<?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.FeatureAggregate</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.GFF-module.html">Package GFF</a> :: Class FeatureAggregate </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.FeatureAggregate-class.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== CLASS DESCRIPTION ==================== --> <h1 class="epydoc">Class FeatureAggregate</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.GFF-pysrc.html#FeatureAggregate">source code</a></span></p> <pre class="base-tree"> object --+ | list --+ | object --+ | | | <a href="Bio.GFF.Feature-class.html">Feature</a> --+ | <strong class="uidshort">FeatureAggregate</strong> </pre> <hr /> <pre class="py-doctest"> <span class="py-prompt">>>> </span>feature1_1 = Feature(location=easy.LocationFromString(<span class="py-string">"NC_001802x.fna:336..1631"</span>), frame=0) <span class="py-comment"># gag-pol</span> <span class="py-prompt">>>> </span>feature1_2 = Feature(location=easy.LocationFromString(<span class="py-string">"NC_001802x.fna:1631..4642"</span>), frame=0) <span class="py-comment"># slippage</span> <span class="py-prompt">>>> </span>aggregate = FeatureAggregate([feature1_1, feature1_2]) <span class="py-prompt">>>> </span><span class="py-keyword">print</span> aggregate.location() <span class="py-output">join(NC_001802x.fna:336..1631,NC_001802x.fna:1631..4642)</span> <span class="py-output"></span><span class="py-prompt">>>> </span>xlate_str = aggregate.translate().tostring() <span class="py-prompt">>>> </span>xlate_str[:5], xlate_str[-5:] <span class="py-output">('MGARA', 'RQDED')</span></pre> <pre class="py-doctest"> <span class="py-prompt">>>> </span>location1 = easy.LocationFromString(<span class="py-string">"NC_001802x.fna:complement(1..6)"</span>) <span class="py-prompt">>>> </span>location2 = easy.LocationFromString(<span class="py-string">"NC_001802x.fna:complement(7..12)"</span>) <span class="py-prompt">>>> </span>feature2_1 = Feature(location=location1, frame=0) <span class="py-prompt">>>> </span>feature2_2 = Feature(location=location2, frame=0) <span class="py-prompt">>>> </span>aggregate2 = FeatureAggregate([feature2_1, feature2_2]) <span class="py-prompt">>>> </span><span class="py-keyword">print</span> aggregate2.location() <span class="py-output">complement(join(NC_001802x.fna:1..6,NC_001802x.fna:7..12))</span> <span class="py-output"></span><span class="py-prompt">>>> </span><span class="py-keyword">print</span> aggregate2.translate() <span class="py-output">Seq('TRET', HasStopCodon(IUPACProtein(), '*'))</span> <span class="py-output"></span><span class="py-prompt">>>> </span>location1.reverse() <span class="py-prompt">>>> </span>location2.reverse() <span class="py-prompt">>>> </span>aggregate3 = FeatureAggregate([Feature(location=x, frame=0) <span class="py-keyword">for</span> x <span class="py-keyword">in</span> [location1, location2]]) <span class="py-prompt">>>> </span><span class="py-keyword">print</span> aggregate3.location() <span class="py-output">join(NC_001802x.fna:1..6,NC_001802x.fna:7..12)</span> <span class="py-output"></span><span class="py-prompt">>>> </span><span class="py-keyword">print</span> aggregate3.translate() <span class="py-output">Seq('GLSG', HasStopCodon(IUPACProtein(), '*'))</span> <span class="py-output"></span><span class="py-prompt">>>> </span>aggregate3[0].frame = 3 <span class="py-prompt">>>> </span><span class="py-keyword">print</span> aggregate3.translate() <span class="py-output">Seq('LSG', HasStopCodon(IUPACProtein(), '*'))</span></pre> <pre class="py-doctest"> <span class="py-prompt">>>> </span>aggregate4 = FeatureAggregate() <span class="py-prompt">>>> </span>aggregate4.append(Feature(location=easy.LocationFromString(<span class="py-string">"NC_001802x.fna:1..5"</span>), frame=0)) <span class="py-prompt">>>> </span>aggregate4.append(Feature(location=easy.LocationFromString(<span class="py-string">"NC_001802x.fna:6..12"</span>), frame=2)) <span class="py-prompt">>>> </span>aggregate4.seq() <span class="py-output">Seq('GGTCTCTCTGGT', Alphabet())</span> <span class="py-output"></span><span class="py-prompt">>>> </span>aggregate4.translate() <span class="py-output">Seq('GLSG', HasStopCodon(IUPACProtein(), '*'))</span></pre> <!-- ==================== 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">new list</span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.GFF.FeatureAggregate-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">feature_query</span>=<span class="summary-sig-default">None</span>)</span><br /> x.__init__(...) initializes x; see x.__class__.__doc__ for signature</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.GFF-pysrc.html#FeatureAggregate.