<?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.Sequencing.Phd</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.Sequencing-module.html">Package Sequencing</a> :: Module Phd </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.Sequencing.Phd-module.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== MODULE DESCRIPTION ==================== --> <h1 class="epydoc">Module Phd</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Sequencing.Phd-pysrc.html">source code</a></span></p> <p>Parser for PHD files output by PHRED and used by PHRAP and CONSED.</p> <p>Works fine with PHRED 0.020425.c</p> <p>Version 1.1, 03/09/2004 written by Cymon J. Cox (cymon@duke.edu) and Frank Kauff (fkauff@duke.edu) Comments, bugs, problems, suggestions to one uf us are welcome!</p> <p>Uses the Biopython Parser interface for parsing: ParserSupport.py</p> <!-- ==================== 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.Sequencing.Phd.Record-class.html" class="summary-name">Record</a><br /> Hold information from a PHD file. </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.Sequencing.Phd.Iterator-class.html" class="summary-name">Iterator</a><br /> Iterates over a file of multiple PHD records. </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.Sequencing.Phd.RecordParser-class.html" class="summary-name">RecordParser</a><br /> Parses PHD file data into a Record object. </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.Sequencing.Phd._Scanner-class.html" class="summary-name" onclick="show_private();">_Scanner</a><br /> Scans a PHD-formatted file. </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.Sequencing.Phd._RecordConsumer-class.html" class="summary-name" onclick="show_private();">_RecordConsumer</a><br /> Consumer that converts a PHD record to a Record object. </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 href="Bio.Sequencing.Phd-module.html#CKEYWORDS" class="summary-name">CKEYWORDS</a> = <code title="['CHROMAT_FILE', 'ABI_THUMBPRINT', 'PHRED_VERSION', 'CALL_METHOD', 'QUALITY_LEVELS', 'TIME', 'TRACE_ARRAY_MIN_INDEX', 'TRACE_ARRAY_MAX_INDEX', ..."><code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">CHROMAT_FILE</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">ABI_THUMBPRINT</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">PHRED_VERSION</code><code class="variable-quote">'</code><code class="variable-ellipsis">...</code></code> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a name="StringTypes"></a><span class="summary-name">StringTypes</span> = <code title="(<type 'str'>, <type 'unicode'>)"><code class="variable-group">(</code><type 'str'><code class="variable-op">, </code><type 'unicode'><code class="variable-group">)</code></code> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a name="xml_support"></a><span class="summary-name">xml_support</span> = <code title="1">1</code> </td> </tr> </table> <!-- ==================== VARIABLES DETAILS ==================== --> <a name="section-VariablesDetails"></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">Variables Details</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-VariablesDetails" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> </table> <a name="CKEYWORDS"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <h3 class="epydoc">CKEYWORDS</h3> <dl class="fields"> </dl> <dl class="fields"> <dt>Value:</dt> <dd><table><tr><td><pre class="variable"> <code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">CHROMAT_FILE</code><code class="variable-quote">'</code><code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">ABI_THUMBPRINT</code><code class="variable-quote">'</code><code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">PHRED_VERSION</code><code class="variable-quote">'</code><code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">CALL_METHOD</code><code class="variable-quote">'</code><code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">QUALITY_LEVELS</code><code class="variable-quote">'</code><code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">TIME</code><code class="variable-quote">'</code><code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">TRACE_ARRAY_MIN_INDEX</code><code class="variable-quote">'</code><code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">TRACE_ARRAY_MAX_INDEX</code><code class="variable-quote">'</code><code class="variable-op">,</code> <code class="variable-ellipsis">...</code> </pre></td></tr></table> </dd> </dl> </td></tr></table> </div> <br /> <!-- ==================== NAVIGATION BAR ==================== --> <table class="navbar" border="0" width="100%" cellpadding="0" 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