<?xml version="1.0" encoding="ascii"?> <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> <head> <title>Bio.SeqIO.InsdcIO</title> <link rel="stylesheet" href="epydoc.css" type="text/css" /> <script type="text/javascript" src="epydoc.js"></script> </head> <body bgcolor="white" text="black" link="blue" vlink="#204080" alink="#204080"> <!-- ==================== NAVIGATION BAR ==================== --> <table class="navbar" border="0" width="100%" cellpadding="0" bgcolor="#a0c0ff" cellspacing="0"> <tr valign="middle"> <!-- Tree link --> <th> <a href="module-tree.html">Trees</a> </th> <!-- Index link --> <th> <a href="identifier-index.html">Indices</a> </th> <!-- Help link --> <th> <a href="help.html">Help</a> </th> <th class="navbar" width="100%"></th> </tr> </table> <table width="100%" cellpadding="0" cellspacing="0"> <tr valign="top"> <td width="100%"> <span class="breadcrumbs"> <a href="Bio-module.html">Package Bio</a> :: <a href="Bio.SeqIO-module.html">Package SeqIO</a> :: Module InsdcIO </span> </td> <td> <table cellpadding="0" cellspacing="0"> <!-- hide/show private --> <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink" onclick="toggle_private();">hide private</a>]</span></td></tr> <tr><td align="right"><span class="options" >[<a href="frames.html" target="_top">frames</a >] | <a href="Bio.SeqIO.InsdcIO-module.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== MODULE DESCRIPTION ==================== --> <h1 class="epydoc">Module InsdcIO</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.SeqIO.InsdcIO-pysrc.html">source code</a></span></p> <p>Bio.SeqIO support for the "genbank" and "embl" file formats.</p> <p>You are expected to use this module via the Bio.SeqIO functions. Note that internally this module calls Bio.GenBank to do the actual parsing of both GenBank and EMBL files.</p> <p>See also:</p> <p>International Nucleotide Sequence Database Collaboration http://www.insdc.org/</p> <p>GenBank http://www.ncbi.nlm.nih.gov/Genbank/</p> <p>EMBL Nucleotide Sequence Database http://www.ebi.ac.uk/embl/</p> <p>DDBJ (DNA Data Bank of Japan) http://www.ddbj.nig.ac.jp/</p> <!-- ==================== FUNCTIONS ==================== --> <a name="section-Functions"></a> <table class="summary" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr bgcolor="#70b0f0" class="table-header"> <td colspan="2" class="table-header"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr valign="top"> <td align="left"><span class="table-header">Functions</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-Functions" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.SeqIO.InsdcIO-module.html#GenBankIterator" class="summary-sig-name">GenBankIterator</a>(<span class="summary-sig-arg">handle</span>)</span><br /> Breaks up a Genbank file into SeqRecord objects.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SeqIO.InsdcIO-pysrc.html#GenBankIterator">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.SeqIO.InsdcIO-module.html#EmblIterator" class="summary-sig-name">EmblIterator</a>(<span class="summary-sig-arg">handle</span>)</span><br /> Breaks up an EMBL file into SeqRecord objects.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SeqIO.InsdcIO-pysrc.html#EmblIterator">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.SeqIO.InsdcIO-module.html#GenBankCdsFeatureIterator" class="summary-sig-name">GenBankCdsFeatureIterator</a>(<span class="summary-sig-arg">handle</span>, <span class="summary-sig-arg">alphabet</span>=<span class="summary-sig-default">ProteinAlphabet()</span>)</span><br /> Breaks up a Genbank file into SeqRecord objects for each CDS feature.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SeqIO.InsdcIO-pysrc.html#GenBankCdsFeatureIterator">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.SeqIO.InsdcIO-module.html#EmblCdsFeatureIterator" class="summary-sig-name">EmblCdsFeatureIterator</a>(<span class="summary-sig-arg">handle</span>, <span class="summary-sig-arg">alphabet</span>=<span class="summary-sig-default">ProteinAlphabet()</span>)</span><br /> Breaks up a EMBL file into SeqRecord objects for each CDS feature.