<?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.SeqFeature.SeqFeature</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.SeqFeature-module.html">Module SeqFeature</a> :: Class SeqFeature </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.SeqFeature.SeqFeature-class.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== CLASS DESCRIPTION ==================== --> <h1 class="epydoc">Class SeqFeature</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.SeqFeature-pysrc.html#SeqFeature">source code</a></span></p> <p>Represent a Sequence Feature on an object.</p> <p>Attributes: o location - the location of the feature on the sequence o type - the specified type of the feature (ie. CDS, exon, repeat...) o location_operator - a string specifying how this SeqFeature may be related to others. For example, in the example GenBank feature shown below, the location_operator would be "join" o strand - A value specifying on which strand (of a DNA sequence, for instance) the feature deals with. 1 indicates the plus strand, -1 indicates the minus strand, 0 indicates both strands, and None indicates that strand doesn't apply (ie. for proteins) or is not known. o id - A string identifier for the feature. o ref - A reference to another sequence. This could be an accession number for some different sequence. o ref_db - A different database for the reference accession number. o qualifier - A dictionary of qualifiers on the feature. These are analagous to the qualifiers from a GenBank feature table. The keys of the dictionary are qualifier names, the values are the qualifier values. o sub_features - Additional SeqFeatures which fall under this 'parent' feature. For instance, if we having something like:</p> <p>CDS join(1..10,30..40,50..60)</p> <p>The the top level feature would be a CDS from 1 to 60, and the sub features would be of 'CDS_join' type and would be from 1 to 10, 30 to 40 and 50 to 60, respectively.</p> <!-- ==================== INSTANCE METHODS ==================== --> <a name="section-InstanceMethods"></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">Instance Methods</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-InstanceMethods" 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="__init__"></a><span class="summary-sig-name">__init__</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">location</span>=<span class="summary-sig-default">None</span>, <span class="summary-sig-arg">type</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>, <span class="summary-sig-arg">location_operator</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>, <span class="summary-sig-arg">strand</span>=<span class="summary-sig-default">None</span>, <span class="summary-sig-arg">id</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string"><unknown id></code><code class="variable-quote">'</code></span>, <span class="summary-sig-arg">qualifiers</span>=<span class="summary-sig-default"><code class="variable-group">{</code><code class="variable-group">}</code></span>, <span class="summary-sig-arg">sub_features</span>=<span class="summary-sig-default"><code class="variable-group">[</code><code class="variable-group">]</code></span>, <span class="summary-sig-arg">ref</span>=<span class="summary-sig-default">None</span>, <span class="summary-sig-arg">ref_db</span>=<span class="summary-sig-default">None</span>)</span><br /> Initialize a SeqFeature on a Sequence.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SeqFeature-pysrc.html#SeqFeature.__init__">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="__str__"></a><span class="summary-sig-name">__str__</span>(<span class="summary-sig-arg">self</span>)</span><br /> Make it easier to debug features.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SeqFeature-pysrc.html#SeqFeature.__str__">source code</a></span> </td> </tr> </table> </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 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 09:26:38 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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