<?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-pysrc.html"
target="_top">no frames</a>]</span></td></tr>
</table>
</td>
</tr>
</table>
<h1 class="epydoc">Source Code for <a href="BioSQL.BioSeqDatabase-module.html">Module BioSQL.BioSeqDatabase</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright 2002 by Andrew Dalke. All rights reserved.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Revisions 2007-2008 by Peter Cock.</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Note that BioSQL (including the database schema and scripts) is</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># available and licensed separately. Please consult www.biosql.org</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-docstring">"""Connect with a BioSQL database and load Biopython like objects from it.</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring">This provides interfaces for loading biological objects from a relational</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring">database, and is compatible with the BioSQL standards.</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-0" class="py-name" targets="Module BioSQL.BioSeq=BioSQL.BioSeq-module.html"><a title="BioSQL.BioSeq" class="py-name" href="#" onclick="return doclink('link-0', 'BioSeq', 'link-0');">BioSeq</a></tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-1" class="py-name" targets="Module BioSQL.Loader=BioSQL.Loader-module.html"><a title="BioSQL.Loader" class="py-name" href="#" onclick="return doclink('link-1', 'Loader', 'link-1');">Loader</a></tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-2" class="py-name" targets="Module BioSQL.DBUtils=BioSQL.DBUtils-module.html"><a title="BioSQL.DBUtils" class="py-name" href="#" onclick="return doclink('link-2', 'DBUtils', 'link-2');">DBUtils</a></tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"> </tt>
<a name="open_database"></a><div id="open_database-def"><a name="L18"></a><tt class="py-lineno"> 18</tt> <a class="py-toggle" href="#" id="open_database-toggle" onclick="return toggle('open_database');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase-module.html#open_database">open_database</a><tt class="py-op">(</tt><tt class="py-param">driver</tt> <tt class="py-op">=</tt> <tt class="py-string">"MySQLdb"</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-param">kwargs</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="open_database-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="open_database-expanded"><a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"> <tt class="py-docstring">"""Main interface for loading a existing BioSQL-style database.</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-docstring"> This function is the easiest way to retrieve a connection to a</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-docstring"> database, doing something like:</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring"> >>> from BioSeq import BioSeqDatabase</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring"> >>> server = BioSeqDatabase.open_database(user = "root", db="minidb")</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring"> the various options are:</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-docstring"> driver -> The name of the database driver to use for connecting. The</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-docstring"> driver should implement the python DB API. By default, the MySQLdb</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring"> driver is used.</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-docstring"> user -> the username to connect to the database with.</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-docstring"> password, passwd -> the password to connect with</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-docstring"> host -> the hostname of the database</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-docstring"> database or db -> the name of the database</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-name">module</tt> <tt class="py-op">=</tt> <tt class="py-name">__import__</tt><tt class="py-op">(</tt><tt class="py-name">driver</tt><tt class="py-op">)</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt class="py-name">connect</tt> <tt class="py-op">=</tt> <tt class="py-name">getattr</tt><tt class="py-op">(</tt><tt class="py-name">module</tt><tt class="py-op">,</tt> <tt class="py-string">"connect"</tt><tt class="py-op">)</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt class="py-comment"># Different drivers use different keywords...</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">kw</tt> <tt class="py-op">=</tt> <tt class="py-name">kwargs</tt><tt class="py-op">.</tt><tt id="link-3" class="py-name" targets="Method Bio.Crystal.Crystal.copy()=Bio.Crystal.Crystal-class.html#copy,Method Bio.GA.Organism.Organism.copy()=Bio.GA.Organism.Organism-class.html#copy,Method Bio.GenBank.NCBIDictionary.copy()=Bio.GenBank.NCBIDictionary-class.html#copy,Method Bio.PDB.Vector'.Vector.copy()=Bio.PDB.Vector%27.Vector-class.html#copy,Method Bio.Prosite.ExPASyDictionary.copy()=Bio.Prosite.ExPASyDictionary-class.html#copy,Method Bio.Prosite.Pattern.PrositeTerm.copy()=Bio.Prosite.Pattern.PrositeTerm-class.html#copy,Method Bio.Prosite.Prodoc.ExPASyDictionary.copy()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#copy,Method Bio.PubMed.Dictionary.copy()=Bio.PubMed.Dictionary-class.html#copy,Method Bio.SwissProt.SProt.ExPASyDictionary.copy()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#copy,Method Martel.Expression.Any.copy()=Martel.Expression.Any-class.html#copy,Method Martel.Expression.AnyEol.copy()=Martel.Expression.AnyEol-class.html#copy,Method Martel.Expression.Assert.copy()=Martel.Expression.Assert-class.html#copy,Method Martel.Expression.AtBeginning.copy()=Martel.Expression.AtBeginning-class.html#copy,Method Martel.Expression.AtEnd.copy()=Martel.Expression.AtEnd-class.html#copy,Method Martel.Expression.Debug.copy()=Martel.Expression.Debug-class.html#copy,Method Martel.Expression.Dot.copy()=Martel.Expression.Dot-class.html#copy,Method Martel.Expression.Expression.copy()=Martel.Expression.Expression-class.html#copy,Method Martel.Expression.ExpressionList.copy()=Martel.Expression.ExpressionList-class.html#copy,Method Martel.Expression.FastFeature.copy()=Martel.Expression.FastFeature-class.html#copy,Method Martel.Expression.Group.copy()=Martel.Expression.Group-class.html#copy,Method Martel.Expression.GroupRef.copy()=Martel.Expression.GroupRef-class.html#copy,Method Martel.Expression.HeaderFooter.copy()=Martel.Expression.HeaderFooter-class.html#copy,Method Martel.Expression.Literal.copy()=Martel.Expression.Literal-class.html#copy,Method Martel.Expression.MaxRepeat.copy()=Martel.Expression.MaxRepeat-class.html#copy,Method Martel.Expression.NullOp.copy()=Martel.Expression.NullOp-class.html#copy,Method Martel.Expression.ParseRecords.copy()=Martel.Expression.ParseRecords-class.html#copy,Method Martel.Expression.PassThrough.copy()=Martel.Expression.PassThrough-class.html#copy,Method Martel.Expression.Str.copy()=Martel.Expression.Str-class.html#copy,Method Martel.IterParser.IterHeaderFooter.copy()=Martel.IterParser.IterHeaderFooter-class.html#copy,Method Martel.IterParser.IterRecords.copy()=Martel.IterParser.IterRecords-class.html#copy,Method Martel.Iterator.IteratorRecords.copy()=Martel.Iterator.IteratorRecords-class.html#copy,Method Martel.Parser.HeaderFooterParser.copy()=Martel.Parser.HeaderFooterParser-class.html#copy,Method Martel.Parser.Parser.copy()=Martel.Parser.Parser-class.html#copy,Method Martel.Parser.RecordParser.copy()=Martel.Parser.RecordParser-class.html#copy"><a title="Bio.Crystal.Crystal.copy
Bio.GA.Organism.Organism.copy
Bio.GenBank.NCBIDictionary.copy
Bio.PDB.Vector'.Vector.copy
Bio.Prosite.ExPASyDictionary.copy
Bio.Prosite.Pattern.PrositeTerm.copy
Bio.Prosite.Prodoc.ExPASyDictionary.copy
Bio.PubMed.Dictionary.copy
Bio.SwissProt.SProt.ExPASyDictionary.copy
Martel.Expression.Any.copy
Martel.Expression.AnyEol.copy
Martel.Expression.Assert.copy
Martel.Expression.AtBeginning.copy
Martel.Expression.AtEnd.copy
Martel.Expression.Debug.copy
Martel.Expression.Dot.copy
Martel.Expression.Expression.copy
Martel.Expression.ExpressionList.copy
Martel.Expression.FastFeature.copy
Martel.Expression.Group.copy
Martel.Expression.GroupRef.copy
Martel.Expression.HeaderFooter.copy
Martel.Expression.Literal.copy
Martel.Expression.MaxRepeat.copy
Martel.Expression.NullOp.copy
Martel.Expression.ParseRecords.copy
Martel.Expression.PassThrough.copy
Martel.Expression.Str.copy
Martel.IterParser.IterHeaderFooter.copy
Martel.IterParser.IterRecords.copy
Martel.Iterator.IteratorRecords.copy
Martel.Parser.HeaderFooterParser.copy
Martel.Parser.Parser.copy
Martel.Parser.RecordParser.copy" class="py-name" href="#" onclick="return doclink('link-3', 'copy', 'link-3');">copy</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">driver</tt> <tt class="py-op">==</tt> <tt class="py-string">"MySQLdb"</tt><tt class="py-op">:</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">kw</tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Method Bio.Crystal.Crystal.has_key()=Bio.Crystal.Crystal-class.html#has_key,Method Bio.EUtils.POM.ElementNode.has_key()=Bio.EUtils.POM.ElementNode-class.html#has_key,Method Bio.GenBank.NCBIDictionary.has_key()=Bio.GenBank.NCBIDictionary-class.html#has_key,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#has_key,Method Bio.PDB.FragmentMapper'.FragmentMapper.has_key()=Bio.PDB.FragmentMapper%27.FragmentMapper-class.html#has_key,Method Bio.Prosite.ExPASyDictionary.has_key()=Bio.Prosite.ExPASyDictionary-class.html#has_key,Method Bio.Prosite.Prodoc.ExPASyDictionary.has_key()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#has_key,Method Bio.PubMed.Dictionary.has_key()=Bio.PubMed.Dictionary-class.html#has_key,Method Bio.SwissProt.SProt.ExPASyDictionary.has_key()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#has_key,Method Martel.Parser.MartelAttributeList.has_key()=Martel.Parser.MartelAttributeList-class.html#has_key"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-4', 'has_key', 'link-4');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-string">"database"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt class="py-name">kw</tt><tt class="py-op">[</tt><tt class="py-string">"db"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">kw</tt><tt class="py-op">[</tt><tt class="py-string">"database"</tt><tt class="py-op">]</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt class="py-keyword">del</tt> <tt class="py-name">kw</tt><tt class="py-op">[</tt><tt class="py-string">"database"</tt><tt class="py-op">]</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">kw</tt><tt class="py-op">.</tt><tt id="link-5" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-5', 'has_key', 'link-4');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-string">"password"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt class="py-name">kw</tt><tt class="py-op">[</tt><tt class="py-string">"passwd"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">kw</tt><tt class="py-op">[</tt><tt class="py-string">"password"</tt><tt class="py-op">]</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-keyword">del</tt> <tt class="py-name">kw</tt><tt class="py-op">[</tt><tt class="py-string">"password"</tt><tt class="py-op">]</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt class="py-comment"># DB-API recommendations</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">kw</tt><tt class="py-op">.</tt><tt id="link-6" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-6', 'has_key', 'link-4');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-string">"db"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt class="py-name">kw</tt><tt class="py-op">[</tt><tt class="py-string">"database"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">kw</tt><tt class="py-op">[</tt><tt class="py-string">"db"</tt><tt class="py-op">]</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> <tt class="py-keyword">del</tt> <tt class="py-name">kw</tt><tt class="py-op">[</tt><tt class="py-string">"db"</tt><tt class="py-op">]</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">kw</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-7', 'has_key', 'link-4');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-string">"passwd"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-name">kw</tt><tt class="py-op">[</tt><tt class="py-string">"password"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">kw</tt><tt class="py-op">[</tt><tt class="py-string">"passwd"</tt><tt class="py-op">]</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-keyword">del</tt> <tt class="py-name">kw</tt><tt class="py-op">[</tt><tt class="py-string">"passwd"</tt><tt class="py-op">]</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">driver</tt> <tt class="py-op">==</tt> <tt class="py-string">"psycopg"</tt> <tt class="py-keyword">and</tt> <tt class="py-keyword">not</tt> <tt class="py-name">kw</tt><tt class="py-op">.</tt><tt id="link-8" class="py-name" targets="Method Bio.Crystal.Crystal.get()=Bio.Crystal.Crystal-class.html#get,Method Bio.Data.CodonTable.AmbiguousForwardTable.get()=Bio.Data.CodonTable.AmbiguousForwardTable-class.html#get,Method Bio.EUtils.MultiDict._BaseMultiDict.get()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#get,Method Bio.EUtils.POM.ElementNode.get()=Bio.EUtils.POM.ElementNode-class.html#get,Method Bio.GenBank.NCBIDictionary.get()=Bio.GenBank.NCBIDictionary-class.html#get,Method Bio.Mindy.BaseDB.DictLookup.get()=Bio.Mindy.BaseDB.DictLookup-class.html#get,Method Bio.Prosite.ExPASyDictionary.get()=Bio.Prosite.ExPASyDictionary-class.html#get,Method Bio.Prosite.Prodoc.ExPASyDictionary.get()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#get,Method Bio.PubMed.Dictionary.get()=Bio.PubMed.Dictionary-class.html#get,Method Bio.Restriction.Restriction.RestrictionBatch.get()=Bio.Restriction.Restriction.RestrictionBatch-class.html#get,Method Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get()=Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder-class.html#get,Method Bio.SeqUtils.MissingTable.get()=Bio.SeqUtils.MissingTable-class.html#get,Method Bio.SwissProt.SProt.ExPASyDictionary.get()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#get,Method Bio.config.DBRegistry.DBGroup.get()=Bio.config.DBRegistry.DBGroup-class.html#get,Method Bio.config.DBRegistry.DBObject.get()=Bio.config.DBRegistry.DBObject-class.html#get,Method Bio.config.Registry.Registry.get()=Bio.config.Registry.Registry-class.html#get,Method Martel.Parser.MartelAttributeList.get()=Martel.Parser.MartelAttributeList-class.html#get,Method Martel.msre_parse.Tokenizer.get()=Martel.msre_parse.Tokenizer-class.html#get"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-8', 'get', 'link-8');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">"database"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-name">kw</tt><tt class="py-op">[</tt><tt class="py-string">"database"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-string">"template1"</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-name">conn</tt> <tt class="py-op">=</tt> <tt class="py-name">connect</tt><tt class="py-op">(</tt><tt class="py-op">**</tt><tt class="py-name">kw</tt><tt class="py-op">)</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">module</tt><tt class="py-op">.