<?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>BioSQL.BioSeqDatabase</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="BioSQL-module.html">Package BioSQL</a> :: Module BioSeqDatabase </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="BioSQL.BioSeqDatabase-module.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== MODULE DESCRIPTION ==================== --> <h1 class="epydoc">Module BioSeqDatabase</h1><p class="nomargin-top"><span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html">source code</a></span></p> <p>Connect with a BioSQL database and load Biopython like objects from it.</p> <p>This provides interfaces for loading biological objects from a relational database, and is compatible with the BioSQL standards.</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="BioSQL.BioSeqDatabase.DBServer-class.html" class="summary-name">DBServer</a> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="BioSQL.BioSeqDatabase.Adaptor-class.html" class="summary-name">Adaptor</a> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="BioSQL.BioSeqDatabase.BioSeqDatabase-class.html" class="summary-name">BioSeqDatabase</a> </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="BioSQL.BioSeqDatabase-module.html#open_database" class="summary-sig-name">open_database</a>(<span class="summary-sig-arg">driver</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">MySQLdb</code><code class="variable-quote">'</code></span>, <span class="summary-sig-arg">**kwargs</span>)</span><br /> Main interface for loading a existing BioSQL-style database.</td> <td align="right" valign="top"> <span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#open_database">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 href="BioSQL.BioSeqDatabase-module.html#_allowed_lookups" class="summary-name" onclick="show_private();">_allowed_lookups</a> = <code title="{'accession': 'fetch_seqid_by_accession', 'display_id': 'fetch_seqid_by_display_id', 'gi': 'fetch_seqid_by_identifier', 'name': 'fetch_seqid_by_display_id', 'primary_id': 'fetch_seqid_by_identifier', 'version': 'fetch_seqid_by_version'}"><code class="variable-group">{</code><code class="variable-quote">'</code><code class="variable-string">accession</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">fetch_seqid_by_accession</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-ellipsis">...</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="open_database"></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">open_database</span>(<span class="sig-arg">driver</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">MySQLdb</code><code class="variable-quote">'</code></span>, <span class="sig-arg">**kwargs</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#open_database">source code</a></span> </td> </tr></table> <p>Main interface for loading a existing BioSQL-style database.</p> <p>This function is the easiest way to retrieve a connection to a database, doing something like:</p> <pre class="py-doctest"> <span class="py-prompt">>>> </span><span class="py-keyword">from</span> BioSeq <span class="py-keyword">import</span> BioSeqDatabase <span class="py-prompt">>>> </span>server = BioSeqDatabase.open_database(user = <span class="py-string">"root"</span>, db=<span class="py-string">"minidb"</span>)</pre> <p>the various options are: driver -> The name of the database driver to use for connecting. The driver should implement the python DB API. By default, the MySQLdb driver is used. user -> the username to connect to the database with. password, passwd -> the password to connect with host -> the hostname of the database database or db -> the name of the database</p> <dl class="fields"> </dl> </td></tr></table> </div> <br /> <!-- ==================== 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="_allowed_lookups"></a> <div class="private"> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <h3 class="epydoc">_allowed_lookups</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">accession</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">fetch_seqid_by_accession</code><code class="variable-quote">'</code><code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">display_id</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">fetch_seqid_by_display_id</code><code class="variable-quote">'</code><code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">gi</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">fetch_seqid_by_identifier</code><code class="variable-quote">'</code><code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">name</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">fetch_seqid_by_display_id</code><code class="variable-quote">'</code><code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">primary_id</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">fetch_seqid_by_identifier</code><code class="variable-quote">'</code><code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">version</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">fetch_seqid_by_version</code><code class="variable-quote">'</code><code class="variable-group">}</code> </pre></td></tr></table> </dd> </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 09:26:29 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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