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<a href="BioSQL-module.html">Package BioSQL</a> ::
Module BioSeqDatabase
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<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"># Revisions 2007-2009 copyright by Peter Cock. All rights reserved.</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"># Revisions 2009 copyright by Cymon J. Cox. All rights reserved.</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-comment"># Note that BioSQL (including the database schema and scripts) is</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-comment"># available and licensed separately. Please consult www.biosql.org</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring">"""Connect with a BioSQL database and load Biopython like objects from it.</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring">This provides interfaces for loading biological objects from a relational</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring">database, and is compatible with the BioSQL standards.</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring">"""</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-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="L16"></a><tt class="py-lineno"> 16</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="L17"></a><tt class="py-lineno"> 17</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="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt id="link-3" class="py-name" targets="Variable BioSQL.BioSeqDatabase._POSTGRES_RULES_PRESENT=BioSQL.BioSeqDatabase-module.html#_POSTGRES_RULES_PRESENT"><a title="BioSQL.BioSeqDatabase._POSTGRES_RULES_PRESENT" class="py-name" href="#" onclick="return doclink('link-3', '_POSTGRES_RULES_PRESENT', 'link-3');">_POSTGRES_RULES_PRESENT</a></tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> <tt class="py-comment"># Hack for BioSQL Bug 2839</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"> </tt>
<a name="open_database"></a><div id="open_database-def"><a name="L21"></a><tt class="py-lineno"> 21</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="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"> <tt class="py-docstring">"""Main interface for loading a existing BioSQL-style database.</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"> This function is the easiest way to retrieve a connection to a</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring"> database, doing something like:</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"> >>> from BioSeq import BioSeqDatabase</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-docstring"> >>> server = BioSeqDatabase.open_database(user="root", db="minidb")</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring"> the various options are:</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</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="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-docstring"> driver should implement the python DB API. By default, the MySQLdb</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-docstring"> driver is used.</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-docstring"> user -> the username to connect to the database with.</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-docstring"> password, passwd -> the password to connect with</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-docstring"> host -> the hostname of the database</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-docstring"> database or db -> the name of the database</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</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-op">:</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</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">"Using BioSQL with psycopg (version one) is no "</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-string">"longer supported. Use psycopg2 instead."</tt><tt class="py-op">)</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</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="L44"></a><tt class="py-lineno"> 44</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="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt class="py-comment"># Different drivers use different keywords...</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <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-4" 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.PDB.Vector'.Vector.copy()=Bio.PDB.Vector%27.Vector-class.html#copy,Method Bio.SeqIO._index._IndexedSeqFileDict.copy()=Bio.SeqIO._index._IndexedSeqFileDict-class.html#copy"><a title="Bio.Crystal.Crystal.copy
Bio.GA.Organism.Organism.copy
Bio.PDB.Vector'.Vector.copy
Bio.SeqIO._index._IndexedSeqFileDict.copy" class="py-name" href="#" onclick="return doclink('link-4', 'copy', 'link-4');">copy</a></tt><tt class="py-op">(</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">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="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-string">"database"</tt> <tt class="py-keyword">in</tt> <tt class="py-name">kw</tt><tt class="py-op">:</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</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="L51"></a><tt class="py-lineno"> 51</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="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-string">"password"</tt> <tt class="py-keyword">in</tt> <tt class="py-name">kw</tt><tt class="py-op">:</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</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="L54"></a><tt class="py-lineno"> 54</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="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt class="py-comment"># DB-API