</tt><tt class="py-name">InterfaceError</tt><tt class="py-op">:</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-comment"># Ok, so let's try building a DSN</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># (older releases of psycopg need this)</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">kw</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-9', 'has_key', 'link-4');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-string">"database"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-name">kw</tt><tt class="py-op">[</tt><tt class="py-string">"dbname"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">kw</tt><tt class="py-op">[</tt><tt class="py-string">"database"</tt><tt class="py-op">]</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-keyword">del</tt> <tt class="py-name">kw</tt><tt class="py-op">[</tt><tt class="py-string">"database"</tt><tt class="py-op">]</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">kw</tt><tt class="py-op">.</tt><tt id="link-10" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-10', 'has_key', 'link-4');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-string">"db"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-name">kw</tt><tt class="py-op">[</tt><tt class="py-string">"dbname"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">kw</tt><tt class="py-op">[</tt><tt class="py-string">"db"</tt><tt class="py-op">]</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-keyword">del</tt> <tt class="py-name">kw</tt><tt class="py-op">[</tt><tt class="py-string">"db"</tt><tt class="py-op">]</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-name">dsn</tt> <tt class="py-op">=</tt> <tt class="py-string">' '</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">'='</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt id="link-11" class="py-name" targets="Variable Bio.PDB.Polypeptide.i=Bio.PDB.Polypeptide-module.html#i"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-11', 'i', 'link-11');">i</a></tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt id="link-12" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-12', 'i', 'link-11');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">kw</tt><tt class="py-op">.</tt><tt id="link-13" class="py-name" targets="Method Bio.Crystal.Crystal.items()=Bio.Crystal.Crystal-class.html#items,Method Bio.EUtils.MultiDict._BaseMultiDict.items()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#items,Variable Bio.Entrez.SerialSet.items=Bio.Entrez.SerialSet-module.html#items,Method Bio.GenBank.NCBIDictionary.items()=Bio.GenBank.NCBIDictionary-class.html#items,Method Bio.Mindy.BaseDB.DictLookup.items()=Bio.Mindy.BaseDB.DictLookup-class.html#items,Method Bio.Prosite.ExPASyDictionary.items()=Bio.Prosite.ExPASyDictionary-class.html#items,Method Bio.Prosite.Prodoc.ExPASyDictionary.items()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#items,Method Bio.PubMed.Dictionary.items()=Bio.PubMed.Dictionary-class.html#items,Method Bio.SwissProt.SProt.ExPASyDictionary.items()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#items,Method Bio.config.Registry.Registry.items()=Bio.config.Registry.Registry-class.html#items,Function Bio.listfns.items()=Bio.listfns-module.html#items,Method BioSQL.BioSeqDatabase.BioSeqDatabase.items()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#items,Method BioSQL.BioSeqDatabase.DBServer.items()=BioSQL.BioSeqDatabase.DBServer-class.html#items,Method Martel.Parser.MartelAttributeList.items()=Martel.Parser.MartelAttributeList-class.html#items"><a title="Bio.Crystal.Crystal.items
Bio.EUtils.MultiDict._BaseMultiDict.items
Bio.Entrez.SerialSet.items
Bio.GenBank.NCBIDictionary.items
Bio.Mindy.BaseDB.DictLookup.items
Bio.Prosite.ExPASyDictionary.items
Bio.Prosite.Prodoc.ExPASyDictionary.items
Bio.PubMed.Dictionary.items
Bio.SwissProt.SProt.ExPASyDictionary.items
Bio.config.Registry.Registry.items
Bio.listfns.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items
Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-13', 'items', 'link-13');">items</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-name">conn</tt> <tt class="py-op">=</tt> <tt class="py-name">connect</tt><tt class="py-op">(</tt><tt class="py-name">dsn</tt><tt class="py-op">)</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-14" class="py-name" targets="Class BioSQL.BioSeqDatabase.DBServer=BioSQL.BioSeqDatabase.DBServer-class.html"><a title="BioSQL.BioSeqDatabase.DBServer" class="py-name" href="#" onclick="return doclink('link-14', 'DBServer', 'link-14');">DBServer</a></tt><tt class="py-op">(</tt><tt class="py-name">conn</tt><tt class="py-op">,</tt> <tt class="py-name">module</tt><tt class="py-op">)</tt> </tt>
</div><a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> </tt>
<a name="DBServer"></a><div id="DBServer-def"><a name="L75"></a><tt class="py-lineno"> 75</tt> <a class="py-toggle" href="#" id="DBServer-toggle" onclick="return toggle('DBServer');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.DBServer-class.html">DBServer</a><tt class="py-op">:</tt> </tt>
</div><div id="DBServer-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="DBServer-expanded"><a name="DBServer.__init__"></a><div id="DBServer.__init__-def"><a name="L76"></a><tt class="py-lineno"> 76</tt> <a class="py-toggle" href="#" id="DBServer.__init__-toggle" onclick="return toggle('DBServer.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.DBServer-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">conn</tt><tt class="py-op">,</tt> <tt class="py-param">module</tt><tt class="py-op">,</tt> <tt class="py-param">module_name</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DBServer.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DBServer.__init__-expanded"><a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">module</tt> <tt class="py-op">=</tt> <tt class="py-name">module</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">module_name</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-name">module_name</tt> <tt class="py-op">=</tt> <tt class="py-name">module</tt><tt class="py-op">.</tt><tt class="py-name">__name__</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt> <tt class="py-op">=</tt> <tt id="link-15" class="py-name" targets="Class BioSQL.BioSeqDatabase.Adaptor=BioSQL.BioSeqDatabase.Adaptor-class.html"><a title="BioSQL.BioSeqDatabase.Adaptor" class="py-name" href="#" onclick="return doclink('link-15', 'Adaptor', 'link-15');">Adaptor</a></tt><tt class="py-op">(</tt><tt class="py-name">conn</tt><tt class="py-op">,</tt> <tt id="link-16" class="py-name"><a title="BioSQL.DBUtils" class="py-name" href="#" onclick="return doclink('link-16', 'DBUtils', 'link-2');">DBUtils</a></tt><tt class="py-op">.</tt><tt id="link-17" class="py-name" targets="Function BioSQL.DBUtils.get_dbutils()=BioSQL.DBUtils-module.html#get_dbutils"><a title="BioSQL.DBUtils.get_dbutils" class="py-name" href="#" onclick="return doclink('link-17', 'get_dbutils', 'link-17');">get_dbutils</a></tt><tt class="py-op">(</tt><tt class="py-name">module_name</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">module_name</tt> <tt class="py-op">=</tt> <tt class="py-name">module_name</tt> </tt>
</div><a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> </tt>
<a name="DBServer.__repr__"></a><div id="DBServer.__repr__-def"><a name="L83"></a><tt class="py-lineno"> 83</tt> <a class="py-toggle" href="#" id="DBServer.__repr__-toggle" onclick="return toggle('DBServer.__repr__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.DBServer-class.html#__repr__">__repr__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DBServer.__repr__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DBServer.__repr__-expanded"><a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__class__</tt><tt class="py-op">.</tt><tt class="py-name">__name__</tt> <tt class="py-op">+</tt> <tt class="py-string">"(%r)"</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt class="py-name">conn</tt> </tt>
</div><a name="DBServer.__getitem__"></a><div id="DBServer.__getitem__-def"><a name="L85"></a><tt class="py-lineno"> 85</tt> <a class="py-toggle" href="#" id="DBServer.__getitem__-toggle" onclick="return toggle('DBServer.__getitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.DBServer-class.html#__getitem__">__getitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DBServer.__getitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DBServer.__getitem__-expanded"><a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-18" class="py-name" targets="Module BioSQL.BioSeqDatabase=BioSQL.BioSeqDatabase-module.html,Class BioSQL.BioSeqDatabase.BioSeqDatabase=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html"><a title="BioSQL.BioSeqDatabase
BioSQL.BioSeqDatabase.BioSeqDatabase" class="py-name" href="#" onclick="return doclink('link-18', 'BioSeqDatabase', 'link-18');">BioSeqDatabase</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">,</tt> <tt id="link-19" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.name=Bio.Encodings.IUPACEncoding-module.html#name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-19', 'name', 'link-19');">name</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="DBServer.keys"></a><div id="DBServer.keys-def"><a name="L87"></a><tt class="py-lineno"> 87</tt> <a class="py-toggle" href="#" id="DBServer.keys-toggle" onclick="return toggle('DBServer.keys');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.DBServer-class.html#keys">keys</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DBServer.keys-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DBServer.keys-expanded"><a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name" targets="Method BioSQL.BioSeqDatabase.Adaptor.list_biodatabase_names()=BioSQL.BioSeqDatabase.Adaptor-class.html#list_biodatabase_names"><a title="BioSQL.BioSeqDatabase.Adaptor.list_biodatabase_names" class="py-name" href="#" onclick="return doclink('link-20', 'list_biodatabase_names', 'link-20');">list_biodatabase_names</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="DBServer.values"></a><div id="DBServer.values-def"><a name="L89"></a><tt class="py-lineno"> 89</tt> <a class="py-toggle" href="#" id="DBServer.values-toggle" onclick="return toggle('DBServer.values');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.DBServer-class.html#values">values</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DBServer.values-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DBServer.values-expanded"><a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">[</tt><tt id="link-21" class="py-name" targets="Variable Bio.Translate.key=Bio.Translate-module.html#key"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-21', 'key', 'link-21');">key</a></tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt id="link-22" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-22', 'key', 'link-21');">key</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name" targets="Method Bio.Crystal.Crystal.keys()=Bio.Crystal.Crystal-class.html#keys,Method Bio.EUtils.MultiDict._BaseMultiDict.keys()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#keys,Method Bio.GenBank.NCBIDictionary.keys()=Bio.GenBank.NCBIDictionary-class.html#keys,Method Bio.Mindy.BaseDB.DictLookup.keys()=Bio.Mindy.BaseDB.DictLookup-class.html#keys,Method Bio.Mindy.BaseDB.OpenDB.keys()=Bio.Mindy.BaseDB.OpenDB-class.html#keys,Method Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys()=Bio.Mindy.BerkeleyDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys()=Bio.Mindy.BerkeleyDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryNamespace.keys()=Bio.Mindy.FlatDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryTable.keys()=Bio.Mindy.FlatDB.PrimaryTable-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryNamespace.keys()=Bio.Mindy.FlatDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryTable.keys()=Bio.Mindy.FlatDB.SecondaryTable-class.html#keys,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#keys,Method Bio.Prosite.ExPASyDictionary.keys()=Bio.Prosite.ExPASyDictionary-class.html#keys,Method Bio.Prosite.Prodoc.ExPASyDictionary.keys()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#keys,Method Bio.PubMed.Dictionary.keys()=Bio.PubMed.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.Dictionary.keys()=Bio.SwissProt.SProt.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.ExPASyDictionary.keys()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#keys,Method Bio.config.Registry.Registry.keys()=Bio.config.Registry.Registry-class.html#keys,Method BioSQL.BioSeqDatabase.BioSeqDatabase.keys()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#keys,Method BioSQL.BioSeqDatabase.DBServer.keys()=BioSQL.BioSeqDatabase.DBServer-class.html#keys,Method Martel.Parser.MartelAttributeList.keys()=Martel.Parser.MartelAttributeList-class.html#keys"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-23', 'keys', 'link-23');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
</div><a name="DBServer.items"></a><div id="DBServer.items-def"><a name="L91"></a><tt class="py-lineno"> 91</tt> <a class="py-toggle" href="#" id="DBServer.items-toggle" onclick="return toggle('DBServer.items');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.DBServer-class.html#items">items</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DBServer.items-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DBServer.items-expanded"><a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">[</tt><tt class="py-op">(</tt><tt id="link-24" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-24', 'key', 'link-21');">key</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">[</tt><tt id="link-25" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-25', 'key', 'link-21');">key</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt id="link-26" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-26', 'key', 'link-21');">key</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-27" class="py-name"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-27', 'keys', 'link-23');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
</div><a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> </tt>
