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Module InsdcIO
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<h1 class="epydoc">Source Code for <a href="Bio.SeqIO.InsdcIO-module.html">Module Bio.SeqIO.InsdcIO</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright 2007, 2008 by Peter Cock. All rights reserved.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package..</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring">"""Bio.SeqIO support for the "genbank" and "embl" file formats.</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">You are expected to use this module via the Bio.SeqIO functions.</tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"><tt class="py-docstring">Note that internally this module calls Bio.GenBank to do the actual</tt> </tt>
<a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"><tt class="py-docstring">parsing of both GenBank and EMBL files.</tt> </tt>
<a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"><tt class="py-docstring">See also:</tt> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"><tt class="py-docstring">International Nucleotide Sequence Database Collaboration</tt> </tt>
<a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"><tt class="py-docstring">http://www.insdc.org/</tt> </tt>
<a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"><tt class="py-docstring">GenBank</tt> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"><tt class="py-docstring">http://www.ncbi.nlm.nih.gov/Genbank/</tt> </tt>
<a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"><tt class="py-docstring">EMBL Nucleotide Sequence Database</tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"><tt class="py-docstring">http://www.ebi.ac.uk/embl/</tt> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"><tt class="py-docstring">DDBJ (DNA Data Bank of Japan)</tt> </tt>
<a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"><tt class="py-docstring">http://www.ddbj.nig.ac.jp/</tt> </tt>
<a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"> </tt>
<a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Package Bio.GenBank=Bio.GenBank-module.html"><a title="Bio.GenBank" class="py-name" href="#" onclick="return doclink('link-1', 'GenBank', 'link-1');">GenBank</a></tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Module Bio.AlignAce.Scanner=Bio.AlignAce.Scanner-module.html,Module Bio.GenBank.Scanner=Bio.GenBank.Scanner-module.html"><a title="Bio.AlignAce.Scanner
Bio.GenBank.Scanner" class="py-name" href="#" onclick="return doclink('link-2', 'Scanner', 'link-2');">Scanner</a></tt> <tt class="py-keyword">import</tt> <tt id="link-3" class="py-name" targets="Class Bio.GenBank.Scanner.GenBankScanner=Bio.GenBank.Scanner.GenBankScanner-class.html"><a title="Bio.GenBank.Scanner.GenBankScanner" class="py-name" href="#" onclick="return doclink('link-3', 'GenBankScanner', 'link-3');">GenBankScanner</a></tt><tt class="py-op">,</tt> <tt id="link-4" class="py-name" targets="Class Bio.GenBank.Scanner.EmblScanner=Bio.GenBank.Scanner.EmblScanner-class.html"><a title="Bio.GenBank.Scanner.EmblScanner" class="py-name" href="#" onclick="return doclink('link-4', 'EmblScanner', 'link-4');">EmblScanner</a></tt> </tt>
<a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-5" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-5', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-6" class="py-name" targets="Package Bio.Alphabet=Bio.Alphabet-module.html,Class Bio.Alphabet.Alphabet=Bio.Alphabet.Alphabet-class.html"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-6', 'Alphabet', 'link-6');">Alphabet</a></tt> <tt class="py-keyword">import</tt> <tt id="link-7" class="py-name" targets="Variable Bio.Alphabet.generic_protein=Bio.Alphabet-module.html#generic_protein"><a title="Bio.Alphabet.generic_protein" class="py-name" href="#" onclick="return doclink('link-7', 'generic_protein', 'link-7');">generic_protein</a></tt> </tt>
<a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"> </tt>
<a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"><tt class="py-comment"># NOTE</tt> </tt>
<a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># ====</tt> </tt>
<a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># The "brains" for parsing GenBank and EMBL files (and any</tt> </tt>
<a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># other flat file variants from the INSDC in future) is in</tt> </tt>
<a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Bio.GenBank.Scanner (plus the _FeatureConsumer in Bio.GenBank)</tt> </tt>
<a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="GenBankIterator"></a><div id="GenBankIterator-def"><a name="L37"></a><tt class="py-lineno">37</tt> <a class="py-toggle" href="#" id="GenBankIterator-toggle" onclick="return toggle('GenBankIterator');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqIO.InsdcIO-module.html#GenBankIterator">GenBankIterator</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="GenBankIterator-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="GenBankIterator-expanded"><a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"> <tt class="py-docstring">"""Breaks up a Genbank file into SeqRecord objects.</tt> </tt>