recommendations</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-string">"db"</tt> <tt class="py-keyword">in</tt> <tt class="py-name">kw</tt><tt class="py-op">:</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</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="L59"></a><tt class="py-lineno"> 59</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="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-string">"passwd"</tt> <tt class="py-keyword">in</tt> <tt class="py-name">kw</tt><tt class="py-op">:</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</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="L62"></a><tt class="py-lineno"> 62</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="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">driver</tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt><tt class="py-string">"psycopg2"</tt><tt class="py-op">,</tt> <tt class="py-string">"pgdb"</tt><tt class="py-op">]</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-5" 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.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.SeqIO._index.SeqFileRandomAccess.get()=Bio.SeqIO._index.SeqFileRandomAccess-class.html#get,Method Bio.SeqIO._index.SffRandomAccess.get()=Bio.SeqIO._index.SffRandomAccess-class.html#get,Method Bio.SeqIO._index.SffTrimedRandomAccess.get()=Bio.SeqIO._index.SffTrimedRandomAccess-class.html#get,Method Bio.SeqIO._index.UniprotRandomAccess.get()=Bio.SeqIO._index.UniprotRandomAccess-class.html#get,Method Bio.SeqIO._index._IndexedSeqFileDict.get()=Bio.SeqIO._index._IndexedSeqFileDict-class.html#get,Method Bio.SeqIO._index._SQLiteManySeqFilesDict.get()=Bio.SeqIO._index._SQLiteManySeqFilesDict-class.html#get"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqIO._index.SeqFileRandomAccess.get
Bio.SeqIO._index.SffRandomAccess.get
Bio.SeqIO._index.SffTrimedRandomAccess.get
Bio.SeqIO._index.UniprotRandomAccess.get
Bio.SeqIO._index._IndexedSeqFileDict.get
Bio.SeqIO._index._SQLiteManySeqFilesDict.get" class="py-name" href="#" onclick="return doclink('link-5', 'get', 'link-5');">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="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">"database"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-string">"template1"</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-comment"># SQLite connect takes the database name as input</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">driver</tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt><tt class="py-string">"sqlite3"</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">conn</tt> <tt class="py-op">=</tt> <tt class="py-name">connect</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 class="py-op">)</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</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="L71"></a><tt class="py-lineno"> 71</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="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-comment"># Ok, so let's try building a DSN</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-comment"># (older releases of psycopg need this)</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-string">"database"</tt> <tt class="py-keyword">in</tt> <tt class="py-name">kw</tt><tt class="py-op">:</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</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="L76"></a><tt class="py-lineno"> 76</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="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-string">"db"</tt> <tt class="py-keyword">in</tt> <tt class="py-name">kw</tt><tt class="py-op">:</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</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="L79"></a><tt class="py-lineno"> 79</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="L80"></a><tt class="py-lineno"> 80</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-6" 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-6', 'i', 'link-6');">i</a></tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt id="link-7" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-7', 'i', 'link-6');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">kw</tt><tt class="py-op">.</tt><tt id="link-8" class="py-name" targets="Method Bio.Crystal.Crystal.items()=Bio.Crystal.Crystal-class.html#items,Method Bio.Phylo.PhyloXML.Events.items()=Bio.Phylo.PhyloXML.Events-class.html#items,Method Bio.SeqIO._index._IndexedSeqFileDict.items()=Bio.SeqIO._index._IndexedSeqFileDict-class.html#items,Method BioSQL.BioSeqDatabase.BioSeqDatabase.items()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#items,Method BioSQL.BioSeqDatabase.DBServer.items()=BioSQL.BioSeqDatabase.DBServer-class.html#items"><a title="Bio.Crystal.Crystal.items
Bio.Phylo.PhyloXML.Events.items
Bio.SeqIO._index._IndexedSeqFileDict.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items" class="py-name" href="#" onclick="return doclink('link-8', 'items', 'link-8');">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="L81"></a><tt class="py-lineno"> 81</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="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-name">server</tt> <tt class="py-op">=</tt> <tt id="link-9" 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-9', 'DBServer', 'link-9');">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>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-comment"># TODO - Remove the following once BioSQL Bug 2839 is fixed.</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-comment"># Test for RULES in PostgreSQL schema, see also Bug 2833.