<a name="DBServer.remove_database"></a><div id="DBServer.remove_database-def"><a name="L94"></a><tt class="py-lineno"> 94</tt> <a class="py-toggle" href="#" id="DBServer.remove_database-toggle" onclick="return toggle('DBServer.remove_database');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.DBServer-class.html#remove_database">remove_database</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">db_name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DBServer.remove_database-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DBServer.remove_database-expanded"><a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-docstring">"""Try to remove all references to items in a database.</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-name">db_id</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-28" class="py-name" targets="Method BioSQL.BioSeqDatabase.Adaptor.fetch_dbid_by_dbname()=BioSQL.BioSeqDatabase.Adaptor-class.html#fetch_dbid_by_dbname"><a title="BioSQL.BioSeqDatabase.Adaptor.fetch_dbid_by_dbname" class="py-name" href="#" onclick="return doclink('link-28', 'fetch_dbid_by_dbname', 'link-28');">fetch_dbid_by_dbname</a></tt><tt class="py-op">(</tt><tt class="py-name">db_name</tt><tt class="py-op">)</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-name">remover</tt> <tt class="py-op">=</tt> <tt id="link-29" class="py-name"><a title="BioSQL.Loader" class="py-name" href="#" onclick="return doclink('link-29', 'Loader', 'link-1');">Loader</a></tt><tt class="py-op">.</tt><tt id="link-30" class="py-name" targets="Class BioSQL.Loader.DatabaseRemover=BioSQL.Loader.DatabaseRemover-class.html"><a title="BioSQL.Loader.DatabaseRemover" class="py-name" href="#" onclick="return doclink('link-30', 'DatabaseRemover', 'link-30');">DatabaseRemover</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">,</tt> <tt class="py-name">db_id</tt><tt class="py-op">)</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-name">remover</tt><tt class="py-op">.</tt><tt id="link-31" class="py-name" targets="Method Bio.Crystal.Chain.remove()=Bio.Crystal.Chain-class.html#remove,Method Bio.GFF.GenericTools.TempFile.remove()=Bio.GFF.GenericTools.TempFile-class.html#remove,Method Bio.Graphics.BasicChromosome._ChromosomeComponent.remove()=Bio.Graphics.BasicChromosome._ChromosomeComponent-class.html#remove,Method Bio.Pathway.Rep.HashSet.HashSet.remove()=Bio.Pathway.Rep.HashSet.HashSet-class.html#remove,Method Bio.Restriction.Restriction.RestrictionBatch.remove()=Bio.Restriction.Restriction.RestrictionBatch-class.html#remove,Method Bio.Seq.MutableSeq.remove()=Bio.Seq.MutableSeq-class.html#remove,Method BioSQL.Loader.DatabaseRemover.remove()=BioSQL.Loader.DatabaseRemover-class.html#remove"><a title="Bio.Crystal.Chain.remove
Bio.GFF.GenericTools.TempFile.remove
Bio.Graphics.BasicChromosome._ChromosomeComponent.remove
Bio.Pathway.Rep.HashSet.HashSet.remove
Bio.Restriction.Restriction.RestrictionBatch.remove
Bio.Seq.MutableSeq.remove
BioSQL.Loader.DatabaseRemover.remove" class="py-name" href="#" onclick="return doclink('link-31', 'remove', 'link-31');">remove</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> </tt>
<a name="DBServer.new_database"></a><div id="DBServer.new_database-def"><a name="L101"></a><tt class="py-lineno">101</tt> <a class="py-toggle" href="#" id="DBServer.new_database-toggle" onclick="return toggle('DBServer.new_database');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.DBServer-class.html#new_database">new_database</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">db_name</tt><tt class="py-op">,</tt> <tt class="py-param">authority</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">description</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DBServer.new_database-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DBServer.new_database-expanded"><a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-docstring">"""Add a new database to the server and return it.</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-comment"># make the database</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">sql</tt> <tt class="py-op">=</tt> <tt class="py-string">r"INSERT INTO biodatabase (name, authority, description)"</tt> \ </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-string">r" VALUES (%s, %s, %s)"</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-32" class="py-name" targets="Method BioSQL.BioSeqDatabase.Adaptor.execute()=BioSQL.BioSeqDatabase.Adaptor-class.html#execute"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-32', 'execute', 'link-32');">execute</a></tt><tt class="py-op">(</tt><tt class="py-name">sql</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">db_name</tt><tt class="py-op">,</tt><tt class="py-name">authority</tt><tt class="py-op">,</tt> <tt id="link-33" class="py-name" targets="Method Bio.Blast.NCBIStandalone._DescriptionConsumer.description()=Bio.Blast.NCBIStandalone._DescriptionConsumer-class.html#description,Method Bio.Enzyme._RecordConsumer.description()=Bio.Enzyme._RecordConsumer-class.html#description,Method Bio.Prosite._RecordConsumer.description()=Bio.Prosite._RecordConsumer-class.html#description,Function Bio.Std.description()=Bio.Std-module.html#description,Method Bio.SwissProt.SProt._RecordConsumer.description()=Bio.SwissProt.SProt._RecordConsumer-class.html#description,Method Bio.SwissProt.SProt._SequenceConsumer.description()=Bio.SwissProt.SProt._SequenceConsumer-class.html#description,Variable Martel.setup.run_local_tests.description=Martel.setup.run_local_tests-class.html#description"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description
Bio.Enzyme._RecordConsumer.description
Bio.Prosite._RecordConsumer.description
Bio.Std.description
Bio.SwissProt.SProt._RecordConsumer.description
Bio.SwissProt.SProt._SequenceConsumer.description
Martel.setup.run_local_tests.description" class="py-name" href="#" onclick="return doclink('link-33', 'description', 'link-33');">description</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-34" class="py-name"><a title="BioSQL.BioSeqDatabase
BioSQL.BioSeqDatabase.BioSeqDatabase" class="py-name" href="#" onclick="return doclink('link-34', 'BioSeqDatabase', 'link-18');">BioSeqDatabase</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">,</tt> <tt class="py-name">db_name</tt><tt class="py-op">)</tt> </tt>
</div><a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> </tt>
<a name="DBServer.load_database_sql"></a><div id="DBServer.load_database_sql-def"><a name="L110"></a><tt class="py-lineno">110</tt> <a class="py-toggle" href="#" id="DBServer.load_database_sql-toggle" onclick="return toggle('DBServer.load_database_sql');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.DBServer-class.html#load_database_sql">load_database_sql</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">sql_file</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DBServer.load_database_sql-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DBServer.load_database_sql-expanded"><a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-docstring">"""Load a database schema into the given database.</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"><tt class="py-docstring"> This is used to create tables, etc when a database is first created.</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"><tt class="py-docstring"> sql_file should specify the complete path to a file containing</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"><tt class="py-docstring"> SQL entries for building the tables.</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt class="py-comment"># Not sophisticated enough for PG schema. Is it needed by MySQL?</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Looks like we need this more complicated way for both. Leaving it</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># the default and removing the simple-minded approach.</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-comment"># read the file with all comment lines removed</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">sql_handle</tt> <tt class="py-op">=</tt> <tt id="link-35" class="py-name" targets="Function Bio.Mindy.FlatDB.open()=Bio.Mindy.FlatDB-module.html#open,Function Bio.Mindy.open()=Bio.Mindy-module.html#open"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-35', 'open', 'link-35');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">sql_file</tt><tt class="py-op">,</tt> <tt class="py-string">"rb"</tt><tt class="py-op">)</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-name">sql</tt> <tt class="py-op">=</tt> <tt class="py-string">r""</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt class="py-name">sql_handle</tt><tt class="py-op">.</tt><tt class="py-name">xreadlines</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-36" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.find()=Bio.EUtils.POM.ElementNode-class.html#find,Method Bio.NeuralNetwork.Gene.Motif.MotifFinder.find()=Bio.NeuralNetwork.Gene.Motif.MotifFinder-class.html#find,Method Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find()=Bio.NeuralNetwork.Gene.Schema.SchemaFinder-class.html#find,Method Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find()=Bio.NeuralNetwork.Gene.Signature.SignatureFinder-class.html#find,Method Bio.biblio.Biblio.find()=Bio.biblio.Biblio-class.html#find,Function Bio.triefind.find()=Bio.triefind-module.html#find"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-36', 'find', 'link-36');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">"--"</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> <tt class="py-comment"># don't include comment lines</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-37', 'find', 'link-36');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">"#"</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> <tt class="py-comment"># ditto for MySQL comments</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-38" class="py-name" targets="Class Bio.EUtils.DTDs.LinkOut.strip=Bio.EUtils.DTDs.LinkOut.strip-class.html,Method Bio.File.SGMLStripper.strip()=Bio.File.SGMLStripper-class.html#strip,Method Bio.SGMLExtractor.SGMLExtractor.strip()=Bio.SGMLExtractor.SGMLExtractor-class.html#strip"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-38', 'strip', 'link-38');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-comment"># only include non-blank lines</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-name">sql</tt> <tt class="py-op">+=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-39" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-39', 'strip', 'link-38');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-name">sql</tt> <tt class="py-op">+=</tt> <tt class="py-string">' '</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-comment"># two ways to load the SQL</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># 1. PostgreSQL can load it all at once and actually needs to</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># due to FUNCTION defines at the end of the SQL which mess up</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># the splitting by semicolons</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">module_name</tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt><tt class="py-string">"psycopg"</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-40" class="py-name" targets="Method Bio.DocSQL.Query.cursor()=Bio.DocSQL.Query-class.html#cursor,Method Bio.DocSQL.QuerySingle.cursor()=Bio.DocSQL.QuerySingle-class.html#cursor"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-40', 'cursor', 'link-40');">cursor</a></tt><tt class="py-op">.</tt><tt id="link-41" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-41', 'execute', 'link-32');">execute</a></tt><tt class="py-op">(</tt><tt class="py-name">sql</tt><tt class="py-op">)</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-comment"># 2. MySQL needs the database loading split up into single lines of</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># SQL executed one at a time</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">elif</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">module_name</tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt><tt class="py-string">"MySQLdb"</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-name">sql_parts</tt> <tt class="py-op">=</tt> <tt class="py-name">sql</tt><tt class="py-op">.</tt><tt id="link-42" class="py-name" targets="Method Bio.Nexus.Trees.Tree.split()=Bio.Nexus.Trees.Tree-class.html#split,Method Bio.Restriction.Restriction.RestrictionBatch.split()=Bio.Restriction.Restriction.RestrictionBatch-class.html#split"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-42', 'split', 'link-42');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">";"</tt><tt class="py-op">)</tt> <tt class="py-comment"># one line per sql command</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">sql_line</tt> <tt class="py-keyword">in</tt> <tt class="py-name">sql_parts</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> <tt class="py-comment"># don't use the last item, it's blank</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-43" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-43', 'cursor', 'link-40');">cursor</a></tt><tt class="py-op">.</tt><tt id="link-44" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-44', 'execute', 'link-32');">execute</a></tt><tt class="py-op">(</tt><tt class="py-name">sql_line</tt><tt class="py-op">)</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Module %s not supported by the loader."</tt> <tt class="py-op">%</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">module_name</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> </tt>
<a name="Adaptor"></a><div id="Adaptor-def"><a name="L149"></a><tt class="py-lineno">149</tt> <a class="py-toggle" href="#" id="Adaptor-toggle" onclick="return toggle('Adaptor');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.Adaptor-class.html">Adaptor</a><tt class="py-op">:</tt> </tt>
</div><div id="Adaptor-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Adaptor-expanded"><a name="Adaptor.__init__"></a><div id="Adaptor.__init__-def"><a name="L150"></a><tt class="py-lineno">150</tt> <a class="py-toggle" href="#" id="Adaptor.__init__-toggle" onclick="return toggle('Adaptor.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.Adaptor-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">conn</tt><tt class="py-op">,</tt> <tt class="py-param">dbutils</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Adaptor.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Adaptor.__init__-expanded"><a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">conn</tt> <tt class="py-op">=</tt> <tt class="py-name">conn</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-45" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-45', 'cursor', 'link-40');">cursor</a></tt> <tt class="py-op">=</tt> <tt class="py-name">conn</tt><tt class="py-op">.</tt><tt id="link-46" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-46', 'cursor', 'link-40');">cursor</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dbutils</tt> <tt class="py-op">=</tt> <tt class="py-name">dbutils</tt> </tt>
</div><a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> </tt>
<a name="Adaptor.last_id"></a><div id="Adaptor.last_id-def"><a name="L155"></a><tt class="py-lineno">155</tt> <a class="py-toggle" href="#" id="Adaptor.last_id-toggle" onclick="return toggle('Adaptor.last_id');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.Adaptor-class.html#last_id">last_id</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">table</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Adaptor.last_id-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Adaptor.last_id-expanded"><a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dbutils</tt><tt class="py-op">.</tt><tt id="link-47" class="py-name" targets="Method BioSQL.BioSeqDatabase.Adaptor.last_id()=BioSQL.BioSeqDatabase.Adaptor-class.html#last_id,Method BioSQL.DBUtils.Generic_dbutils.last_id()=BioSQL.DBUtils.Generic_dbutils-class.html#last_id,Method BioSQL.DBUtils.Mysql_dbutils.last_id()=BioSQL.DBUtils.Mysql_dbutils-class.html#last_id,Method BioSQL.DBUtils.Pgdb_dbutils.last_id()=BioSQL.DBUtils.Pgdb_dbutils-class.html#last_id,Method BioSQL.DBUtils.Psycopg_dbutils.last_id()=BioSQL.DBUtils.Psycopg_dbutils-class.html#last_id"><a title="BioSQL.BioSeqDatabase.Adaptor.last_id