<a name="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L40"></a><tt class="py-lineno">40</tt> <tt class="py-line"><tt class="py-docstring"> Every section from the LOCUS line to the terminating // becomes</tt> </tt>
<a name="L41"></a><tt class="py-lineno">41</tt> <tt class="py-line"><tt class="py-docstring"> a single SeqRecord with associated annotation and features.</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-docstring"> Note that for genomes or chromosomes, there is typically only</tt> </tt>
<a name="L44"></a><tt class="py-lineno">44</tt> <tt class="py-line"><tt class="py-docstring"> one record."""</tt> </tt>
<a name="L45"></a><tt class="py-lineno">45</tt> <tt class="py-line"> <tt class="py-comment">#This calls a generator function:</tt> </tt>
<a name="L46"></a><tt class="py-lineno">46</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt id="link-8" class="py-name"><a title="Bio.GenBank.Scanner.GenBankScanner" class="py-name" href="#" onclick="return doclink('link-8', 'GenBankScanner', 'link-3');">GenBankScanner</a></tt><tt class="py-op">(</tt><tt class="py-name">debug</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Method Bio.GenBank.Scanner.InsdcScanner.parse_records()=Bio.GenBank.Scanner.InsdcScanner-class.html#parse_records"><a title="Bio.GenBank.Scanner.InsdcScanner.parse_records" class="py-name" href="#" onclick="return doclink('link-9', 'parse_records', 'link-9');">parse_records</a></tt><tt class="py-op">(</tt><tt id="link-10" 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-10', 'handle', 'link-10');">handle</a></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="EmblIterator"></a><div id="EmblIterator-def"><a name="L48"></a><tt class="py-lineno">48</tt> <a class="py-toggle" href="#" id="EmblIterator-toggle" onclick="return toggle('EmblIterator');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqIO.InsdcIO-module.html#EmblIterator">EmblIterator</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="EmblIterator-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="EmblIterator-expanded"><a name="L49"></a><tt class="py-lineno">49</tt> <tt class="py-line"> <tt class="py-docstring">"""Breaks up an EMBL file into SeqRecord objects.</tt> </tt>
<a name="L50"></a><tt class="py-lineno">50</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L51"></a><tt class="py-lineno">51</tt> <tt class="py-line"><tt class="py-docstring"> Every section from the LOCUS line to the terminating // becomes</tt> </tt>
<a name="L52"></a><tt class="py-lineno">52</tt> <tt class="py-line"><tt class="py-docstring"> a single SeqRecord with associated annotation and features.</tt> </tt>
<a name="L53"></a><tt class="py-lineno">53</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L54"></a><tt class="py-lineno">54</tt> <tt class="py-line"><tt class="py-docstring"> Note that for genomes or chromosomes, there is typically only</tt> </tt>
<a name="L55"></a><tt class="py-lineno">55</tt> <tt class="py-line"><tt class="py-docstring"> one record."""</tt> </tt>
<a name="L56"></a><tt class="py-lineno">56</tt> <tt class="py-line"> <tt class="py-comment">#This calls a generator function:</tt> </tt>
<a name="L57"></a><tt class="py-lineno">57</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt id="link-11" class="py-name"><a title="Bio.GenBank.Scanner.EmblScanner" class="py-name" href="#" onclick="return doclink('link-11', 'EmblScanner', 'link-4');">EmblScanner</a></tt><tt class="py-op">(</tt><tt class="py-name">debug</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-12" class="py-name"><a title="Bio.GenBank.Scanner.InsdcScanner.parse_records" class="py-name" href="#" onclick="return doclink('link-12', 'parse_records', 'link-9');">parse_records</a></tt><tt class="py-op">(</tt><tt id="link-13" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-13', 'handle', 'link-10');">handle</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L58"></a><tt class="py-lineno">58</tt> <tt class="py-line"> </tt>
<a name="GenBankCdsFeatureIterator"></a><div id="GenBankCdsFeatureIterator-def"><a name="L59"></a><tt class="py-lineno">59</tt> <a class="py-toggle" href="#" id="GenBankCdsFeatureIterator-toggle" onclick="return toggle('GenBankCdsFeatureIterator');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqIO.InsdcIO-module.html#GenBankCdsFeatureIterator">GenBankCdsFeatureIterator</a><tt class="py-op">(</tt><tt class="py-param">handle</tt><tt class="py-op">,</tt> <tt class="py-param">alphabet</tt><tt class="py-op">=</tt><tt id="link-14" class="py-name"><a title="Bio.Alphabet.generic_protein" class="py-name" href="#" onclick="return doclink('link-14', 'generic_protein', 'link-7');">generic_protein</a></tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="GenBankCdsFeatureIterator-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="GenBankCdsFeatureIterator-expanded"><a name="L60"></a><tt class="py-lineno">60</tt> <tt class="py-line"> <tt class="py-docstring">"""Breaks up a Genbank file into SeqRecord objects for each CDS feature.</tt> </tt>