</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">driver</tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt><tt class="py-string">"psycopg2"</tt><tt class="py-op">,</tt> <tt class="py-string">"pgdb"</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-name">sql</tt> <tt class="py-op">=</tt> <tt class="py-string">"SELECT ev_class FROM pg_rewrite WHERE "</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-string">"rulename='rule_bioentry_i1' OR "</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-string">"rulename='rule_bioentry_i2';"</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">server</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-10" class="py-name" targets="Method BioSQL.BioSeqDatabase.Adaptor.execute_and_fetchall()=BioSQL.BioSeqDatabase.Adaptor-class.html#execute_and_fetchall"><a title="BioSQL.BioSeqDatabase.Adaptor.execute_and_fetchall" class="py-name" href="#" onclick="return doclink('link-10', 'execute_and_fetchall', 'link-10');">execute_and_fetchall</a></tt><tt class="py-op">(</tt><tt class="py-name">sql</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">warnings</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-name">warnings</tt><tt class="py-op">.</tt><tt class="py-name">warn</tt><tt class="py-op">(</tt><tt class="py-string">"Your BioSQL PostgreSQL schema includes some "</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-string">"rules currently required for bioperl-db but "</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-string">"which may cause problems loading data using "</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-string">"Biopython (see BioSQL Bug 2839). If you do not "</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-string">"use BioPerl, please remove these rules. "</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-string">"Biopython should cope with the rules present, "</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-string">"but with a performance penalty when loading "</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-string">"new records."</tt><tt class="py-op">)</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-keyword">global</tt> <tt id="link-11" class="py-name"><a title="BioSQL.BioSeqDatabase._POSTGRES_RULES_PRESENT" class="py-name" href="#" onclick="return doclink('link-11', '_POSTGRES_RULES_PRESENT', 'link-3');">_POSTGRES_RULES_PRESENT</a></tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt id="link-12" class="py-name"><a title="BioSQL.BioSeqDatabase._POSTGRES_RULES_PRESENT" class="py-name" href="#" onclick="return doclink('link-12', '_POSTGRES_RULES_PRESENT', 'link-3');">_POSTGRES_RULES_PRESENT</a></tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">server</tt> </tt>
</div><a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> </tt>
<a name="DBServer"></a><div id="DBServer-def"><a name="L106"></a><tt class="py-lineno">106</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="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-docstring">"""Represents a BioSQL database continaing namespaces (sub-databases).</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"><tt class="py-docstring"> This acts like a Python dictionary, giving access to each namespace</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"><tt class="py-docstring"> (defined by a row in the biodatabase table) as a BioSeqDatabase object.</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="DBServer.__init__"></a><div id="DBServer.__init__-def"><a name="L112"></a><tt class="py-lineno">112</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="L113"></a><tt class="py-lineno">113</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="L114"></a><tt class="py-lineno">114</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="L115"></a><tt class="py-lineno">115</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="L116"></a><tt class="py-lineno">116</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-13" 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-13', 'Adaptor', 'link-13');">Adaptor</a></tt><tt class="py-op">(</tt><tt class="py-name">conn</tt><tt class="py-op">,</tt> <tt id="link-14" class="py-name"><a title="BioSQL.DBUtils" class="py-name" href="#" onclick="return doclink('link-14', 'DBUtils', 'link-2');">DBUtils</a></tt><tt class="py-op">.</tt><tt id="link-15" 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-15', 'get_dbutils', 'link-15');">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="L117"></a><tt class="py-lineno">117</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="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> </tt>
<a name="DBServer.__repr__"></a><div id="DBServer.__repr__-def"><a name="L119"></a><tt class="py-lineno">119</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="L120"></a><tt class="py-lineno">120</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="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> </tt>
<a name="DBServer.__getitem__"></a><div id="DBServer.__getitem__-def"><a name="L122"></a><tt class="py-lineno">122</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="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-16" 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-16', 'BioSeqDatabase', 'link-16');">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-17" class="py-name" targets="Method Bio.Phylo.PhyloXMLIO.Writer.name()=Bio.Phylo.PhyloXMLIO.Writer-class.html#name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-17', 'name', 'link-17');">name</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> </tt>