BioSQL.DBUtils.Generic_dbutils.last_id
BioSQL.DBUtils.Mysql_dbutils.last_id
BioSQL.DBUtils.Pgdb_dbutils.last_id
BioSQL.DBUtils.Psycopg_dbutils.last_id" class="py-name" href="#" onclick="return doclink('link-47', 'last_id', 'link-47');">last_id</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-48" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-48', 'cursor', 'link-40');">cursor</a></tt><tt class="py-op">,</tt> <tt id="link-49" class="py-name" targets="Variable Bio.CDD.cdd_format.table=Bio.CDD.cdd_format-module.html#table,Variable Bio.expressions.blast.ncbiblast.table=Bio.expressions.blast.ncbiblast-module.html#table"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-49', 'table', 'link-49');">table</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> </tt>
<a name="Adaptor.autocommit"></a><div id="Adaptor.autocommit-def"><a name="L158"></a><tt class="py-lineno">158</tt> <a class="py-toggle" href="#" id="Adaptor.autocommit-toggle" onclick="return toggle('Adaptor.autocommit');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.Adaptor-class.html#autocommit">autocommit</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">y</tt><tt class="py-op">=</tt><tt id="link-50" class="py-name" targets="Variable Bio.EUtils.POM.True=Bio.EUtils.POM-module.html#True"><a title="Bio.EUtils.POM.True" class="py-name" href="#" onclick="return doclink('link-50', 'True', 'link-50');">True</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Adaptor.autocommit-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Adaptor.autocommit-expanded"><a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dbutils</tt><tt class="py-op">.</tt><tt id="link-51" class="py-name" targets="Method BioSQL.BioSeqDatabase.Adaptor.autocommit()=BioSQL.BioSeqDatabase.Adaptor-class.html#autocommit,Method BioSQL.DBUtils.Generic_dbutils.autocommit()=BioSQL.DBUtils.Generic_dbutils-class.html#autocommit,Method BioSQL.DBUtils.Pgdb_dbutils.autocommit()=BioSQL.DBUtils.Pgdb_dbutils-class.html#autocommit,Method BioSQL.DBUtils.Psycopg_dbutils.autocommit()=BioSQL.DBUtils.Psycopg_dbutils-class.html#autocommit"><a title="BioSQL.BioSeqDatabase.Adaptor.autocommit
BioSQL.DBUtils.Generic_dbutils.autocommit
BioSQL.DBUtils.Pgdb_dbutils.autocommit
BioSQL.DBUtils.Psycopg_dbutils.autocommit" class="py-name" href="#" onclick="return doclink('link-51', 'autocommit', 'link-51');">autocommit</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">conn</tt><tt class="py-op">,</tt> <tt class="py-name">y</tt><tt class="py-op">)</tt> </tt>
</div><a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> </tt>
<a name="Adaptor.commit"></a><div id="Adaptor.commit-def"><a name="L161"></a><tt class="py-lineno">161</tt> <a class="py-toggle" href="#" id="Adaptor.commit-toggle" onclick="return toggle('Adaptor.commit');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.Adaptor-class.html#commit">commit</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Adaptor.commit-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Adaptor.commit-expanded"><a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">conn</tt><tt class="py-op">.</tt><tt id="link-52" class="py-name" targets="Method BioSQL.BioSeqDatabase.Adaptor.commit()=BioSQL.BioSeqDatabase.Adaptor-class.html#commit"><a title="BioSQL.BioSeqDatabase.Adaptor.commit" class="py-name" href="#" onclick="return doclink('link-52', 'commit', 'link-52');">commit</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> </tt>
<a name="Adaptor.rollback"></a><div id="Adaptor.rollback-def"><a name="L164"></a><tt class="py-lineno">164</tt> <a class="py-toggle" href="#" id="Adaptor.rollback-toggle" onclick="return toggle('Adaptor.rollback');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.Adaptor-class.html#rollback">rollback</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Adaptor.rollback-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Adaptor.rollback-expanded"><a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">conn</tt><tt class="py-op">.</tt><tt id="link-53" class="py-name" targets="Method BioSQL.BioSeqDatabase.Adaptor.rollback()=BioSQL.BioSeqDatabase.Adaptor-class.html#rollback"><a title="BioSQL.BioSeqDatabase.Adaptor.rollback" class="py-name" href="#" onclick="return doclink('link-53', 'rollback', 'link-53');">rollback</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> </tt>
<a name="Adaptor.close"></a><div id="Adaptor.close-def"><a name="L167"></a><tt class="py-lineno">167</tt> <a class="py-toggle" href="#" id="Adaptor.close-toggle" onclick="return toggle('Adaptor.close');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.Adaptor-class.html#close">close</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Adaptor.close-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Adaptor.close-expanded"><a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">conn</tt><tt class="py-op">.</tt><tt id="link-54" class="py-name" targets="Method Bio.FilteredReader.FilteredReader.close()=Bio.FilteredReader.FilteredReader-class.html#close,Method Bio.Mindy.BerkeleyDB.BerkeleyDB.close()=Bio.Mindy.BerkeleyDB.BerkeleyDB-class.html#close,Method Bio.Mindy.FlatDB.MemoryFlatDB.close()=Bio.Mindy.FlatDB.MemoryFlatDB-class.html#close,Method BioSQL.BioSeqDatabase.Adaptor.close()=BioSQL.BioSeqDatabase.Adaptor-class.html#close,Method Martel.Parser.Parser.close()=Martel.Parser.Parser-class.html#close,Method Martel.Parser.RecordParser.close()=Martel.Parser.RecordParser-class.html#close"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-54', 'close', 'link-54');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> </tt>
<a name="Adaptor.fetch_dbid_by_dbname"></a><div id="Adaptor.fetch_dbid_by_dbname-def"><a name="L170"></a><tt class="py-lineno">170</tt> <a class="py-toggle" href="#" id="Adaptor.fetch_dbid_by_dbname-toggle" onclick="return toggle('Adaptor.fetch_dbid_by_dbname');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.Adaptor-class.html#fetch_dbid_by_dbname">fetch_dbid_by_dbname</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">dbname</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Adaptor.fetch_dbid_by_dbname-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Adaptor.fetch_dbid_by_dbname-expanded"><a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-55" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-55', 'cursor', 'link-40');">cursor</a></tt><tt class="py-op">.</tt><tt id="link-56" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-56', 'execute', 'link-32');">execute</a></tt><tt class="py-op">(</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt class="py-string">r"select biodatabase_id from biodatabase where name = %s"</tt><tt class="py-op">,</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">dbname</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-name">rv</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-57" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-57', 'cursor', 'link-40');">cursor</a></tt><tt class="py-op">.</tt><tt class="py-name">fetchall</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">rv</tt><tt class="py-op">:</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">KeyError</tt><tt class="py-op">(</tt><tt class="py-string">"Cannot find biodatabase with name %r"</tt> <tt class="py-op">%</tt> <tt class="py-name">dbname</tt><tt class="py-op">)</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-comment"># Cannot happen (UK)</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## assert len(rv) == 1, "More than one biodatabase with name %r" % dbname</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt class="py-name">rv</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
</div><a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> </tt>
<a name="Adaptor.fetch_seqid_by_display_id"></a><div id="Adaptor.fetch_seqid_by_display_id-def"><a name="L181"></a><tt class="py-lineno">181</tt> <a class="py-toggle" href="#" id="Adaptor.fetch_seqid_by_display_id-toggle" onclick="return toggle('Adaptor.fetch_seqid_by_display_id');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.Adaptor-class.html#fetch_seqid_by_display_id">fetch_seqid_by_display_id</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">dbid</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Adaptor.fetch_seqid_by_display_id-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Adaptor.fetch_seqid_by_display_id-expanded"><a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt class="py-name">sql</tt> <tt class="py-op">=</tt> <tt class="py-string">r"select bioentry_id from bioentry where name = %s"</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> <tt class="py-name">fields</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-58" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-58', 'name', 'link-19');">name</a></tt><tt class="py-op">]</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-59" class="py-name" targets="Function Bio.Std.dbid()=Bio.Std-module.html#dbid"><a title="Bio.Std.dbid" class="py-name" href="#" onclick="return doclink('link-59', 'dbid', 'link-59');">dbid</a></tt><tt class="py-op">:</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-name">sql</tt> <tt class="py-op">+=</tt> <tt class="py-string">" and biodatabase_id = %s"</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> <tt class="py-name">fields</tt><tt class="py-op">.</tt><tt id="link-60" class="py-name" targets="Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-class.html#append,Method Bio.EUtils.POM.ElementNode.append()=Bio.EUtils.POM.ElementNode-class.html#append,Method Bio.EUtils.sourcegen.SourceFile.append()=Bio.EUtils.sourcegen.SourceFile-class.html#append,Method Bio.SCOP.Raf.SeqMap.append()=Bio.SCOP.Raf.SeqMap-class.html#append,Method Bio.Seq.MutableSeq.append()=Bio.Seq.MutableSeq-class.html#append,Method Bio.Wise.psw.Alignment.append()=Bio.Wise.psw.Alignment-class.html#append,Method Bio.Wise.psw.AlignmentColumn.append()=Bio.Wise.psw.AlignmentColumn-class.html#append,Method Martel.msre_parse.SubPattern.append()=Martel.msre_parse.SubPattern-class.html#append"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-60', 'append', 'link-60');">append</a></tt><tt class="py-op">(</tt><tt id="link-61" class="py-name"><a title="Bio.Std.dbid" class="py-name" href="#" onclick="return doclink('link-61', 'dbid', 'link-59');">dbid</a></tt><tt class="py-op">)</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-62" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-62', 'cursor', 'link-40');">cursor</a></tt><tt class="py-op">.</tt><tt id="link-63" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-63', 'execute', 'link-32');">execute</a></tt><tt class="py-op">(</tt><tt class="py-name">sql</tt><tt class="py-op">,</tt> <tt class="py-name">fields</tt><tt class="py-op">)</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> <tt class="py-name">rv</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-64" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-64', 'cursor', 'link-40');">cursor</a></tt><tt class="py-op">.</tt><tt class="py-name">fetchall</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">rv</tt><tt class="py-op">:</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">IndexError</tt><tt class="py-op">(</tt><tt class="py-string">"Cannot find display id %r"</tt> <tt class="py-op">%</tt> <tt id="link-65" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-65', 'name', 'link-19');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">rv</tt><tt class="py-op">)</tt> <tt class="py-op">></tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">IndexError</tt><tt class="py-op">(</tt><tt class="py-string">"More than one entry with display id %r"</tt> <tt class="py-op">%</tt> <tt id="link-66" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-66', 'name', 'link-19');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">rv</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
</div><a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> </tt>
<a name="Adaptor.fetch_seqid_by_accession"></a><div id="Adaptor.fetch_seqid_by_accession-def"><a name="L195"></a><tt class="py-lineno">195</tt> <a class="py-toggle" href="#" id="Adaptor.fetch_seqid_by_accession-toggle" onclick="return toggle('Adaptor.fetch_seqid_by_accession');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.Adaptor-class.html#fetch_seqid_by_accession">fetch_seqid_by_accession</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">dbid</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Adaptor.fetch_seqid_by_accession-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Adaptor.fetch_seqid_by_accession-expanded"><a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-name">sql</tt> <tt class="py-op">=</tt> <tt class="py-string">r"select bioentry_id from bioentry where accession = %s"</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt class="py-name">fields</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-67" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-67', 'name', 'link-19');">name</a></tt><tt class="py-op">]</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-68" class="py-name"><a title="Bio.Std.dbid" class="py-name" href="#" onclick="return doclink('link-68', 'dbid', 'link-59');">dbid</a></tt><tt class="py-op">:</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> <tt class="py-name">sql</tt> <tt class="py-op">+=</tt> <tt class="py-string">" and biodatabase_id = %s"</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt class="py-name">fields</tt><tt class="py-op">.</tt><tt id="link-69" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-69', 'append', 'link-60');">append</a></tt><tt class="py-op">(</tt><tt id="link-70" class="py-name"><a title="Bio.Std.dbid" class="py-name" href="#" onclick="return doclink('link-70', 'dbid', 'link-59');">dbid</a></tt><tt class="py-op">)</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-71" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-71', 'cursor', 'link-40');">cursor</a></tt><tt class="py-op">.</tt><tt id="link-72" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-72', 'execute', 'link-32');">execute</a></tt><tt class="py-op">(</tt><tt class="py-name">sql</tt><tt class="py-op">,</tt> <tt class="py-name">fields</tt><tt class="py-op">)</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt class="py-name">rv</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-73" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-73', 'cursor', 'link-40');">cursor</a></tt><tt class="py-op">.</tt><tt class="py-name">fetchall</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">rv</tt><tt class="py-op">:</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">IndexError</tt><tt class="py-op">(</tt><tt class="py-string">"Cannot find accession %r"</tt> <tt class="py-op">%</tt> <tt id="link-74" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-74', 'name', 'link-19');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">rv</tt><tt class="py-op">)</tt> <tt class="py-op">></tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">IndexError</tt><tt class="py-op">(</tt><tt class="py-string">"More than one entry with accession %r"</tt> <tt class="py-op">%</tt> <tt id="link-75" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-75', 'name', 'link-19');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">rv</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
