<?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.Blast.NCBIXML</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.Blast-module.html">Package Blast</a> :: Module NCBIXML </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.Blast.NCBIXML-module.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== MODULE DESCRIPTION ==================== --> <h1 class="epydoc">Module NCBIXML</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html">source code</a></span></p> <pre class="literalblock"> This module provides code to work with the BLAST XML output following the DTD available on the NCBI FTP ftp://ftp.ncbi.nlm.nih.gov/blast/documents/xml/NCBI_BlastOutput.dtd Classes: BlastParser Parses XML output from BLAST (direct use discouraged). This (now) returns a list of Blast records. Historically it returned a single Blast record. You are expected to use this via the parse or read functions. _XMLParser Generic SAX parser (private). Functions: parse Incremental parser, this is an iterator that returns Blast records. It uses the BlastParser internally. read Returns a single Blast record. Uses the BlastParser internally. </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 class="private"> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.Blast.NCBIXML._XMLparser-class.html" class="summary-name" onclick="show_private();">_XMLparser</a><br /> Generic SAX Parser </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.Blast.NCBIXML.BlastParser-class.html" class="summary-name">BlastParser</a><br /> Parse XML BLAST data into a Record.Blast object </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 href="Bio.Blast.NCBIXML-module.html#read" class="summary-sig-name">read</a>(<span class="summary-sig-arg">handle</span>, <span class="summary-sig-arg">debug</span>=<span class="summary-sig-default">0</span>)</span><br /> Returns a single Blast record (assumes just one query).</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#read">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.Blast.NCBIXML-module.html#parse" class="summary-sig-name">parse</a>(<span class="summary-sig-arg">handle</span>, <span class="summary-sig-arg">debug</span>=<span class="summary-sig-default">0</span>)</span><br /> Returns an iterator a Blast record for each query.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#parse">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="__package__"></a><span class="summary-name">__package__</span> = <code title="'Bio.Blast'"><code class="variable-quote">'</code><code class="variable-string">Bio.Blast</code><code class="variable-quote">'</code></code> </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="read"></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">read</span>(<span class="sig-arg">handle</span>, <span class="sig-arg">debug</span>=<span class="sig-default">0</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#read">source code</a></span> </td> </tr></table> <p>Returns a single Blast record (assumes just one query).</p> <p>This function is for use when there is one and only one BLAST result in your XML file.</p> <p>Use the Bio.Blast.NCBIXML.parse() function if you expect more than one BLAST record (i.e. if you have more than one query sequence).</p> <dl class="fields"> </dl> </td></tr></table> </div> <a name="parse"></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">parse</span>(<span class="sig-arg">handle</span>, <span class="sig-arg">debug</span>=<span class="sig-default">0</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#parse">source code</a></span> </td> </tr></table> <p>Returns an iterator a Blast record for each query.</p> <p>handle - file handle to and XML file to parse debug - integer, amount of debug information to print</p> <p>This is a generator function that returns multiple Blast records objects - one for each query sequence given to blast. The file is read incrementally, returning complete records as they are read in.</p> <p>Should cope with new BLAST 2.2.14+ which gives a single XML file for mutliple query records.</p> <p>Should also cope with XML output from older versions BLAST which gave multiple XML files concatenated together (giving a single file which strictly speaking wasn't valid XML).</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 Thu Aug 18 18:19:19 2011 </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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