<a name="DBServer.__len__"></a><div id="DBServer.__len__-def"><a name="L125"></a><tt class="py-lineno">125</tt> <a class="py-toggle" href="#" id="DBServer.__len__-toggle" onclick="return toggle('DBServer.__len__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.DBServer-class.html#__len__">__len__</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.__len__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DBServer.__len__-expanded"><a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt class="py-docstring">"""Number of namespaces (sub-databases) in this database."""</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-name">sql</tt> <tt class="py-op">=</tt> <tt class="py-string">"SELECT COUNT(name) FROM biodatabase;"</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">int</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-18" 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-18', 'execute_and_fetch_col0', 'link-18');">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-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
</div><a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> </tt>
<a name="DBServer.__contains__"></a><div id="DBServer.__contains__-def"><a name="L130"></a><tt class="py-lineno">130</tt> <a class="py-toggle" href="#" id="DBServer.__contains__-toggle" onclick="return toggle('DBServer.__contains__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.DBServer-class.html#__contains__">__contains__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">value</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DBServer.__contains__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DBServer.__contains__-expanded"><a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-docstring">"""Check if a namespace (sub-database) in this database."""</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-name">sql</tt> <tt class="py-op">=</tt> <tt class="py-string">"SELECT COUNT(name) FROM biodatabase WHERE name=%s;"</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">bool</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"><a title="BioSQL.BioSeqDatabase.Adaptor.execute_and_fetch_col0" class="py-name" href="#" onclick="return doclink('link-19', 'execute_and_fetch_col0', 'link-18');">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-op">(</tt><tt id="link-20" class="py-name" targets="Method Bio.Phylo.PhyloXMLIO.Writer.value()=Bio.Phylo.PhyloXMLIO.Writer-class.html#value"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-20', 'value', 'link-20');">value</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">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
</div><a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> </tt>
<a name="DBServer.__iter__"></a><div id="DBServer.__iter__-def"><a name="L135"></a><tt class="py-lineno">135</tt> <a class="py-toggle" href="#" id="DBServer.__iter__-toggle" onclick="return toggle('DBServer.__iter__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.DBServer-class.html#__iter__">__iter__</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.__iter__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DBServer.__iter__-expanded"><a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-docstring">"""Iterate over namespaces (sub-databases) in the database."""</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-comment">#TODO - Iterate over the cursor, much more efficient</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">iter</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-21" 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-21', 'list_biodatabase_names', 'link-21');">list_biodatabase_names</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">hasattr</tt><tt class="py-op">(</tt><tt class="py-name">dict</tt><tt class="py-op">,</tt> <tt class="py-string">"iteritems"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-comment">#Python 2, use iteritems etc </tt> </tt>
<a name="DBServer.keys"></a><div id="DBServer.keys-def"><a name="L142"></a><tt class="py-lineno">142</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="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt class="py-docstring">"""List of namespaces (sub-databases) in the database."""</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</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-22" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.list_biodatabase_names" class="py-name" href="#" onclick="return doclink('link-22', 'list_biodatabase_names', 'link-21');">list_biodatabase_names</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> </tt>
<a name="DBServer.values"></a><div id="DBServer.values-def"><a name="L146"></a><tt class="py-lineno">146</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="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-docstring">"""List of BioSeqDatabase objects in the database."""</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</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 class="py-name">key</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">key</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.PDB.AbstractPropertyMap.AbstractPropertyMap.keys()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#keys,Method Bio.Phylo.PhyloXML.Events.keys()=Bio.Phylo.PhyloXML.Events-class.html#keys,Method Bio.SeqIO._index._IndexedSeqFileDict.keys()=Bio.SeqIO._index._IndexedSeqFileDict-class.html#keys,Method Bio.SeqIO._index._SQLiteManySeqFilesDict.keys()=Bio.SeqIO._index._SQLiteManySeqFilesDict-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"><a title="Bio.Crystal.Crystal.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Phylo.PhyloXML.Events.keys
Bio.SeqIO._index._IndexedSeqFileDict.keys
Bio.SeqIO._index._SQLiteManySeqFilesDict.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.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="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> </tt>