</div><a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> </tt>
<a name="Adaptor.fetch_seqids_by_accession"></a><div id="Adaptor.fetch_seqids_by_accession-def"><a name="L209"></a><tt class="py-lineno">209</tt> <a class="py-toggle" href="#" id="Adaptor.fetch_seqids_by_accession-toggle" onclick="return toggle('Adaptor.fetch_seqids_by_accession');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.Adaptor-class.html#fetch_seqids_by_accession">fetch_seqids_by_accession</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">dbid</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Adaptor.fetch_seqids_by_accession-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Adaptor.fetch_seqids_by_accession-expanded"><a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> <tt class="py-name">sql</tt> <tt class="py-op">=</tt> <tt class="py-string">r"select bioentry_id from bioentry where accession = %s"</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt class="py-name">fields</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-76" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-76', 'name', 'link-19');">name</a></tt><tt class="py-op">]</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-77" class="py-name"><a title="Bio.Std.dbid" class="py-name" href="#" onclick="return doclink('link-77', 'dbid', 'link-59');">dbid</a></tt><tt class="py-op">:</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-name">sql</tt> <tt class="py-op">+=</tt> <tt class="py-string">" and biodatabase_id = %s"</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt class="py-name">fields</tt><tt class="py-op">.</tt><tt id="link-78" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-78', 'append', 'link-60');">append</a></tt><tt class="py-op">(</tt><tt id="link-79" class="py-name"><a title="Bio.Std.dbid" class="py-name" href="#" onclick="return doclink('link-79', 'dbid', 'link-59');">dbid</a></tt><tt class="py-op">)</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-80" class="py-name" targets="Method BioSQL.BioSeqDatabase.Adaptor.execute_and_fetch_col0()=BioSQL.BioSeqDatabase.Adaptor-class.html#execute_and_fetch_col0"><a title="BioSQL.BioSeqDatabase.Adaptor.execute_and_fetch_col0" class="py-name" href="#" onclick="return doclink('link-80', 'execute_and_fetch_col0', 'link-80');">execute_and_fetch_col0</a></tt><tt class="py-op">(</tt><tt class="py-name">sql</tt><tt class="py-op">,</tt> <tt class="py-name">fields</tt><tt class="py-op">)</tt> </tt>
</div><a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> </tt>
<a name="Adaptor.fetch_seqid_by_version"></a><div id="Adaptor.fetch_seqid_by_version-def"><a name="L217"></a><tt class="py-lineno">217</tt> <a class="py-toggle" href="#" id="Adaptor.fetch_seqid_by_version-toggle" onclick="return toggle('Adaptor.fetch_seqid_by_version');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.Adaptor-class.html#fetch_seqid_by_version">fetch_seqid_by_version</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">dbid</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Adaptor.fetch_seqid_by_version-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Adaptor.fetch_seqid_by_version-expanded"><a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt class="py-name">acc_version</tt> <tt class="py-op">=</tt> <tt id="link-81" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-81', 'name', 'link-19');">name</a></tt><tt class="py-op">.</tt><tt id="link-82" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-82', 'split', 'link-42');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">"."</tt><tt class="py-op">)</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">acc_version</tt><tt class="py-op">)</tt> <tt class="py-op">></tt> <tt class="py-number">2</tt><tt class="py-op">:</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">IndexError</tt><tt class="py-op">(</tt><tt class="py-string">"Bad version %r"</tt> <tt class="py-op">%</tt> <tt id="link-83" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-83', 'name', 'link-19');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt id="link-84" class="py-name" targets="Variable Bio.FSSP.fssp_rec.align.acc=Bio.FSSP.fssp_rec.align-class.html#acc"><a title="Bio.FSSP.fssp_rec.align.acc" class="py-name" href="#" onclick="return doclink('link-84', 'acc', 'link-84');">acc</a></tt> <tt class="py-op">=</tt> <tt class="py-name">acc_version</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">acc_version</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">2</tt><tt class="py-op">:</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt id="link-85" class="py-name" targets="Method Bio.AlignAce.Parser.AlignAceConsumer.version()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#version,Method Bio.Blast.NCBIStandalone._HeaderConsumer.version()=Bio.Blast.NCBIStandalone._HeaderConsumer-class.html#version,Method Bio.GenBank._FeatureConsumer.version()=Bio.GenBank._FeatureConsumer-class.html#version,Method Bio.GenBank._RecordConsumer.version()=Bio.GenBank._RecordConsumer-class.html#version,Variable Bio.MetaTool.metatool_format.version=Bio.MetaTool.metatool_format-module.html#version,Variable Bio.expressions.genbank.version=Bio.expressions.genbank-module.html#version"><a title="Bio.AlignAce.Parser.AlignAceConsumer.version
Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version
Bio.MetaTool.metatool_format.version
Bio.expressions.genbank.version" class="py-name" href="#" onclick="return doclink('link-85', 'version', 'link-85');">version</a></tt> <tt class="py-op">=</tt> <tt class="py-name">acc_version</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> <tt id="link-86" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.version
Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version
Bio.MetaTool.metatool_format.version
Bio.expressions.genbank.version" class="py-name" href="#" onclick="return doclink('link-86', 'version', 'link-85');">version</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"0"</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> <tt class="py-name">sql</tt> <tt class="py-op">=</tt> <tt class="py-string">r"SELECT bioentry_id FROM bioentry WHERE accession = %s"</tt> \ </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt class="py-string">r" AND version = %s"</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt class="py-name">fields</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-87" class="py-name"><a title="Bio.FSSP.fssp_rec.align.acc" class="py-name" href="#" onclick="return doclink('link-87', 'acc', 'link-84');">acc</a></tt><tt class="py-op">,</tt> <tt id="link-88" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.version
Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version
Bio.MetaTool.metatool_format.version
Bio.expressions.genbank.version" class="py-name" href="#" onclick="return doclink('link-88', 'version', 'link-85');">version</a></tt><tt class="py-op">]</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-89" class="py-name"><a title="Bio.Std.dbid" class="py-name" href="#" onclick="return doclink('link-89', 'dbid', 'link-59');">dbid</a></tt><tt class="py-op">:</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"> <tt class="py-name">sql</tt> <tt class="py-op">+=</tt> <tt class="py-string">" and biodatabase_id = %s"</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> <tt class="py-name">fields</tt><tt class="py-op">.</tt><tt id="link-90" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-90', 'append', 'link-60');">append</a></tt><tt class="py-op">(</tt><tt id="link-91" class="py-name"><a title="Bio.Std.dbid" class="py-name" href="#" onclick="return doclink('link-91', 'dbid', 'link-59');">dbid</a></tt><tt class="py-op">)</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-92" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-92', 'cursor', 'link-40');">cursor</a></tt><tt class="py-op">.</tt><tt id="link-93" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-93', 'execute', 'link-32');">execute</a></tt><tt class="py-op">(</tt><tt class="py-name">sql</tt><tt class="py-op">,</tt> <tt class="py-name">fields</tt><tt class="py-op">)</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> <tt class="py-name">rv</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-94" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-94', 'cursor', 'link-40');">cursor</a></tt><tt class="py-op">.</tt><tt class="py-name">fetchall</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">rv</tt><tt class="py-op">:</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">IndexError</tt><tt class="py-op">(</tt><tt class="py-string">"Cannot find version %r"</tt> <tt class="py-op">%</tt> <tt id="link-95" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-95', 'name', 'link-19');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">rv</tt><tt class="py-op">)</tt> <tt class="py-op">></tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">IndexError</tt><tt class="py-op">(</tt><tt class="py-string">"More than one entry with version %r"</tt> <tt class="py-op">%</tt> <tt id="link-96" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-96', 'name', 'link-19');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">rv</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
</div><a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> </tt>
<a name="Adaptor.fetch_seqid_by_identifier"></a><div id="Adaptor.fetch_seqid_by_identifier-def"><a name="L240"></a><tt class="py-lineno">240</tt> <a class="py-toggle" href="#" id="Adaptor.fetch_seqid_by_identifier-toggle" onclick="return toggle('Adaptor.fetch_seqid_by_identifier');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.Adaptor-class.html#fetch_seqid_by_identifier">fetch_seqid_by_identifier</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">dbid</tt><tt class="py-op">,</tt> <tt class="py-param">identifier</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Adaptor.fetch_seqid_by_identifier-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Adaptor.fetch_seqid_by_identifier-expanded"><a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt class="py-comment"># YB: was fetch_seqid_by_seqid</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">sql</tt> <tt class="py-op">=</tt> <tt class="py-string">"SELECT bioentry_id FROM bioentry WHERE identifier = %s"</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> <tt class="py-name">fields</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-97" class="py-name" targets="Variable Bio.expressions.blocks.identifier=Bio.expressions.blocks-module.html#identifier"><a title="Bio.expressions.blocks.identifier" class="py-name" href="#" onclick="return doclink('link-97', 'identifier', 'link-97');">identifier</a></tt><tt class="py-op">]</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-98" class="py-name"><a title="Bio.Std.dbid" class="py-name" href="#" onclick="return doclink('link-98', 'dbid', 'link-59');">dbid</a></tt><tt class="py-op">:</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> <tt class="py-name">sql</tt> <tt class="py-op">+=</tt> <tt class="py-string">" and biodatabase_id = %s"</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> <tt class="py-name">fields</tt><tt class="py-op">.</tt><tt id="link-99" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-99', 'append', 'link-60');">append</a></tt><tt class="py-op">(</tt><tt id="link-100" class="py-name"><a title="Bio.Std.dbid" class="py-name" href="#" onclick="return doclink('link-100', 'dbid', 'link-59');">dbid</a></tt><tt class="py-op">)</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-101" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-101', 'cursor', 'link-40');">cursor</a></tt><tt class="py-op">.</tt><tt id="link-102" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-102', 'execute', 'link-32');">execute</a></tt><tt class="py-op">(</tt><tt class="py-name">sql</tt><tt class="py-op">,</tt> <tt class="py-name">fields</tt><tt class="py-op">)</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> <tt class="py-name">rv</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-103" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-103', 'cursor', 'link-40');">cursor</a></tt><tt class="py-op">.</tt><tt class="py-name">fetchall</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">rv</tt><tt class="py-op">:</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">IndexError</tt><tt class="py-op">(</tt><tt class="py-string">"Cannot find display id %r"</tt> <tt class="py-op">%</tt> <tt id="link-104" class="py-name"><a title="Bio.expressions.blocks.identifier" class="py-name" href="#" onclick="return doclink('link-104', 'identifier', 'link-97');">identifier</a></tt><tt class="py-op">)</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">rv</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
</div><a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> </tt>
<a name="Adaptor.list_biodatabase_names"></a><div id="Adaptor.list_biodatabase_names-def"><a name="L253"></a><tt class="py-lineno">253</tt> <a class="py-toggle" href="#" id="Adaptor.list_biodatabase_names-toggle" onclick="return toggle('Adaptor.list_biodatabase_names');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.Adaptor-class.html#list_biodatabase_names">list_biodatabase_names</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Adaptor.list_biodatabase_names-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Adaptor.list_biodatabase_names-expanded"><a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-105" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute_and_fetch_col0" class="py-name" href="#" onclick="return doclink('link-105', 'execute_and_fetch_col0', 'link-80');">execute_and_fetch_col0</a></tt><tt class="py-op">(</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"> <tt class="py-string">"SELECT name FROM biodatabase"</tt><tt class="py-op">)</tt> </tt>
</div><a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> </tt>
<a name="Adaptor.list_bioentry_ids"></a><div id="Adaptor.list_bioentry_ids-def"><a name="L257"></a><tt class="py-lineno">257</tt> <a class="py-toggle" href="#" id="Adaptor.list_bioentry_ids-toggle" onclick="return toggle('Adaptor.list_bioentry_ids');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.Adaptor-class.html#list_bioentry_ids">list_bioentry_ids</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">dbid</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Adaptor.list_bioentry_ids-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Adaptor.list_bioentry_ids-expanded"><a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-106" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute_and_fetch_col0" class="py-name" href="#" onclick="return doclink('link-106', 'execute_and_fetch_col0', 'link-80');">execute_and_fetch_col0</a></tt><tt class="py-op">(</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> <tt class="py-string">"SELECT bioentry_id FROM bioentry WHERE biodatabase_id = %s"</tt><tt class="py-op">,</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt id="link-107" class="py-name"><a title="Bio.Std.dbid" class="py-name" href="#" onclick="return doclink('link-107', 'dbid', 'link-59');">dbid</a></tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> </tt>