<a name="L61"></a><tt class="py-lineno">61</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L62"></a><tt class="py-lineno">62</tt> <tt class="py-line"><tt class="py-docstring"> Every section from the LOCUS line to the terminating // can contain</tt> </tt>
<a name="L63"></a><tt class="py-lineno">63</tt> <tt class="py-line"><tt class="py-docstring"> many CDS features. These are returned as with the stated amino acid</tt> </tt>
<a name="L64"></a><tt class="py-lineno">64</tt> <tt class="py-line"><tt class="py-docstring"> translation sequence (if given).</tt> </tt>
<a name="L65"></a><tt class="py-lineno">65</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L66"></a><tt class="py-lineno">66</tt> <tt class="py-line"> <tt class="py-comment">#This calls a generator function:</tt> </tt>
<a name="L67"></a><tt class="py-lineno">67</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt id="link-15" class="py-name"><a title="Bio.GenBank.Scanner.GenBankScanner" class="py-name" href="#" onclick="return doclink('link-15', 'GenBankScanner', 'link-3');">GenBankScanner</a></tt><tt class="py-op">(</tt><tt class="py-name">debug</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-16" class="py-name" targets="Method Bio.GenBank.Scanner.InsdcScanner.parse_cds_features()=Bio.GenBank.Scanner.InsdcScanner-class.html#parse_cds_features"><a title="Bio.GenBank.Scanner.InsdcScanner.parse_cds_features" class="py-name" href="#" onclick="return doclink('link-16', 'parse_cds_features', 'link-16');">parse_cds_features</a></tt><tt class="py-op">(</tt><tt id="link-17" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-17', 'handle', 'link-10');">handle</a></tt><tt class="py-op">,</tt> <tt id="link-18" class="py-name" targets="Variable Bio.Prosite.Pattern.Prosite.alphabet=Bio.Prosite.Pattern.Prosite-class.html#alphabet,Function Bio.Std.alphabet()=Bio.Std-module.html#alphabet"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-18', 'alphabet', 'link-18');">alphabet</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L68"></a><tt class="py-lineno">68</tt> <tt class="py-line"> </tt>
<a name="EmblCdsFeatureIterator"></a><div id="EmblCdsFeatureIterator-def"><a name="L69"></a><tt class="py-lineno">69</tt> <a class="py-toggle" href="#" id="EmblCdsFeatureIterator-toggle" onclick="return toggle('EmblCdsFeatureIterator');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqIO.InsdcIO-module.html#EmblCdsFeatureIterator">EmblCdsFeatureIterator</a><tt class="py-op">(</tt><tt class="py-param">handle</tt><tt class="py-op">,</tt> <tt class="py-param">alphabet</tt><tt class="py-op">=</tt><tt id="link-19" class="py-name"><a title="Bio.Alphabet.generic_protein" class="py-name" href="#" onclick="return doclink('link-19', 'generic_protein', 'link-7');">generic_protein</a></tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="EmblCdsFeatureIterator-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="EmblCdsFeatureIterator-expanded"><a name="L70"></a><tt class="py-lineno">70</tt> <tt class="py-line"> <tt class="py-docstring">"""Breaks up a EMBL file into SeqRecord objects for each CDS feature.</tt> </tt>
<a name="L71"></a><tt class="py-lineno">71</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L72"></a><tt class="py-lineno">72</tt> <tt class="py-line"><tt class="py-docstring"> Every section from the LOCUS line to the terminating // can contain</tt> </tt>
<a name="L73"></a><tt class="py-lineno">73</tt> <tt class="py-line"><tt class="py-docstring"> many CDS features. These are returned as with the stated amino acid</tt> </tt>
<a name="L74"></a><tt class="py-lineno">74</tt> <tt class="py-line"><tt class="py-docstring"> translation sequence (if given).</tt> </tt>
<a name="L75"></a><tt class="py-lineno">75</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L76"></a><tt class="py-lineno">76</tt> <tt class="py-line"> <tt class="py-comment">#This calls a generator function:</tt> </tt>
<a name="L77"></a><tt class="py-lineno">77</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt id="link-20" class="py-name"><a title="Bio.GenBank.Scanner.EmblScanner" class="py-name" href="#" onclick="return doclink('link-20', 'EmblScanner', 'link-4');">EmblScanner</a></tt><tt class="py-op">(</tt><tt class="py-name">debug</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-21" class="py-name"><a title="Bio.GenBank.Scanner.InsdcScanner.parse_cds_features" class="py-name" href="#" onclick="return doclink('link-21', 'parse_cds_features', 'link-16');">parse_cds_features</a></tt><tt class="py-op">(</tt><tt id="link-22" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-22', 'handle', 'link-10');">handle</a></tt><tt class="py-op">,</tt> <tt id="link-23" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-23', 'alphabet', 'link-18');">alphabet</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L78"></a><tt class="py-lineno">78</tt> <tt class="py-line"> </tt><script type="text/javascript">
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