__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 href="Bio.GFF.FeatureAggregate-class.html#location" class="summary-sig-name">location</a>(<span class="summary-sig-arg">self</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.GFF-pysrc.html#FeatureAggregate.location">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="map"></a><span class="summary-sig-name">map</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">func</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.GFF-pysrc.html#FeatureAggregate.map">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.GFF.FeatureAggregate-class.html#seq" class="summary-sig-name">seq</a>(<span class="summary-sig-arg">self</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.GFF-pysrc.html#FeatureAggregate.seq">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.GFF.FeatureAggregate-class.html#translate" class="summary-sig-name">translate</a>(<span class="summary-sig-arg">self</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.GFF-pysrc.html#FeatureAggregate.translate">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td colspan="2" class="summary"> <p class="indent-wrapped-lines"><b>Inherited from <code>list</code></b>: <code>__add__</code>, <code>__contains__</code>, <code>__delitem__</code>, <code>__delslice__</code>, <code>__eq__</code>, <code>__ge__</code>, <code>__getattribute__</code>, <code>__getitem__</code>, <code>__getslice__</code>, <code>__gt__</code>, <code>__hash__</code>, <code>__iadd__</code>, <code>__imul__</code>, <code>__iter__</code>, <code>__le__</code>, <code>__len__</code>, <code>__lt__</code>, <code>__mul__</code>, <code>__ne__</code>, <code>__new__</code>, <code>__repr__</code>, <code>__reversed__</code>, <code>__rmul__</code>, <code>__setitem__</code>, <code>__setslice__</code>, <code>append</code>, <code>count</code>, <code>extend</code>, <code>index</code>, <code>insert</code>, <code>pop</code>, <code>remove</code>, <code>reverse</code>, <code>sort</code> </p> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.GFF.Feature-class.html">Feature</a></code></b>: <code><a href="Bio.GFF.Feature-class.html#__str__">__str__</a></code>, <code><a href="Bio.GFF.Feature-class.html#id">id</a></code>, <code><a href="Bio.GFF.Feature-class.html#record">record</a></code>, <code><a href="Bio.GFF.Feature-class.html#target_location">target_location</a></code>, <code><a href="Bio.GFF.Feature-class.html#xrange">xrange</a></code> </p> <p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>: <code>__delattr__</code>, <code>__reduce__</code>, <code>__reduce_ex__</code>, <code>__setattr__</code> </p> </td> </tr> </table> <!-- ==================== PROPERTIES ==================== --> <a name="section-Properties"></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">Properties</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-Properties" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> <tr> <td colspan="2" class="summary"> <p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>: <code>__class__</code> </p> </td> </tr> </table> <!-- ==================== METHOD DETAILS ==================== --> <a name="section-MethodDetails"></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">Method Details</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-MethodDetails" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> </table> <a name="__init__"></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">__init__</span>(<span class="sig-arg">self</span>, <span class="sig-arg">feature_query</span>=<span class="sig-default">None</span>)</span> <br /><em class="fname">(Constructor)</em> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.GFF-pysrc.html#FeatureAggregate.__init__">source code</a></span> </td> </tr></table> <p>x.__init__(...) initializes x; see x.__class__.__doc__ for signature</p> <dl class="fields"> <dt>Returns: new list</dt> <dt>Overrides: object.__init__ <dd><em class="note">(inherited documentation)</em></dd> </dt> </dl> </td></tr></table> </div> <a name="location"></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">location</span>(<span class="sig-arg">self</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.GFF-pysrc.html#FeatureAggregate.location">source code</a></span> </td> </tr></table> <dl class="fields"> <dt>Overrides: <a href="Bio.GFF.Feature-class.html#location">Feature.location</a> </dt> </dl> </td></tr></table> </div> <a name="seq"></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">seq</span>(<span class="sig-arg">self</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.GFF-pysrc.html#FeatureAggregate.seq">source code</a></span> </td> </tr></table> <dl class="fields"> <dt>Overrides: <a href="Bio.GFF.Feature-class.html#seq">Feature.seq</a> </dt> </dl> </td></tr></table> </div> <a name="translate"></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">translate</span>(<span class="sig-arg">self</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.GFF-pysrc.html#FeatureAggregate.translate">source code</a></span> </td> </tr></table> <dl class="fields"> <dt>Overrides: <a href="Bio.GFF.Feature-class.html#translate">Feature.translate</a> </dt> </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 09:26:34 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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