<?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.GFF</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> :: Package GFF </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.GFF-module.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== PACKAGE DESCRIPTION ==================== --> <h1 class="epydoc">Package GFF</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.GFF-pysrc.html">source code</a></span></p> <p>Access to General Feature Format databases created with Bio::DB:GFF</p> <p>based on documentation for Lincoln Stein's Perl Bio::DB::GFF</p> <pre class="py-doctest"> <span class="py-prompt">>>> </span><span class="py-keyword">import</span> os <span class="py-prompt">>>> </span><span class="py-keyword">import</span> Bio.GFF <span class="py-prompt">>>> </span>PASSWORD = os.environ[<span class="py-string">'MYSQLPASS'</span>] <span class="py-prompt">>>> </span>DATABASE_GFF = <span class="py-string">'wormbase_ws93'</span> <span class="py-prompt">>>> </span>FASTADIR = <span class="py-string">'/local/wormbase_ws93/'</span> <span class="py-prompt">>>> </span>gff = Bio.GFF.Connection(passwd=PASSWORD, db=DATABASE_GFF, fastadir=FASTADIR)</pre> <hr /> <div class="fields"> <p><strong>Version:</strong> $Revision: 1.8 $ </p> </div><!-- ==================== SUBMODULES ==================== --> <a name="section-Submodules"></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">Submodules</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-Submodules" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> <tr><td class="summary"> <ul class="nomargin"> <li> <strong class="uidlink"><a href="Bio.GFF.GenericTools-module.html">Bio.GFF.GenericTools</a></strong>: <em class="summary">Docstring</em> </li> <li> <strong class="uidlink"><a href="Bio.GFF.binning-module.html">Bio.GFF.binning</a></strong>: <em class="summary">Binning support for Bio.GFF</em> </li> <li> <strong class="uidlink"><a href="Bio.GFF.easy-module.html">Bio.GFF.easy</a></strong>: <em class="summary">Bio.GFF.easy: some functions to ease the use of Biopython</em> </li> </ul></td></tr> </table> <br /> <!-- ==================== CLASSES ==================== --> <a name="section-Classes"></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">Classes</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-Classes" 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"> <a href="Bio.GFF.Segment-class.html" class="summary-name">Segment</a><br /> this will only work for the simplest of easy.Location objects </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.GFF.Connection-class.html" class="summary-name">Connection</a><br /> Connection to GFF database </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.GFF.RetrieveSeqname-class.html" class="summary-name">RetrieveSeqname</a><br /> Singleton: contain records of loaded FASTA files </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.GFF.Feature-class.html" class="summary-name">Feature</a><br /> strand may be: +/0 = Watson -/1 = Crick </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.GFF.FeatureQueryRow-class.html" class="summary-name">FeatureQueryRow</a><br /> row of FeatureQuery results works like a Feature </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.GFF.FeatureQuery-class.html" class="summary-name">FeatureQuery</a><br /> SELECT fdata.fref AS seqname,... </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.GFF.FeatureAggregate-class.html" class="summary-name">FeatureAggregate</a> </td> </tr> </table> <!-- ==================== 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 name="object2fgroup_sql"></a><span class="summary-sig-name">object2fgroup_sql</span>(<span class="summary-sig-arg">object</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.GFF-pysrc.html#object2fgroup_sql">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 name="object_split"></a><span class="summary-sig-name">object_split</span>(<span class="summary-sig-arg">object</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.GFF-pysrc.html#object_split">source code</a></span> </td> </tr> </table> </td> </tr> <tr class="private"> <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 name="_test"></a><span class="summary-sig-name">_test</span>(<span class="summary-sig-arg">*args</span>, <span class="summary-sig-arg">**keywds</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.GFF-pysrc.html#_test">source code</a></span> </td> </tr> </table> </td> </tr> </table> <!-- ==================== VARIABLES ==================== --> <a name="section-Variables"></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">Variables</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-Variables" 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"> <a name="DEFAULT_ALPHABET"></a><span class="summary-name">DEFAULT_ALPHABET</span> = <code title="IUPACUnambiguousDNA()">IUPACUnambiguousDNA()</code> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a name="standard_translator"></a><span class="summary-name">standard_translator</span> = <code title="Translate.unambiguous_dna_by_id [1]">Translate.unambiguous_dna_by_id [1]</code> </td> </tr> </table> <!-- ==================== 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 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