<?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.SCOP.Astral</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.SCOP-module.html">Package SCOP</a> :: Class Astral </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.SCOP.Astral-class.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== CLASS DESCRIPTION ==================== --> <h1 class="epydoc">Class Astral</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.SCOP-pysrc.html#Astral">source code</a></span></p> <p>Abstraction of the ASTRAL database, which has sequences for all the SCOP domains, as well as clusterings by percent id or evalue.</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.SCOP.Astral-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">dir_path</span>=<span class="summary-sig-default">None</span>, <span class="summary-sig-arg">version</span>=<span class="summary-sig-default">None</span>, <span class="summary-sig-arg">scop</span>=<span class="summary-sig-default">None</span>, <span class="summary-sig-arg">ind_file</span>=<span class="summary-sig-default">None</span>, <span class="summary-sig-arg">astral_file</span>=<span class="summary-sig-default">None</span>, <span class="summary-sig-arg">db_handle</span>=<span class="summary-sig-default">None</span>)</span><br /> Initialise the astral database.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SCOP-pysrc.html#Astral.__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 name="domainsClusteredByEv"></a><span class="summary-sig-name">domainsClusteredByEv</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">id</span>)</span><br /> get domains clustered by evalue</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SCOP-pysrc.html#Astral.domainsClusteredByEv">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="domainsClusteredById"></a><span class="summary-sig-name">domainsClusteredById</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">id</span>)</span><br /> get domains clustered by percent id</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SCOP-pysrc.html#Astral.domainsClusteredById">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="getAstralDomainsFromFile"></a><span class="summary-sig-name">getAstralDomainsFromFile</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">filename</span>=<span class="summary-sig-default">None</span>, <span class="summary-sig-arg">file_handle</span>=<span class="summary-sig-default">None</span>)</span><br /> Get the scop domains from a file containing a list of sids</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SCOP-pysrc.html#Astral.getAstralDomainsFromFile">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="getAstralDomainsFromSQL"></a><span class="summary-sig-name">getAstralDomainsFromSQL</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">column</span>)</span><br /> Load a set of astral domains from a column in the astral table of a MYSQL database (which can be created with writeToSQL(...)</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SCOP-pysrc.html#Astral.getAstralDomainsFromSQL">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="getSeqBySid"></a><span class="summary-sig-name">getSeqBySid</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">domain</span>)</span><br /> get the seq record of a given domain from its sid</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SCOP-pysrc.html#Astral.getSeqBySid">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="getSeq"></a><span class="summary-sig-name">getSeq</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">domain</span>)</span><br /> Return seq associated with domain</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SCOP-pysrc.html#Astral.getSeq">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="hashedDomainsById"></a><span class="summary-sig-name">hashedDomainsById</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">id</span>)</span><br /> Get domains clustered by sequence identity in a dict</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SCOP-pysrc.html#Astral.hashedDomainsById">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="hashedDomainsByEv"></a><span class="summary-sig-name">hashedDomainsByEv</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">id</span>)</span><br /> Get domains clustered by evalue in a dict</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SCOP-pysrc.html#Astral.hashedDomainsByEv">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="isDomainInId"></a><span class="summary-sig-name">isDomainInId</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">dom</span>, <span class="summary-sig-arg">id</span>)</span><br /> Returns true if the domain is in the astral clusters for percent ID</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SCOP-pysrc.html#Astral.isDomainInId">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="isDomainInEv"></a><span class="summary-sig-name">isDomainInEv</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">dom</span>, <span class="summary-sig-arg">id</span>)</span><br /> Returns true if the domain is in the ASTRAL clusters for evalues</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SCOP-pysrc.html#Astral.isDomainInEv">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="writeToSQL"></a><span class="summary-sig-name">writeToSQL</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">db_handle</span>)</span><br /> Write the ASTRAL database to a MYSQL database</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SCOP-pysrc.html#Astral.writeToSQL">source code</a></span> </td> </tr> </table> </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">dir_path</span>=<span class="sig-default">None</span>, <span class="sig-arg">version</span>=<span class="sig-default">None</span>, <span class="sig-arg">scop</span>=<span class="sig-default">None</span>, <span class="sig-arg">ind_file</span>=<span class="sig-default">None</span>, <span class="sig-arg">astral_file</span>=<span class="sig-default">None</span>, <span class="sig-arg">db_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.SCOP-pysrc.html#Astral.__init__">source code</a></span> </td> </tr></table> <pre class="literalblock"> Initialise the astral database. You must provide either a directory of SCOP files: dir_path - string, the path to location of the scopseq-x.xx directory (not the directory itself), and version -a version number. or, a FASTA file: astral_file - string, a path to a fasta file (which will be loaded in memory) or, a MYSQL database: db_handle - a database handle for a MYSQL database containing a table 'astral' with the astral data in it. This can be created using writeToSQL. Note that the ind_file argument is deprecated. </pre> <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 09:26:38 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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