<a name="DBServer.items"></a><div id="DBServer.items-def"><a name="L150"></a><tt class="py-lineno">150</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="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-docstring">"""List of (namespace, BioSeqDatabase) for entries in the database."""</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">key</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">[</tt><tt class="py-name">key</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">key</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-24" class="py-name"><a title="Bio.Crystal.Crystal.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Phylo.PhyloXML.Events.keys
Bio.SeqIO._index._IndexedSeqFileDict.keys
Bio.SeqIO._index._SQLiteManySeqFilesDict.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys" class="py-name" href="#" onclick="return doclink('link-24', '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="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> </tt>
<a name="DBServer.iterkeys"></a><div id="DBServer.iterkeys-def"><a name="L154"></a><tt class="py-lineno">154</tt> <a class="py-toggle" href="#" id="DBServer.iterkeys-toggle" onclick="return toggle('DBServer.iterkeys');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.DBServer-class.html#iterkeys">iterkeys</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.iterkeys-collapsed" style="display:none;" pad="+++" indent="++++++++++++++++"></div><div id="DBServer.iterkeys-expanded"><a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt class="py-docstring">"""Iterate over namespaces (sub-databases) in the database."""</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">iter</tt><tt class="py-op">(</tt><tt class="py-name">self</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="DBServer.itervalues"></a><div id="DBServer.itervalues-def"><a name="L158"></a><tt class="py-lineno">158</tt> <a class="py-toggle" href="#" id="DBServer.itervalues-toggle" onclick="return toggle('DBServer.itervalues');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.DBServer-class.html#itervalues">itervalues</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.itervalues-collapsed" style="display:none;" pad="+++" indent="++++++++++++++++"></div><div id="DBServer.itervalues-expanded"><a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-docstring">"""Iterate over BioSeqDatabase objects in the database."""</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">key</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">:</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-name">self</tt><tt class="py-op">[</tt><tt class="py-name">key</tt><tt class="py-op">]</tt> </tt>
</div><a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> </tt>
<a name="DBServer.iteritems"></a><div id="DBServer.iteritems-def"><a name="L163"></a><tt class="py-lineno">163</tt> <a class="py-toggle" href="#" id="DBServer.iteritems-toggle" onclick="return toggle('DBServer.iteritems');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.DBServer-class.html#iteritems">iteritems</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.iteritems-collapsed" style="display:none;" pad="+++" indent="++++++++++++++++"></div><div id="DBServer.iteritems-expanded"><a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-docstring">"""Iterate over (namespace, BioSeqDatabase) in the database."""</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">key</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">:</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-name">key</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">[</tt><tt class="py-name">key</tt><tt class="py-op">]</tt> </tt>
</div><a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> <tt class="py-comment">#Python 3, items etc are all iterators</tt> </tt>
<a name="DBServer.keys"></a><div id="DBServer.keys-def"><a name="L169"></a><tt class="py-lineno">169</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="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt class="py-docstring">"""Iterate over namespaces (sub-databases) in the database."""</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">iter</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> </tt>
</div><a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> </tt>
<a name="DBServer.values"></a><div id="DBServer.values-def"><a name="L173"></a><tt class="py-lineno">173</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="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-docstring">"""Iterate over BioSeqDatabase objects in the database."""</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">key</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</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">yield</tt> <tt class="py-name">self</tt><tt class="py-op">[</tt><tt class="py-name">key</tt><tt class="py-op">]</tt> </tt>
</div><a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> </tt>
<a name="DBServer.items"></a><div id="DBServer.items-def"><a name="L178"></a><tt class="py-lineno">178</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="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-docstring">"""Iterate over (namespace, BioSeqDatabase) in the database."""</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">key</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">:</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-name">key</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">[</tt><tt class="py-name">key</tt><tt class="py-op">]</tt> </tt>
</div><a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> </tt>
