<?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</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> :: Module 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-module.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== MODULE DESCRIPTION ==================== --> <h1 class="epydoc">Module SeqFeature</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.SeqFeature-pysrc.html">source code</a></span></p> <pre class="literalblock"> Represent a Sequence Feature holding info about a part of a sequence. This is heavily modeled after the Biocorba SeqFeature objects, and may be pretty biased towards GenBank stuff since I'm writing it for the GenBank parser output... What's here: Base class to hold a Feature. ---------------------------- classes: o SeqFeature Hold information about a Reference. ---------------------------------- This is an attempt to create a General class to hold Reference type information. classes: o Reference Specify locations of a feature on a Sequence. --------------------------------------------- This aims to handle, in Ewan's words, 'the dreaded fuzziness issue' in much the same way as Biocorba. This has the advantages of allowing us to handle fuzzy stuff in case anyone needs it, and also be compatible with Biocorba. classes: o FeatureLocation - Specify the start and end location of a feature. o ExactPosition - Specify the position as being exact. o WithinPosition - Specify a position occuring within some range. o BetweenPosition - Specify a position occuring between a range. o BeforePosition - Specify the position as being found before some base. o AfterPosition - Specify the position as being found after some base. </pre> <!-- ==================== 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.SeqFeature.SeqFeature-class.html" class="summary-name">SeqFeature</a><br /> Represent a Sequence Feature on an object. </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.SeqFeature.Reference-class.html" class="summary-name">Reference</a><br /> Represent a Generic Reference object. </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.SeqFeature.FeatureLocation-class.html" class="summary-name">FeatureLocation</a><br /> Specify the location of a feature along a sequence. </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.SeqFeature.AbstractPosition-class.html" class="summary-name">AbstractPosition</a><br /> Abstract base class representing a position. </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.SeqFeature.ExactPosition-class.html" class="summary-name">ExactPosition</a><br /> Specify the specific position of a boundary. </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.SeqFeature.WithinPosition-class.html" class="summary-name">WithinPosition</a><br /> Specify the position of a boundary within some coordinates. </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.SeqFeature.BetweenPosition-class.html" class="summary-name">BetweenPosition</a><br /> Specify the position of a boundary between two coordinates. </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.SeqFeature.BeforePosition-class.html" class="summary-name">BeforePosition</a><br /> Specify a position where the actual location occurs before it. </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.SeqFeature.AfterPosition-class.html" class="summary-name">AfterPosition</a><br /> Specify a position where the actual location is found after it. </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.SeqFeature.OneOfPosition-class.html" class="summary-name">OneOfPosition</a><br /> Specify a position where the location can be multiple positions. </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.SeqFeature.PositionGap-class.html" class="summary-name">PositionGap</a><br /> Simple class to hold information about a gap between positions. </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 09:26:25 2008 </td> <td align="right" 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