<a name="Adaptor.list_bioentry_display_ids"></a><div id="Adaptor.list_bioentry_display_ids-def"><a name="L262"></a><tt class="py-lineno">262</tt> <a class="py-toggle" href="#" id="Adaptor.list_bioentry_display_ids-toggle" onclick="return toggle('Adaptor.list_bioentry_display_ids');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.Adaptor-class.html#list_bioentry_display_ids">list_bioentry_display_ids</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">dbid</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Adaptor.list_bioentry_display_ids-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Adaptor.list_bioentry_display_ids-expanded"><a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-108" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute_and_fetch_col0" class="py-name" href="#" onclick="return doclink('link-108', 'execute_and_fetch_col0', 'link-80');">execute_and_fetch_col0</a></tt><tt class="py-op">(</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> <tt class="py-string">"SELECT name FROM bioentry WHERE biodatabase_id = %s"</tt><tt class="py-op">,</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt id="link-109" class="py-name"><a title="Bio.Std.dbid" class="py-name" href="#" onclick="return doclink('link-109', 'dbid', 'link-59');">dbid</a></tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> </tt>
<a name="Adaptor.list_any_ids"></a><div id="Adaptor.list_any_ids-def"><a name="L267"></a><tt class="py-lineno">267</tt> <a class="py-toggle" href="#" id="Adaptor.list_any_ids-toggle" onclick="return toggle('Adaptor.list_any_ids');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.Adaptor-class.html#list_any_ids">list_any_ids</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">sql</tt><tt class="py-op">,</tt> <tt class="py-param">args</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Adaptor.list_any_ids-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Adaptor.list_any_ids-expanded"><a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"> <tt class="py-docstring">"""Return ids given a SQL statement to select for them.</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"><tt class="py-docstring"> This assumes that the given SQL does a SELECT statement that</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"><tt class="py-docstring"> returns a list of items. This parses them out of the 2D list</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"><tt class="py-docstring"> they come as and just returns them in a list.</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-110" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-110', 'cursor', 'link-40');">cursor</a></tt><tt class="py-op">.</tt><tt id="link-111" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute_and_fetch_col0" class="py-name" href="#" onclick="return doclink('link-111', 'execute_and_fetch_col0', 'link-80');">execute_and_fetch_col0</a></tt><tt class="py-op">(</tt><tt class="py-name">sql</tt><tt class="py-op">,</tt> <tt class="py-name">args</tt><tt class="py-op">)</tt> </tt>
</div><a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"> </tt>
<a name="Adaptor.execute_one"></a><div id="Adaptor.execute_one-def"><a name="L276"></a><tt class="py-lineno">276</tt> <a class="py-toggle" href="#" id="Adaptor.execute_one-toggle" onclick="return toggle('Adaptor.execute_one');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.Adaptor-class.html#execute_one">execute_one</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">sql</tt><tt class="py-op">,</tt> <tt class="py-param">args</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Adaptor.execute_one-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Adaptor.execute_one-expanded"><a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-112" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-112', 'cursor', 'link-40');">cursor</a></tt><tt class="py-op">.</tt><tt id="link-113" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-113', 'execute', 'link-32');">execute</a></tt><tt class="py-op">(</tt><tt class="py-name">sql</tt><tt class="py-op">,</tt> <tt class="py-name">args</tt> <tt class="py-keyword">or</tt> <tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> <tt class="py-name">rv</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-114" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-114', 'cursor', 'link-40');">cursor</a></tt><tt class="py-op">.</tt><tt class="py-name">fetchall</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">rv</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-string">"Expected 1 response, got %d"</tt> <tt class="py-op">%</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">rv</tt><tt class="py-op">)</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">rv</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
</div><a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"> </tt>
<a name="Adaptor.execute"></a><div id="Adaptor.execute-def"><a name="L282"></a><tt class="py-lineno">282</tt> <a class="py-toggle" href="#" id="Adaptor.execute-toggle" onclick="return toggle('Adaptor.execute');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.Adaptor-class.html#execute">execute</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">sql</tt><tt class="py-op">,</tt> <tt class="py-param">args</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Adaptor.execute-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Adaptor.execute-expanded"><a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"> <tt class="py-docstring">"""Just execute an sql command.</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-115" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-115', 'cursor', 'link-40');">cursor</a></tt><tt class="py-op">.</tt><tt id="link-116" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-116', 'execute', 'link-32');">execute</a></tt><tt class="py-op">(</tt><tt class="py-name">sql</tt><tt class="py-op">,</tt> <tt class="py-name">args</tt> <tt class="py-keyword">or</tt> <tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"> </tt>
<a name="Adaptor.get_subseq_as_string"></a><div id="Adaptor.get_subseq_as_string-def"><a name="L287"></a><tt class="py-lineno">287</tt> <a class="py-toggle" href="#" id="Adaptor.get_subseq_as_string-toggle" onclick="return toggle('Adaptor.get_subseq_as_string');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.Adaptor-class.html#get_subseq_as_string">get_subseq_as_string</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">seqid</tt><tt class="py-op">,</tt> <tt class="py-param">start</tt><tt class="py-op">,</tt> <tt class="py-param">end</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Adaptor.get_subseq_as_string-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Adaptor.get_subseq_as_string-expanded"><a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"> <tt id="link-117" class="py-name" targets="Method Bio.Blast.NCBIStandalone._AlignmentConsumer.length()=Bio.Blast.NCBIStandalone._AlignmentConsumer-class.html#length,Method Bio.GFF.easy.Location.length()=Bio.GFF.easy.Location-class.html#length"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-117', 'length', 'link-117');">length</a></tt> <tt class="py-op">=</tt> <tt id="link-118" class="py-name" targets="Method Bio.GFF.easy.Location.end()=Bio.GFF.easy.Location-class.html#end,Method Bio.Prosite.Pattern.PrositeMatch.end()=Bio.Prosite.Pattern.PrositeMatch-class.html#end,Variable Bio.expressions.blocks.end=Bio.expressions.blocks-module.html#end,Variable Bio.expressions.embl.embl65.end=Bio.expressions.embl.embl65-module.html#end,Variable Bio.expressions.swissprot.sprot38.end=Bio.expressions.swissprot.sprot38-module.html#end,Method Martel.LAX.LAX.end()=Martel.LAX.LAX-class.html#end,Variable Martel.test.test_swissprot38.end=Martel.test.test_swissprot38-module.html#end,Variable Martel.test.testformats.swissprot38.end=Martel.test.testformats.swissprot38-module.html#end"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-118', 'end', 'link-118');">end</a></tt> <tt class="py-op">-</tt> <tt id="link-119" class="py-name" targets="Method Bio.GFF.easy.Location.start()=Bio.GFF.easy.Location-class.html#start,Method Bio.Prosite.Pattern.PrositeMatch.start()=Bio.Prosite.Pattern.PrositeMatch-class.html#start,Variable Bio.Restriction._Update.RestrictionCompiler.start=Bio.Restriction._Update.RestrictionCompiler-module.html#start,Method Martel.LAX.LAX.start()=Martel.LAX.LAX-class.html#start"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-119', 'start', 'link-119');">start</a></tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-120" class="py-name" targets="Method BioSQL.BioSeqDatabase.Adaptor.execute_one()=BioSQL.BioSeqDatabase.Adaptor-class.html#execute_one"><a title="BioSQL.BioSeqDatabase.Adaptor.execute_one" class="py-name" href="#" onclick="return doclink('link-120', 'execute_one', 'link-120');">execute_one</a></tt><tt class="py-op">(</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"> <tt class="py-string">"""select SUBSTRING(seq FROM %s FOR %s)</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"><tt class="py-string"> from biosequence where bioentry_id = %s"""</tt><tt class="py-op">,</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt id="link-121" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-121', 'start', 'link-119');">start</a></tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt id="link-122" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-122', 'length', 'link-117');">length</a></tt><tt class="py-op">,</tt> <tt class="py-name">seqid</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
</div><a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"> </tt>
<a name="Adaptor.execute_and_fetch_col0"></a><div id="Adaptor.execute_and_fetch_col0-def"><a name="L294"></a><tt class="py-lineno">294</tt> <a class="py-toggle" href="#" id="Adaptor.execute_and_fetch_col0-toggle" onclick="return toggle('Adaptor.execute_and_fetch_col0');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.Adaptor-class.html#execute_and_fetch_col0">execute_and_fetch_col0</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">sql</tt><tt class="py-op">,</tt> <tt class="py-param">args</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Adaptor.execute_and_fetch_col0-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Adaptor.execute_and_fetch_col0-expanded"><a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-123" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-123', 'cursor', 'link-40');">cursor</a></tt><tt class="py-op">.</tt><tt id="link-124" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-124', 'execute', 'link-32');">execute</a></tt><tt class="py-op">(</tt><tt class="py-name">sql</tt><tt class="py-op">,</tt> <tt class="py-name">args</tt> <tt class="py-keyword">or</tt> <tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">[</tt><tt class="py-name">field</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">field</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-125" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-125', 'cursor', 'link-40');">cursor</a></tt><tt class="py-op">.</tt><tt class="py-name">fetchall</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
</div><a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"> </tt>
<a name="Adaptor.execute_and_fetchall"></a><div id="Adaptor.execute_and_fetchall-def"><a name="L298"></a><tt class="py-lineno">298</tt> <a class="py-toggle" href="#" id="Adaptor.execute_and_fetchall-toggle" onclick="return toggle('Adaptor.execute_and_fetchall');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.Adaptor-class.html#execute_and_fetchall">execute_and_fetchall</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">sql</tt><tt class="py-op">,</tt> <tt class="py-param">args</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Adaptor.execute_and_fetchall-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Adaptor.execute_and_fetchall-expanded"><a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-126" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-126', 'cursor', 'link-40');">cursor</a></tt><tt class="py-op">.</tt><tt id="link-127" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-127', 'execute', 'link-32');">execute</a></tt><tt class="py-op">(</tt><tt class="py-name">sql</tt><tt class="py-op">,</tt> <tt class="py-name">args</tt> <tt class="py-keyword">or</tt> <tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-128" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-128', 'cursor', 'link-40');">cursor</a></tt><tt class="py-op">.</tt><tt class="py-name">fetchall</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"><tt id="link-129" class="py-name" targets="Variable BioSQL.BioSeqDatabase._allowed_lookups=BioSQL.BioSeqDatabase-module.html#_allowed_lookups"><a title="BioSQL.BioSeqDatabase._allowed_lookups" class="py-name" href="#" onclick="return doclink('link-129', '_allowed_lookups', 'link-129');">_allowed_lookups</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"> <tt class="py-comment"># Lookup name / function name to get id, function to list all ids</tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"> <tt class="py-string">'primary_id'</tt><tt class="py-op">:</tt> <tt class="py-string">"fetch_seqid_by_identifier"</tt><tt class="py-op">,</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"> <tt class="py-string">'gi'</tt><tt class="py-op">:</tt> <tt class="py-string">"fetch_seqid_by_identifier"</tt><tt class="py-op">,</tt> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"> <tt class="py-string">'display_id'</tt><tt class="py-op">:</tt> <tt class="py-string">"fetch_seqid_by_display_id"</tt><tt class="py-op">,</tt> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"> <tt class="py-string">'name'</tt><tt class="py-op">:</tt> <tt class="py-string">"fetch_seqid_by_display_id"</tt><tt class="py-op">,</tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"> <tt class="py-string">'accession'</tt><tt class="py-op">:</tt> <tt class="py-string">"fetch_seqid_by_accession"</tt><tt class="py-op">,</tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"> <tt class="py-string">'version'</tt><tt class="py-op">:</tt> <tt class="py-string">"fetch_seqid_by_version"</tt><tt class="py-op">,</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"> <tt class="py-op">}</tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"> </tt>
<a name="BioSeqDatabase"></a><div id="BioSeqDatabase-def"><a name="L312"></a><tt class="py-lineno">312</tt> <a class="py-toggle" href="#" id="BioSeqDatabase-toggle" onclick="return toggle('BioSeqDatabase');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.BioSeqDatabase-class.html">BioSeqDatabase</a><tt class="py-op">:</tt> </tt>