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SeqIO.InsdcIO-pysrc.html#EmblCdsFeatureIterator">source code</a></span> </td> </tr> </table> </td> </tr> </table> <!-- ==================== FUNCTION DETAILS ==================== --> <a name="section-FunctionDetails"></a> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr bgcolor="#70b0f0" class="table-header"> <td colspan="2" class="table-header"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr valign="top"> <td align="left"><span class="table-header">Function Details</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-FunctionDetails" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> </table> <a name="GenBankIterator"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">GenBankIterator</span>(<span class="sig-arg">handle</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.SeqIO.InsdcIO-pysrc.html#GenBankIterator">source code</a></span> </td> </tr></table> <p>Breaks up a Genbank file into SeqRecord objects.</p> <p>Every section from the LOCUS line to the terminating // becomes a single SeqRecord with associated annotation and features.</p> <p>Note that for genomes or chromosomes, there is typically only one record.</p> <dl class="fields"> </dl> </td></tr></table> </div> <a name="EmblIterator"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">EmblIterator</span>(<span class="sig-arg">handle</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.SeqIO.InsdcIO-pysrc.html#EmblIterator">source code</a></span> </td> </tr></table> <p>Breaks up an EMBL file into SeqRecord objects.</p> <p>Every section from the LOCUS line to the terminating // becomes a single SeqRecord with associated annotation and features.</p> <p>Note that for genomes or chromosomes, there is typically only one record.</p> <dl class="fields"> </dl> </td></tr></table> </div> <a name="GenBankCdsFeatureIterator"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">GenBankCdsFeatureIterator</span>(<span class="sig-arg">handle</span>, <span class="sig-arg">alphabet</span>=<span class="sig-default">ProteinAlphabet()</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.SeqIO.InsdcIO-pysrc.html#GenBankCdsFeatureIterator">source code</a></span> </td> </tr></table> <p>Breaks up a Genbank file into SeqRecord objects for each CDS feature.</p> <p>Every section from the LOCUS line to the terminating // can contain many CDS features. These are returned as with the stated amino acid translation sequence (if given).</p> <dl class="fields"> </dl> </td></tr></table> </div> <a name="EmblCdsFeatureIterator"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">EmblCdsFeatureIterator</span>(<span class="sig-arg">handle</span>, <span class="sig-arg">alphabet</span>=<span class="sig-default">ProteinAlphabet()</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.SeqIO.InsdcIO-pysrc.html#EmblCdsFeatureIterator">source code</a></span> </td> </tr></table> <p>Breaks up a EMBL file into SeqRecord objects for each CDS feature.</p> <p>Every section from the LOCUS line to the terminating // can contain many CDS features. These are returned as with the stated amino acid translation sequence (if given).</p> <dl class="fields"> </dl> </td></tr></table> </div> <br /> <!-- ==================== NAVIGATION BAR ==================== --> <table class="navbar" border="0" width="100%" cellpadding="0" bgcolor="#a0c0ff" cellspacing="0"> <tr valign="middle"> <!-- Tree link --> <th> <a href="module-tree.html">Trees</a> </th> <!-- Index link --> <th> <a href="identifier-index.html">Indices</a> </th> <!-- Help link --> <th> <a href="help.html">Help</a> </th> <th class="navbar" width="100%"></th> </tr> </table> <table border="0" cellpadding="0" cellspacing="0" width="100%%"> <tr> <td align="left" class="footer"> Generated by Epydoc 3.0.1 on Mon Sep 15 09:26:25 2008 </td> <td align="right" class="footer"> <a target="mainFrame" href="http://epydoc.sourceforge.net" >http://epydoc.sourceforge.net</a> </td> </tr> </table> <script type="text/javascript"> <!-- // Private objects are initially displayed (because if // javascript is turned off then we want them to be // visible); but by default, we want to hide them. 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