<?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.NCBIStandalone.BlastErrorParser</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> :: <a href="Bio.Blast.NCBIStandalone-module.html">Module NCBIStandalone</a> :: Class BlastErrorParser </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.NCBIStandalone.BlastErrorParser-class.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== CLASS DESCRIPTION ==================== --> <h1 class="epydoc">Class BlastErrorParser</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Blast.NCBIStandalone-pysrc.html#BlastErrorParser">source code</a></span></p> <pre class="base-tree"> <a href="Bio.ParserSupport.AbstractParser-class.html">ParserSupport.AbstractParser</a> --+ | <strong class="uidshort">BlastErrorParser</strong> </pre> <hr /> <p>Attempt to catch and diagnose BLAST errors while parsing.</p> <p>This utilizes the BlastParser module but adds an additional layer of complexity on top of it by attempting to diagnose ValueErrors that may actually indicate problems during BLAST parsing.</p> <p>Current BLAST problems this detects are: o LowQualityBlastError - When BLASTing really low quality sequences (ie. some GenBank entries which are just short streches of a single nucleotide), BLAST will report an error with the sequence and be unable to search with this. This will lead to a badly formatted BLAST report that the parsers choke on. The parser will convert the ValueError to a LowQualityBlastError and attempt to provide useful information.</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 href="Bio.Blast.NCBIStandalone.BlastErrorParser-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">bad_report_handle</span>=<span class="summary-sig-default">None</span>)</span><br /> Initialize a parser that tries to catch BlastErrors.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Blast.NCBIStandalone-pysrc.html#BlastErrorParser.__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.Blast.NCBIStandalone.BlastErrorParser-class.html#parse" class="summary-sig-name">parse</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">handle</span>)</span><br /> Parse a handle, attempting to diagnose errors.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Blast.NCBIStandalone-pysrc.html#BlastErrorParser.parse">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 href="Bio.Blast.NCBIStandalone.BlastErrorParser-class.html#_diagnose_error" class="summary-sig-name" onclick="show_private();">_diagnose_error</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">handle</span>, <span class="summary-sig-arg">data_record</span>)</span><br /> Attempt to diagnose an error in the passed handle.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Blast.NCBIStandalone-pysrc.html#BlastErrorParser._diagnose_error">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td colspan="2" class="summary"> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.ParserSupport.AbstractParser-class.html">ParserSupport.AbstractParser</a></code></b>: <code><a href="Bio.ParserSupport.AbstractParser-class.html#parse_file">parse_file</a></code>, <code><a href="Bio.ParserSupport.AbstractParser-class.html#parse_str">parse_str</a></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">bad_report_handle</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.Blast.NCBIStandalone-pysrc.html#BlastErrorParser.__init__">source code</a></span> </td> </tr></table> <p>Initialize a parser that tries to catch BlastErrors.</p> <p>Arguments: o bad_report_handle - An optional argument specifying a handle where bad reports should be sent. This would allow you to save all of the bad reports to a file, for instance. If no handle is specified, the bad reports will not be saved.</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">self</span>, <span class="sig-arg">handle</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Blast.NCBIStandalone-pysrc.html#BlastErrorParser.parse">source code</a></span> </td> </tr></table> <p>Parse a handle, attempting to diagnose errors.</p> <dl class="fields"> <dt>Overrides: <a href="Bio.ParserSupport.AbstractParser-class.html#parse">ParserSupport.AbstractParser.parse</a> </dt> </dl> </td></tr></table> </div> <a name="_diagnose_error"></a> <div class="private"> <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">_diagnose_error</span>(<span class="sig-arg">self</span>, <span class="sig-arg">handle</span>, <span class="sig-arg">data_record</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Blast.NCBIStandalone-pysrc.html#BlastErrorParser._diagnose_error">source code</a></span> </td> </tr></table> <p>Attempt to diagnose an error in the passed handle.</p> <p>Arguments: o handle - The handle potentially containing the error o data_record - The data record partially created by the consumer.</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 Mon Sep 15 09:26:30 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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