</div><div id="BioSeqDatabase-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="BioSeqDatabase-expanded"><a name="BioSeqDatabase.__init__"></a><div id="BioSeqDatabase.__init__-def"><a name="L313"></a><tt class="py-lineno">313</tt> <a class="py-toggle" href="#" id="BioSeqDatabase.__init__-toggle" onclick="return toggle('BioSeqDatabase.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">adaptor</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BioSeqDatabase.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSeqDatabase.__init__-expanded"><a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt> <tt class="py-op">=</tt> <tt class="py-name">adaptor</tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-130" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-130', 'name', 'link-19');">name</a></tt> <tt class="py-op">=</tt> <tt id="link-131" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-131', 'name', 'link-19');">name</a></tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-132" class="py-name"><a title="Bio.Std.dbid" class="py-name" href="#" onclick="return doclink('link-132', 'dbid', 'link-59');">dbid</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-133" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.fetch_dbid_by_dbname" class="py-name" href="#" onclick="return doclink('link-133', 'fetch_dbid_by_dbname', 'link-28');">fetch_dbid_by_dbname</a></tt><tt class="py-op">(</tt><tt id="link-134" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-134', 'name', 'link-19');">name</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="BioSeqDatabase.__repr__"></a><div id="BioSeqDatabase.__repr__-def"><a name="L317"></a><tt class="py-lineno">317</tt> <a class="py-toggle" href="#" id="BioSeqDatabase.__repr__-toggle" onclick="return toggle('BioSeqDatabase.__repr__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#__repr__">__repr__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BioSeqDatabase.__repr__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSeqDatabase.__repr__-expanded"><a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"BioSeqDatabase(%r, %r)"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-135" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-135', 'name', 'link-19');">name</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"> </tt>
<a name="BioSeqDatabase.get_Seq_by_id"></a><div id="BioSeqDatabase.get_Seq_by_id-def"><a name="L320"></a><tt class="py-lineno">320</tt> <a class="py-toggle" href="#" id="BioSeqDatabase.get_Seq_by_id-toggle" onclick="return toggle('BioSeqDatabase.get_Seq_by_id');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#get_Seq_by_id">get_Seq_by_id</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BioSeqDatabase.get_Seq_by_id-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSeqDatabase.get_Seq_by_id-expanded"><a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"> <tt class="py-docstring">"""Gets a Bio::Seq object by its name</tt> </tt>
<a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt> <tt class="py-line"><tt class="py-docstring"> Example: seq = db.get_Seq_by_id('ROA1_HUMAN')</tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"> <tt class="py-name">seqid</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-136" class="py-name" targets="Method BioSQL.BioSeqDatabase.Adaptor.fetch_seqid_by_display_id()=BioSQL.BioSeqDatabase.Adaptor-class.html#fetch_seqid_by_display_id"><a title="BioSQL.BioSeqDatabase.Adaptor.fetch_seqid_by_display_id" class="py-name" href="#" onclick="return doclink('link-136', 'fetch_seqid_by_display_id', 'link-136');">fetch_seqid_by_display_id</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-137" class="py-name"><a title="Bio.Std.dbid" class="py-name" href="#" onclick="return doclink('link-137', 'dbid', 'link-59');">dbid</a></tt><tt class="py-op">,</tt> <tt id="link-138" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-138', 'name', 'link-19');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-139" class="py-name"><a title="BioSQL.BioSeq" class="py-name" href="#" onclick="return doclink('link-139', 'BioSeq', 'link-0');">BioSeq</a></tt><tt class="py-op">.</tt><tt id="link-140" class="py-name" targets="Class BioSQL.BioSeq.DBSeqRecord=BioSQL.BioSeq.DBSeqRecord-class.html"><a title="BioSQL.BioSeq.DBSeqRecord" class="py-name" href="#" onclick="return doclink('link-140', 'DBSeqRecord', 'link-140');">DBSeqRecord</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">,</tt> <tt class="py-name">seqid</tt><tt class="py-op">)</tt> </tt>
</div><a name="L328"></a><tt class="py-lineno">328</tt> <tt class="py-line"> </tt>
<a name="BioSeqDatabase.get_Seq_by_acc"></a><div id="BioSeqDatabase.get_Seq_by_acc-def"><a name="L329"></a><tt class="py-lineno">329</tt> <a class="py-toggle" href="#" id="BioSeqDatabase.get_Seq_by_acc-toggle" onclick="return toggle('BioSeqDatabase.get_Seq_by_acc');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#get_Seq_by_acc">get_Seq_by_acc</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BioSeqDatabase.get_Seq_by_acc-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSeqDatabase.get_Seq_by_acc-expanded"><a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"> <tt class="py-docstring">"""Gets a Bio::Seq object by accession number</tt> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"><tt class="py-docstring"> Example: seq = db.get_Seq_by_acc('X77802')</tt> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"> <tt class="py-name">seqid</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-141" class="py-name" targets="Method BioSQL.BioSeqDatabase.Adaptor.fetch_seqid_by_accession()=BioSQL.BioSeqDatabase.Adaptor-class.html#fetch_seqid_by_accession"><a title="BioSQL.BioSeqDatabase.Adaptor.fetch_seqid_by_accession" class="py-name" href="#" onclick="return doclink('link-141', 'fetch_seqid_by_accession', 'link-141');">fetch_seqid_by_accession</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-142" class="py-name"><a title="Bio.Std.dbid" class="py-name" href="#" onclick="return doclink('link-142', 'dbid', 'link-59');">dbid</a></tt><tt class="py-op">,</tt> <tt id="link-143" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-143', 'name', 'link-19');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-144" class="py-name"><a title="BioSQL.BioSeq" class="py-name" href="#" onclick="return doclink('link-144', 'BioSeq', 'link-0');">BioSeq</a></tt><tt class="py-op">.</tt><tt id="link-145" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord" class="py-name" href="#" onclick="return doclink('link-145', 'DBSeqRecord', 'link-140');">DBSeqRecord</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">,</tt> <tt class="py-name">seqid</tt><tt class="py-op">)</tt> </tt>
</div><a name="L337"></a><tt class="py-lineno">337</tt> <tt class="py-line"> </tt>
<a name="BioSeqDatabase.get_Seq_by_ver"></a><div id="BioSeqDatabase.get_Seq_by_ver-def"><a name="L338"></a><tt class="py-lineno">338</tt> <a class="py-toggle" href="#" id="BioSeqDatabase.get_Seq_by_ver-toggle" onclick="return toggle('BioSeqDatabase.get_Seq_by_ver');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#get_Seq_by_ver">get_Seq_by_ver</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BioSeqDatabase.get_Seq_by_ver-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSeqDatabase.get_Seq_by_ver-expanded"><a name="L339"></a><tt class="py-lineno">339</tt> <tt class="py-line"> <tt class="py-docstring">"""Gets a Bio::Seq object by version number</tt> </tt>
<a name="L340"></a><tt class="py-lineno">340</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt> <tt class="py-line"><tt class="py-docstring"> Example: seq = db.get_Seq_by_ver('X77802.1')</tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt> <tt class="py-line"> <tt class="py-name">seqid</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-146" class="py-name" targets="Method BioSQL.BioSeqDatabase.Adaptor.fetch_seqid_by_version()=BioSQL.BioSeqDatabase.Adaptor-class.html#fetch_seqid_by_version"><a title="BioSQL.BioSeqDatabase.Adaptor.fetch_seqid_by_version" class="py-name" href="#" onclick="return doclink('link-146', 'fetch_seqid_by_version', 'link-146');">fetch_seqid_by_version</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-147" class="py-name"><a title="Bio.Std.dbid" class="py-name" href="#" onclick="return doclink('link-147', 'dbid', 'link-59');">dbid</a></tt><tt class="py-op">,</tt> <tt id="link-148" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-148', 'name', 'link-19');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-149" class="py-name"><a title="BioSQL.BioSeq" class="py-name" href="#" onclick="return doclink('link-149', 'BioSeq', 'link-0');">BioSeq</a></tt><tt class="py-op">.</tt><tt id="link-150" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord" class="py-name" href="#" onclick="return doclink('link-150', 'DBSeqRecord', 'link-140');">DBSeqRecord</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">,</tt> <tt class="py-name">seqid</tt><tt class="py-op">)</tt> </tt>
</div><a name="L346"></a><tt class="py-lineno">346</tt> <tt class="py-line"> </tt>
<a name="BioSeqDatabase.get_Seqs_by_acc"></a><div id="BioSeqDatabase.get_Seqs_by_acc-def"><a name="L347"></a><tt class="py-lineno">347</tt> <a class="py-toggle" href="#" id="BioSeqDatabase.get_Seqs_by_acc-toggle" onclick="return toggle('BioSeqDatabase.get_Seqs_by_acc');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#get_Seqs_by_acc">get_Seqs_by_acc</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BioSeqDatabase.get_Seqs_by_acc-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSeqDatabase.get_Seqs_by_acc-expanded"><a name="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"> <tt class="py-docstring">"""Gets a *list* of Bio::Seq objects by accession number</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt> <tt class="py-line"><tt class="py-docstring"> Example: seqs = db.get_Seq_by_acc('X77802')</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt> <tt class="py-line"> <tt class="py-name">seqids</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-151" class="py-name" targets="Method BioSQL.BioSeqDatabase.Adaptor.fetch_seqids_by_accession()=BioSQL.BioSeqDatabase.Adaptor-class.html#fetch_seqids_by_accession"><a title="BioSQL.BioSeqDatabase.Adaptor.fetch_seqids_by_accession" class="py-name" href="#" onclick="return doclink('link-151', 'fetch_seqids_by_accession', 'link-151');">fetch_seqids_by_accession</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-152" class="py-name"><a title="Bio.Std.dbid" class="py-name" href="#" onclick="return doclink('link-152', 'dbid', 'link-59');">dbid</a></tt><tt class="py-op">,</tt> <tt id="link-153" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-153', 'name', 'link-19');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">[</tt><tt id="link-154" class="py-name"><a title="BioSQL.BioSeq" class="py-name" href="#" onclick="return doclink('link-154', 'BioSeq', 'link-0');">BioSeq</a></tt><tt class="py-op">.</tt><tt id="link-155" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord" class="py-name" href="#" onclick="return doclink('link-155', 'DBSeqRecord', 'link-140');">DBSeqRecord</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">,</tt> <tt class="py-name">seqid</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">seqid</tt> <tt class="py-keyword">in</tt> <tt class="py-name">seqids</tt><tt class="py-op">]</tt> </tt>
</div><a name="L355"></a><tt class="py-lineno">355</tt> <tt class="py-line"> </tt>
<a name="BioSeqDatabase.get_PrimarySeq_stream"></a><div id="BioSeqDatabase.get_PrimarySeq_stream-def"><a name="L356"></a><tt class="py-lineno">356</tt> <a class="py-toggle" href="#" id="BioSeqDatabase.get_PrimarySeq_stream-toggle" onclick="return toggle('BioSeqDatabase.get_PrimarySeq_stream');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#get_PrimarySeq_stream">get_PrimarySeq_stream</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BioSeqDatabase.get_PrimarySeq_stream-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSeqDatabase.get_PrimarySeq_stream-expanded"><a name="L357"></a><tt class="py-lineno">357</tt> <tt class="py-line"> <tt class="py-comment"># my @array = $self->get_all_primary_ids;</tt> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># my $stream = Bio::DB::BioDatabasePSeqStream->new(</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># -adaptor => $self->_adaptor->db->get_PrimarySeqAdaptor,</tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># -idlist => \@array);</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">raise</tt> <tt class="py-name">NotImplementedError</tt><tt class="py-op">(</tt><tt class="py-string">"waiting for Python 2.2's iter"</tt><tt class="py-op">)</tt> </tt>
</div><a name="L362"></a><tt class="py-lineno">362</tt> <tt class="py-line"> </tt>
<a name="BioSeqDatabase.get_all_primary_ids"></a><div id="BioSeqDatabase.get_all_primary_ids-def"><a name="L363"></a><tt class="py-lineno">363</tt> <a class="py-toggle" href="#" id="BioSeqDatabase.get_all_primary_ids-toggle" onclick="return toggle('BioSeqDatabase.get_all_primary_ids');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#get_all_primary_ids">get_all_primary_ids</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BioSeqDatabase.get_all_primary_ids-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSeqDatabase.get_all_primary_ids-expanded"><a name="L364"></a><tt class="py-lineno">364</tt> <tt class="py-line"> <tt class="py-docstring">"""Array of all the primary_ids of the sequences in the database.</tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"><tt class="py-docstring"> These maybe ids (display style) or accession numbers or</tt> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt> <tt class="py-line"><tt class="py-docstring"> something else completely different - they *are not*</tt> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt> <tt class="py-line"><tt class="py-docstring"> meaningful outside of this database implementation.</tt> </tt>
<a name="L369"></a><tt class="py-lineno">369</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L370"></a><tt class="py-lineno">370</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-156" class="py-name" targets="Method BioSQL.BioSeqDatabase.Adaptor.list_bioentry_ids()=BioSQL.BioSeqDatabase.Adaptor-class.html#list_bioentry_ids"><a title="BioSQL.BioSeqDatabase.Adaptor.list_bioentry_ids" class="py-name" href="#" onclick="return doclink('link-156', 'list_bioentry_ids', 'link-156');">list_bioentry_ids</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-157" class="py-name"><a title="Bio.Std.dbid" class="py-name" href="#" onclick="return doclink('link-157', 'dbid', 'link-59');">dbid</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L371"></a><tt class="py-lineno">371</tt> <tt class="py-line"> </tt>