<a name="DBServer.__delitem__"></a><div id="DBServer.__delitem__-def"><a name="L183"></a><tt class="py-lineno">183</tt> <a class="py-toggle" href="#" id="DBServer.__delitem__-toggle" onclick="return toggle('DBServer.__delitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.DBServer-class.html#__delitem__">__delitem__</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.__delitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DBServer.__delitem__-expanded"><a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-docstring">"""Remove a namespace and all its entries."""</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-25" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-25', 'name', 'link-17');">name</a></tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">:</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">KeyError</tt><tt class="py-op">(</tt><tt id="link-26" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-26', 'name', 'link-17');">name</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-27" class="py-name" targets="Method BioSQL.BioSeqDatabase.DBServer.remove_database()=BioSQL.BioSeqDatabase.DBServer-class.html#remove_database"><a title="BioSQL.BioSeqDatabase.DBServer.remove_database" class="py-name" href="#" onclick="return doclink('link-27', 'remove_database', 'link-27');">remove_database</a></tt><tt class="py-op">(</tt><tt id="link-28" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-28', 'name', 'link-17');">name</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> </tt>
<a name="DBServer.remove_database"></a><div id="DBServer.remove_database-def"><a name="L189"></a><tt class="py-lineno">189</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="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt class="py-docstring">"""Remove a namespace and all its entries (OBSOLETE).</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"><tt class="py-docstring"> Try to remove all references to items in a database.</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"><tt class="py-docstring"> server.remove_database(name)</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"><tt class="py-docstring"> In keeping with the dictionary interface, you can now do this:</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"><tt class="py-docstring"> del server[name]</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">warnings</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-name">warnings</tt><tt class="py-op">.</tt><tt class="py-name">warn</tt><tt class="py-op">(</tt><tt class="py-string">"This method is obsolete. In keeping with the dictionary interface, you can now use 'del server[name]' instead"</tt><tt class="py-op">,</tt> <tt class="py-name">PendingDeprecationWarning</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">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-29" 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-29', 'fetch_dbid_by_dbname', 'link-29');">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="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-name">remover</tt> <tt class="py-op">=</tt> <tt id="link-30" class="py-name"><a title="BioSQL.Loader" class="py-name" href="#" onclick="return doclink('link-30', 'Loader', 'link-1');">Loader</a></tt><tt class="py-op">.</tt><tt id="link-31" 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-31', 'DatabaseRemover', 'link-31');">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="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-name">remover</tt><tt class="py-op">.</tt><tt id="link-32" class="py-name" targets="Method Bio.Crystal.Chain.remove()=Bio.Crystal.Chain-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.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-32', 'remove', 'link-32');">remove</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> </tt>
<a name="DBServer.new_database"></a><div id="DBServer.new_database-def"><a name="L206"></a><tt class="py-lineno">206</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="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> <tt class="py-docstring">"""Add a new database to the server and return it.</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> <tt class="py-comment"># make the database</tt> </tt>
<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"INSERT INTO biodatabase (name, authority, description)"</tt> \ </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt class="py-string">r" VALUES (%s, %s, %s)"</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</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-33" class="py-name" targets="Method BioSQL.BioSeqDatabase.Adaptor.execute()=BioSQL.BioSeqDatabase.Adaptor-class.html#execute,Method BioSQL.DBUtils.Generic_dbutils.execute()=BioSQL.DBUtils.Generic_dbutils-class.html#execute,Method BioSQL.DBUtils.Sqlite_dbutils.execute()=BioSQL.DBUtils.Sqlite_dbutils-class.html#execute"><a title="BioSQL.BioSeqDatabase.Adaptor.execute
BioSQL.DBUtils.Generic_dbutils.execute
BioSQL.DBUtils.Sqlite_dbutils.execute" class="py-name" href="#" onclick="return doclink('link-33', 'execute', 'link-33');">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-34" class="py-name" targets="Method Bio.Blast.NCBIStandalone._DescriptionConsumer.description()=Bio.Blast.NCBIStandalone._DescriptionConsumer-class.html#description,Method Bio.Phylo.PhyloXMLIO.Writer.description()=Bio.Phylo.PhyloXMLIO.Writer-class.html#description"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description
Bio.Phylo.PhyloXMLIO.Writer.description" class="py-name" href="#" onclick="return doclink('link-34', 'description', 'link-34');">description</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-35" class="py-name"><a title="BioSQL.BioSeqDatabase
BioSQL.BioSeqDatabase.BioSeqDatabase" class="py-name" href="#" onclick="return doclink('link-35', 'BioSeqDatabase', 'link-16');">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="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> </tt>
