<?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.Wise.dnal</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.Wise-module.html">Package Wise</a> :: Module dnal </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.Wise.dnal-module.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== MODULE DESCRIPTION ==================== --> <h1 class="epydoc">Module dnal</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Wise.dnal-pysrc.html">source code</a></span></p> <hr /> <div class="fields"> <p><strong>Version:</strong> $Revision: 1.11 $ </p> </div><!-- ==================== 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.Wise.dnal.Statistics-class.html" class="summary-name">Statistics</a><br /> Calculate statistics from an ALB report </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 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 name="_build_dnal_cmdline"></a><span class="summary-sig-name">_build_dnal_cmdline</span>(<span class="summary-sig-arg">match</span>, <span class="summary-sig-arg">mismatch</span>, <span class="summary-sig-arg">gap</span>, <span class="summary-sig-arg">extension</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Wise.dnal-pysrc.html#_build_dnal_cmdline">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 name="_fgrep_count"></a><span class="summary-sig-name">_fgrep_count</span>(<span class="summary-sig-arg">pattern</span>, <span class="summary-sig-arg">file</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Wise.dnal-pysrc.html#_fgrep_count">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 name="_alb_line2coords"></a><span class="summary-sig-name">_alb_line2coords</span>(<span class="summary-sig-arg">line</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Wise.dnal-pysrc.html#_alb_line2coords">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 name="_get_coords"></a><span class="summary-sig-name">_get_coords</span>(<span class="summary-sig-arg">filename</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Wise.dnal-pysrc.html#_get_coords">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 name="_any"></a><span class="summary-sig-name">_any</span>(<span class="summary-sig-arg">seq</span>, <span class="summary-sig-arg">pred</span>=<span class="summary-sig-default"><type 'bool'></span>)</span><br /> Returns True if pred(x) is True at least one element in the iterable</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Wise.dnal-pysrc.html#_any">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="align"></a><span class="summary-sig-name">align</span>(<span class="summary-sig-arg">pair</span>, <span class="summary-sig-arg">match</span>=<span class="summary-sig-default">4</span>, <span class="summary-sig-arg">mismatch</span>=<span class="summary-sig-default">-1</span>, <span class="summary-sig-arg">gap</span>=<span class="summary-sig-default">-5</span>, <span class="summary-sig-arg">extension</span>=<span class="summary-sig-default">-1</span>, <span class="summary-sig-arg">**keywds</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Wise.dnal-pysrc.html#align">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="main"></a><span class="summary-sig-name">main</span>()</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Wise.dnal-pysrc.html#main">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 name="_test"></a><span class="summary-sig-name">_test</span>(<span class="summary-sig-arg">*args</span>, <span class="summary-sig-arg">**keywds</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Wise.dnal-pysrc.html#_test">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 class="private"> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a name="_SCORE_MATCH"></a><span class="summary-name">_SCORE_MATCH</span> = <code title="4">4</code> </td> </tr> <tr class="private"> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a name="_SCORE_MISMATCH"></a><span class="summary-name">_SCORE_MISMATCH</span> = <code title="-1">-1</code> </td> </tr> <tr class="private"> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a name="_SCORE_GAP_START"></a><span class="summary-name">_SCORE_GAP_START</span> = <code title="-5">-5</code> </td> </tr> <tr class="private"> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a name="_SCORE_GAP_EXTENSION"></a><span class="summary-name">_SCORE_GAP_EXTENSION</span> = <code title="-1">-1</code> </td> </tr> <tr class="private"> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a name="_CMDLINE_DNAL"></a><span class="summary-name">_CMDLINE_DNAL</span> = <code title="['dnal', '-alb', '-nopretty']"><code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">dnal</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">-alb</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">-nopretty</code><code class="variable-quote">'</code><code class="variable-group">]</code></code> </td> </tr> <tr class="private"> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a name="_CMDLINE_FGREP_COUNT"></a><span class="summary-name">_CMDLINE_FGREP_COUNT</span> = <code title="'fgrep -c \'%s\' %s'"><code class="variable-quote">'</code><code class="variable-string">fgrep -c \'%s\' %s</code><code class="variable-quote">'</code></code> </td> </tr> <tr class="private"> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a name="_re_alb_line2coords"></a><span class="summary-name">_re_alb_line2coords</span> = <code title="re.compile(r'^\[([^:]+):[^\[]+\[([^:]+):')">re.compile(r'^\[<code class="re-group">(</code><code class="re-group">[^</code>:<code class="re-group">]</code><code class="re-op">+</code><code class="re-group">)</code>:<code class="re-group">[^</code>\[<code class="re-group">]</code><code class="re-op">+</code>\[<code class="re-group">(</code><code class="re-group">[^</code>:<code class="re-group">]</code><code class="re-op">+</code><code class="re-group">)</code>:')</code> </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 09:26:26 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 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