<a name="BioSeqDatabase.__getitem__"></a><div id="BioSeqDatabase.__getitem__-def"><a name="L372"></a><tt class="py-lineno">372</tt> <a class="py-toggle" href="#" id="BioSeqDatabase.__getitem__-toggle" onclick="return toggle('BioSeqDatabase.__getitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#__getitem__">__getitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">key</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BioSeqDatabase.__getitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSeqDatabase.__getitem__-expanded"><a name="L373"></a><tt class="py-lineno">373</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-158" class="py-name"><a title="BioSQL.BioSeq" class="py-name" href="#" onclick="return doclink('link-158', 'BioSeq', 'link-0');">BioSeq</a></tt><tt class="py-op">.</tt><tt id="link-159" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord" class="py-name" href="#" onclick="return doclink('link-159', 'DBSeqRecord', 'link-140');">DBSeqRecord</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">,</tt> <tt id="link-160" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-160', 'key', 'link-21');">key</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="BioSeqDatabase.keys"></a><div id="BioSeqDatabase.keys-def"><a name="L374"></a><tt class="py-lineno">374</tt> <a class="py-toggle" href="#" id="BioSeqDatabase.keys-toggle" onclick="return toggle('BioSeqDatabase.keys');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#keys">keys</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BioSeqDatabase.keys-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSeqDatabase.keys-expanded"><a name="L375"></a><tt class="py-lineno">375</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-161" class="py-name" targets="Method BioSQL.BioSeqDatabase.BioSeqDatabase.get_all_primary_ids()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#get_all_primary_ids"><a title="BioSQL.BioSeqDatabase.BioSeqDatabase.get_all_primary_ids" class="py-name" href="#" onclick="return doclink('link-161', 'get_all_primary_ids', 'link-161');">get_all_primary_ids</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="BioSeqDatabase.values"></a><div id="BioSeqDatabase.values-def"><a name="L376"></a><tt class="py-lineno">376</tt> <a class="py-toggle" href="#" id="BioSeqDatabase.values-toggle" onclick="return toggle('BioSeqDatabase.values');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#values">values</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BioSeqDatabase.values-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSeqDatabase.values-expanded"><a name="L377"></a><tt class="py-lineno">377</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">[</tt><tt id="link-162" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-162', 'key', 'link-21');">key</a></tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt id="link-163" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-163', 'key', 'link-21');">key</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-164" class="py-name"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-164', 'keys', 'link-23');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
</div><a name="BioSeqDatabase.items"></a><div id="BioSeqDatabase.items-def"><a name="L378"></a><tt class="py-lineno">378</tt> <a class="py-toggle" href="#" id="BioSeqDatabase.items-toggle" onclick="return toggle('BioSeqDatabase.items');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#items">items</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BioSeqDatabase.items-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSeqDatabase.items-expanded"><a name="L379"></a><tt class="py-lineno">379</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">[</tt><tt class="py-op">(</tt><tt id="link-165" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-165', 'key', 'link-21');">key</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">[</tt><tt id="link-166" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-166', 'key', 'link-21');">key</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt id="link-167" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-167', 'key', 'link-21');">key</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-168" class="py-name"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-168', 'keys', 'link-23');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
</div><a name="L380"></a><tt class="py-lineno">380</tt> <tt class="py-line"> </tt>
<a name="BioSeqDatabase.lookup"></a><div id="BioSeqDatabase.lookup-def"><a name="L381"></a><tt class="py-lineno">381</tt> <a class="py-toggle" href="#" id="BioSeqDatabase.lookup-toggle" onclick="return toggle('BioSeqDatabase.lookup');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#lookup">lookup</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-param">kwargs</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BioSeqDatabase.lookup-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSeqDatabase.lookup-expanded"><a name="L382"></a><tt class="py-lineno">382</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">kwargs</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L383"></a><tt class="py-lineno">383</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">"single key/value parameter expected"</tt><tt class="py-op">)</tt> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt> <tt class="py-line"> <tt class="py-name">k</tt><tt class="py-op">,</tt> <tt id="link-169" class="py-name" targets="Variable Martel.Time.v=Martel.Time-module.html#v"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-169', 'v', 'link-169');">v</a></tt> <tt class="py-op">=</tt> <tt class="py-name">kwargs</tt><tt class="py-op">.</tt><tt id="link-170" class="py-name"><a title="Bio.Crystal.Crystal.items
Bio.EUtils.MultiDict._BaseMultiDict.items
Bio.Entrez.SerialSet.items
Bio.GenBank.NCBIDictionary.items
Bio.Mindy.BaseDB.DictLookup.items
Bio.Prosite.ExPASyDictionary.items
Bio.Prosite.Prodoc.ExPASyDictionary.items
Bio.PubMed.Dictionary.items
Bio.SwissProt.SProt.ExPASyDictionary.items
Bio.config.Registry.Registry.items
Bio.listfns.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items
Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-170', 'items', 'link-13');">items</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L385"></a><tt class="py-lineno">385</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-171" class="py-name"><a title="BioSQL.BioSeqDatabase._allowed_lookups" class="py-name" href="#" onclick="return doclink('link-171', '_allowed_lookups', 'link-129');">_allowed_lookups</a></tt><tt class="py-op">.</tt><tt id="link-172" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-172', 'has_key', 'link-4');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">k</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L386"></a><tt class="py-lineno">386</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">"lookup() expects one of %s, not %r"</tt> <tt class="py-op">%</tt> \ </tt>
<a name="L387"></a><tt class="py-lineno">387</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">repr</tt><tt class="py-op">(</tt><tt id="link-173" class="py-name"><a title="BioSQL.BioSeqDatabase._allowed_lookups" class="py-name" href="#" onclick="return doclink('link-173', '_allowed_lookups', 'link-129');">_allowed_lookups</a></tt><tt class="py-op">.</tt><tt id="link-174" class="py-name"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-174', 'keys', 'link-23');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt class="py-name">k</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L388"></a><tt class="py-lineno">388</tt> <tt class="py-line"> <tt class="py-name">lookup_name</tt> <tt class="py-op">=</tt> <tt id="link-175" class="py-name"><a title="BioSQL.BioSeqDatabase._allowed_lookups" class="py-name" href="#" onclick="return doclink('link-175', '_allowed_lookups', 'link-129');">_allowed_lookups</a></tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt> </tt>
<a name="L389"></a><tt class="py-lineno">389</tt> <tt class="py-line"> <tt class="py-name">lookup_func</tt> <tt class="py-op">=</tt> <tt class="py-name">getattr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">,</tt> <tt class="py-name">lookup_name</tt><tt class="py-op">)</tt> </tt>
<a name="L390"></a><tt class="py-lineno">390</tt> <tt class="py-line"> <tt class="py-name">seqid</tt> <tt class="py-op">=</tt> <tt class="py-name">lookup_func</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-176" class="py-name"><a title="Bio.Std.dbid" class="py-name" href="#" onclick="return doclink('link-176', 'dbid', 'link-59');">dbid</a></tt><tt class="py-op">,</tt> <tt id="link-177" class="py-name"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-177', 'v', 'link-169');">v</a></tt><tt class="py-op">)</tt> </tt>
<a name="L391"></a><tt class="py-lineno">391</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-178" class="py-name"><a title="BioSQL.BioSeq" class="py-name" href="#" onclick="return doclink('link-178', 'BioSeq', 'link-0');">BioSeq</a></tt><tt class="py-op">.</tt><tt id="link-179" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord" class="py-name" href="#" onclick="return doclink('link-179', 'DBSeqRecord', 'link-140');">DBSeqRecord</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">,</tt> <tt class="py-name">seqid</tt><tt class="py-op">)</tt> </tt>
</div><a name="L392"></a><tt class="py-lineno">392</tt> <tt class="py-line"> </tt>
<a name="BioSeqDatabase.get_Seq_by_primary_id"></a><div id="BioSeqDatabase.get_Seq_by_primary_id-def"><a name="L393"></a><tt class="py-lineno">393</tt> <a class="py-toggle" href="#" id="BioSeqDatabase.get_Seq_by_primary_id-toggle" onclick="return toggle('BioSeqDatabase.get_Seq_by_primary_id');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#get_Seq_by_primary_id">get_Seq_by_primary_id</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">seqid</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BioSeqDatabase.get_Seq_by_primary_id-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSeqDatabase.get_Seq_by_primary_id-expanded"><a name="L394"></a><tt class="py-lineno">394</tt> <tt class="py-line"> <tt class="py-docstring">"""Gets a Bio::Seq object by the primary (internal) id.</tt> </tt>
<a name="L395"></a><tt class="py-lineno">395</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L396"></a><tt class="py-lineno">396</tt> <tt class="py-line"><tt class="py-docstring"> The primary id in these cases has to come from</tt> </tt>
<a name="L397"></a><tt class="py-lineno">397</tt> <tt class="py-line"><tt class="py-docstring"> $db->get_all_primary_ids. There is no other way to get (or</tt> </tt>
<a name="L398"></a><tt class="py-lineno">398</tt> <tt class="py-line"><tt class="py-docstring"> guess) the primary_ids in a database.</tt> </tt>
<a name="L399"></a><tt class="py-lineno">399</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L400"></a><tt class="py-lineno">400</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">[</tt><tt class="py-name">seqid</tt><tt class="py-op">]</tt> </tt>
</div><a name="L401"></a><tt class="py-lineno">401</tt> <tt class="py-line"> </tt>
<a name="BioSeqDatabase.load"></a><div id="BioSeqDatabase.load-def"><a name="L402"></a><tt class="py-lineno">402</tt> <a class="py-toggle" href="#" id="BioSeqDatabase.load-toggle" onclick="return toggle('BioSeqDatabase.load');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#load">load</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">record_iterator</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BioSeqDatabase.load-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSeqDatabase.load-expanded"><a name="L403"></a><tt class="py-lineno">403</tt> <tt class="py-line"> <tt class="py-docstring">"""Load a set of SeqRecords into the BioSQL database.</tt> </tt>
<a name="L404"></a><tt class="py-lineno">404</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L405"></a><tt class="py-lineno">405</tt> <tt class="py-line"><tt class="py-docstring"> record_iterator is either a list of SeqRecord objects, or an</tt> </tt>
<a name="L406"></a><tt class="py-lineno">406</tt> <tt class="py-line"><tt class="py-docstring"> Iterator object that returns SeqRecord objects (such as the</tt> </tt>
<a name="L407"></a><tt class="py-lineno">407</tt> <tt class="py-line"><tt class="py-docstring"> output from the Bio.SeqIO.parse() function), which will be</tt> </tt>
<a name="L408"></a><tt class="py-lineno">408</tt> <tt class="py-line"><tt class="py-docstring"> used to populate the database.</tt> </tt>
<a name="L409"></a><tt class="py-lineno">409</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L410"></a><tt class="py-lineno">410</tt> <tt class="py-line"><tt class="py-docstring"> Example:</tt> </tt>
<a name="L411"></a><tt class="py-lineno">411</tt> <tt class="py-line"><tt class="py-docstring"> from Bio import SeqIO</tt> </tt>
<a name="L412"></a><tt class="py-lineno">412</tt> <tt class="py-line"><tt class="py-docstring"> count = db.load(SeqIO.parse(open(filename), format))</tt> </tt>
<a name="L413"></a><tt class="py-lineno">413</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L414"></a><tt class="py-lineno">414</tt> <tt class="py-line"><tt class="py-docstring"> Returns the number of records loaded.</tt> </tt>
<a name="L415"></a><tt class="py-lineno">415</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L416"></a><tt class="py-lineno">416</tt> <tt class="py-line"> <tt class="py-name">db_loader</tt> <tt class="py-op">=</tt> <tt id="link-180" class="py-name"><a title="BioSQL.Loader" class="py-name" href="#" onclick="return doclink('link-180', 'Loader', 'link-1');">Loader</a></tt><tt class="py-op">.</tt><tt id="link-181" class="py-name" targets="Class BioSQL.Loader.DatabaseLoader=BioSQL.Loader.DatabaseLoader-class.html"><a title="BioSQL.Loader.DatabaseLoader" class="py-name" href="#" onclick="return doclink('link-181', 'DatabaseLoader', 'link-181');">DatabaseLoader</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-182" class="py-name"><a title="Bio.Std.dbid" class="py-name" href="#" onclick="return doclink('link-182', 'dbid', 'link-59');">dbid</a></tt><tt class="py-op">)</tt> </tt>
<a name="L417"></a><tt class="py-lineno">417</tt> <tt class="py-line"> <tt class="py-name">num_records</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L418"></a><tt class="py-lineno">418</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">cur_record</tt> <tt class="py-keyword">in</tt> <tt class="py-name">record_iterator</tt> <tt class="py-op">:</tt> </tt>
<a name="L419"></a><tt class="py-lineno">419</tt> <tt class="py-line"> <tt class="py-name">num_records</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L420"></a><tt class="py-lineno">420</tt> <tt class="py-line"> <tt class="py-name">db_loader</tt><tt class="py-op">.</tt><tt id="link-183" class="py-name" targets="Method BioSQL.Loader.DatabaseLoader.load_seqrecord()=BioSQL.Loader.DatabaseLoader-class.html#load_seqrecord"><a title="BioSQL.Loader.DatabaseLoader.load_seqrecord" class="py-name" href="#" onclick="return doclink('link-183', 'load_seqrecord', 'link-183');">load_seqrecord</a></tt><tt class="py-op">(</tt><tt class="py-name">cur_record</tt><tt class="py-op">)</tt> </tt>
<a name="L421"></a><tt class="py-lineno">421</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">num_records</tt> </tt>
</div></div><a name="L422"></a><tt class="py-lineno">422</tt> <tt class="py-line"> </tt><script type="text/javascript">
<!--
expandto(location.href);
// -->
</script>
</pre>
<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 09:28:14 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. So hide
// them unless we have a cookie that says to show them.
checkCookie();
// -->
</script>
</body>
</html>
