tt><tt class="py-op">)</tt> </tt>
<a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"> <tt id="link-5" 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-5', 'handle', 'link-5');">handle</a></tt> <tt class="py-op">=</tt> <tt class="py-name">urllib</tt><tt class="py-op">.</tt><tt class="py-name">urlopen</tt><tt class="py-op">(</tt><tt class="py-name">CGI</tt><tt class="py-op">,</tt> <tt class="py-name">options</tt><tt class="py-op">)</tt> </tt>
<a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">parse_results</tt><tt class="py-op">:</tt> </tt>
<a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"> <tt class="py-name">results</tt> <tt class="py-op">=</tt> <tt id="link-6" class="py-name" targets="Function Bio.EZRetrieve.parse_single()=Bio.EZRetrieve-module.html#parse_single"><a title="Bio.EZRetrieve.parse_single" class="py-name" href="#" onclick="return doclink('link-6', 'parse_single', 'link-6');">parse_single</a></tt><tt class="py-op">(</tt><tt id="link-7" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-7', 'handle', 'link-5');">handle</a></tt><tt class="py-op">)</tt> </tt>
<a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"> <tt class="py-name">results</tt> <tt class="py-op">=</tt> <tt id="link-8" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-8', 'handle', 'link-5');">handle</a></tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Method Bio.AlignAce.Motif.Motif.read()=Bio.AlignAce.Motif.Motif-class.html#read,Function Bio.AlignIO.read()=Bio.AlignIO-module.html#read,Function Bio.Cluster.read()=Bio.Cluster-module.html#read,Method Bio.EUtils.ReseekFile.ReseekFile.read()=Bio.EUtils.ReseekFile.ReseekFile-class.html#read,Function Bio.Entrez.read()=Bio.Entrez-module.html#read,Method Bio.File.SGMLHandle.read()=Bio.File.SGMLHandle-class.html#read,Method Bio.File.UndoHandle.read()=Bio.File.UndoHandle-class.html#read,Method Bio.FilteredReader.FilteredReader.read()=Bio.FilteredReader.FilteredReader-class.html#read,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.read()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#read,Method Bio.Nexus.Nexus.Nexus.read()=Bio.Nexus.Nexus.Nexus-class.html#read,Function Bio.Prosite.Prodoc.read()=Bio.Prosite.Prodoc-module.html#read,Function Bio.Prosite.read()=Bio.Prosite-module.html#read,Method Bio.SGMLExtractor.SGMLExtractorHandle.read()=Bio.SGMLExtractor.SGMLExtractorHandle-class.html#read,Function Bio.SeqIO.read()=Bio.SeqIO-module.html#read,Function Bio.SwissProt.read()=Bio.SwissProt-module.html#read"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-9', 'read', 'link-9');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">results</tt> </tt>
</div><a name="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"> </tt>
<a name="parse_single"></a><div id="parse_single-def"><a name="L38"></a><tt class="py-lineno">38</tt> <a class="py-toggle" href="#" id="parse_single-toggle" onclick="return toggle('parse_single');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EZRetrieve-module.html#parse_single">parse_single</a><tt class="py-op">(</tt><tt class="py-param">handle</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="parse_single-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="parse_single-expanded"><a name="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"> <tt class="py-docstring">"""Return a FASTA-formatted string for the sequence. May raise an</tt> </tt>
<a name="L40"></a><tt class="py-lineno">40</tt> <tt class="py-line"><tt class="py-docstring"> AssertionError if there was a problem retrieving the sequence.</tt> </tt>
<a name="L41"></a><tt class="py-lineno">41</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L42"></a><tt class="py-lineno">42</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L43"></a><tt class="py-lineno">43</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">re</tt> </tt>
<a name="L44"></a><tt class="py-lineno">44</tt> <tt class="py-line"> <tt class="py-name">results</tt> <tt class="py-op">=</tt> <tt id="link-10" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-10', 'handle', 'link-5');">handle</a></tt><tt class="py-op">.</tt><tt id="link-11" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-11', 'read', 'link-9');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L45"></a><tt class="py-lineno">45</tt> <tt class="py-line"> <tt class="py-name">lresults</tt> <tt class="py-op">=</tt> <tt class="py-name">results</tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L46"></a><tt class="py-lineno">46</tt> <tt class="py-line"> </tt>
<a name="L47"></a><tt class="py-lineno">47</tt> <tt class="py-line"> <tt id="link-12" class="py-name" targets="Variable Bio.PDB.Polypeptide.i=Bio.PDB.Polypeptide-module.html#i"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-12', 'i', 'link-12');">i</a></tt> <tt class="py-op">=</tt> <tt class="py-name">results</tt><tt class="py-op">.</tt><tt id="link-13" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.find()=Bio.EUtils.POM.ElementNode-class.html#find,Method Bio.NeuralNetwork.Gene.Motif.MotifFinder.find()=Bio.NeuralNetwork.Gene.Motif.MotifFinder-class.html#find,Method Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find()=Bio.NeuralNetwork.Gene.Schema.SchemaFinder-class.html#find,Method Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find()=Bio.NeuralNetwork.Gene.Signature.SignatureFinder-class.html#find,Method Bio.biblio.Biblio.find()=Bio.biblio.Biblio-class.html#find,Function Bio.triefind.find()=Bio.triefind-module.html#find"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-13', 'find', 'link-13');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">"Error: "</tt><tt class="py-op">)</tt> </tt>
<a name="L48"></a><tt class="py-lineno">48</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-14" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-14', 'i', 'link-12');">i</a></tt> <tt class="py-op">>=</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L49"></a><tt class="py-lineno">49</tt> <tt class="py-line"> <tt class="py-name">j</tt> <tt class="py-op">=</tt> <tt class="py-name">lresults</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name" targets="Method Bio.Crystal.Chain.index()=Bio.Crystal.Chain-class.html#index,Method Bio.EUtils.POM.ElementNode.index()=Bio.EUtils.POM.ElementNode-class.html#index,Method Bio.SCOP.Raf.SeqMap.index()=Bio.SCOP.Raf.SeqMap-class.html#index,Method Bio.Seq.MutableSeq.index()=Bio.Seq.MutableSeq-class.html#index"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-15', 'index', 'link-15');">index</a></tt><tt class="py-op">(</tt><tt class="py-string">"<br>"</tt><tt class="py-op">,</tt> <tt id="link-16" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-16', 'i', 'link-12');">i</a></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">errmsg</tt> <tt class="py-op">=</tt> <tt class="py-name">results</tt><tt class="py-op">[</tt><tt id="link-17" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-17', 'i', 'link-12');">i</a></tt><tt class="py-op">:</tt><tt class="py-name">j</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-18" 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-18', 'strip', 'link-18');">strip</a></tt><tt class="py-op">(</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">raise</tt> <tt class="py-name">AssertionError</tt><tt class="py-op">,</tt> <tt class="py-name">errmsg</tt> </tt>
<a name="L52"></a><tt class="py-lineno">52</tt> <tt class="py-line"> </tt>
<a name="L53"></a><tt class="py-lineno">53</tt> <tt class="py-line"> <tt id="link-19" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-19', 'i', 'link-12');">i</a></tt> <tt class="py-op">=</tt> <tt class="py-name">lresults</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-20', 'find', 'link-13');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">"<b>>"</tt><tt class="py-op">)</tt> </tt>
<a name="L54"></a><tt class="py-lineno">54</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-21" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-21', 'i', 'link-12');">i</a></tt> <tt class="py-op">>=</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">"Couldn't find sequence."</tt> </tt>
<a name="L55"></a><tt class="py-lineno">55</tt> <tt class="py-line"> <tt class="py-name">j</tt> <tt class="py-op">=</tt> <tt class="py-name">lresults</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-22', 'find', 'link-13');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">"<br><br>"</tt><tt class="py-op">,</tt> <tt id="link-23" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-23', 'i', 'link-12');">i</a></tt><tt class="py-op">)</tt> </tt>
<a name="L56"></a><tt class="py-lineno">56</tt> <tt class="py-line"> <tt class="py-name">seqdata</tt> <tt class="py-op">=</tt> <tt class="py-name">results</tt><tt class="py-op">[</tt><tt id="link-24" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-24', 'i', 'link-12');">i</a></tt><tt class="py-op">:</tt><tt class="py-name">j</tt><tt class="py-op">]</tt> </tt>
<a name="L57"></a><tt class="py-lineno">57</tt> <tt class="py-line"> <tt class="py-name">reobj</tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-25" class="py-name" targets="Function Bio.Prosite.Pattern.compile()=Bio.Prosite.Pattern-module.html#compile"><a title="Bio.Prosite.Pattern.compile" class="py-name" href="#" onclick="return doclink('link-25', 'compile', 'link-25');">compile</a></tt><tt class="py-op">(</tt><tt class="py-string">r"<[^>]*>"</tt><tt class="py-op">,</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">IGNORECASE</tt><tt class="py-op">|</tt><tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">DOTALL</tt><tt class="py-op">)</tt> </tt>
<a name="L58"></a><tt class="py-lineno">58</tt> <tt class="py-line"> <tt class="py-name">seqdata</tt> <tt class="py-op">=</tt> <tt class="py-name">reobj</tt><tt class="py-op">.</tt><tt class="py-name">sub</tt><tt class="py-op">(</tt><tt class="py-string">""</tt><tt class="py-op">,</tt> <tt class="py-name">seqdata</tt><tt class="py-op">)</tt> </tt>
<a name="L59"></a><tt class="py-lineno">59</tt> <tt class="py-line"> <tt class="py-name">seqdata</tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">sub</tt><tt class="py-op">(</tt><tt class="py-string">r"\s+"</tt><tt class="py-op">,</tt> <tt class="py-string">r"\n"</tt><tt class="py-op">,</tt> <tt class="py-name">seqdata</tt><tt class="py-op">)</tt> </tt>
<a name="L60"></a><tt class="py-lineno">60</tt> <tt class="py-line"> <tt class="py-name">seqdata</tt> <tt class="py-op">=</tt> <tt class="py-name">seqdata</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-26', 'strip', 'link-18');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">"\n"</tt> </tt>
<a name="L61"></a><tt class="py-lineno">61</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">seqdata</tt> </tt>
</div><a name="L62"></a><tt class="py-lineno">62</tt> <tt class="py-line"> </tt><script type="text/javascript">
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