<a name="DBServer.load_database_sql"></a><div id="DBServer.load_database_sql-def"><a name="L215"></a><tt class="py-lineno">215</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="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt class="py-docstring">"""Load a database schema into the given database.</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</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="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"><tt class="py-docstring"> sql_file should specify the complete path to a file containing</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"><tt class="py-docstring"> SQL entries for building the tables.</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt class="py-comment"># Not sophisticated enough for PG schema. Is it needed by MySQL?</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt class="py-comment"># Looks like we need this more complicated way for both. Leaving it</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> <tt class="py-comment"># the default and removing the simple-minded approach.</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> <tt class="py-comment"># read the file with all comment lines removed</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt class="py-name">sql_handle</tt> <tt class="py-op">=</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">sql_file</tt><tt class="py-op">,</tt> <tt class="py-string">"rU"</tt><tt class="py-op">)</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</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="L229"></a><tt class="py-lineno">229</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>
<a name="L230"></a><tt class="py-lineno">230</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.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.Seq.Seq.find()=Bio.Seq.Seq-class.html#find,Function Bio.triefind.find()=Bio.triefind-module.html#find"><a title="Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.Seq.Seq.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="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</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.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.Seq.Seq.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="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</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="Method Bio.File.SGMLStripper.strip()=Bio.File.SGMLStripper-class.html#strip,Method Bio.Seq.Seq.strip()=Bio.Seq.Seq-class.html#strip"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.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="L235"></a><tt class="py-lineno">235</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.File.SGMLStripper.strip
Bio.Seq.Seq.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="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> <tt class="py-name">sql</tt> <tt class="py-op">+=</tt> <tt class="py-string">' '</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> <tt class="py-comment"># two ways to load the SQL</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> <tt class="py-comment"># 1. PostgreSQL can load it all at once and actually needs to</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> <tt class="py-comment"># due to FUNCTION defines at the end of the SQL which mess up</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt class="py-comment"># the splitting by semicolons</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> <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">"psycopg2"</tt><tt class="py-op">,</tt> <tt class="py-string">"pgdb"</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</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
BioSQL.DBUtils.Generic_dbutils.execute
BioSQL.DBUtils.Sqlite_dbutils.execute" class="py-name" href="#" onclick="return doclink('link-41', 'execute', 'link-33');">execute</a></tt><tt class="py-op">(</tt><tt class="py-name">sql</tt><tt class="py-op">)</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</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="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> <tt class="py-comment"># SQL executed one at a time</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> <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-string">"sqlite3"</tt><tt class="py-op">]</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">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.Phylo.BaseTree.TreeMixin.split()=Bio.Phylo.BaseTree.TreeMixin-class.html#split,Method Bio.Restriction.Restriction.RestrictionBatch.split()=Bio.Restriction.Restriction.RestrictionBatch-class.html#split,Method Bio.Seq.Seq.split()=Bio.Seq.Seq-class.html#split"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.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="L248"></a><tt class="py-lineno">248</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="L249"></a><tt class="py-lineno">249</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
BioSQL.DBUtils.Generic_dbutils.execute
BioSQL.DBUtils.Sqlite_dbutils.execute" class="py-name" href="#" onclick="return doclink('link-44', 'execute', 'link-33');">execute</a></tt><tt class="py-op">(</tt><tt class="py-name">sql_line</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">else</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">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="L252"></a><tt class="py-lineno">252</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><a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> </tt>
<a name="DBServer.commit"></a><div id="DBServer.commit-def"><a name="L254"></a><tt class="py-lineno">254</tt> <a class="py-toggle" href="#" id="DBServer.commit-toggle" onclick="return toggle('DBServer.commit');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.DBServer-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="DBServer.commit-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DBServer.commit-expanded"><a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"> <tt class="py-docstring">"""Commits the current transaction to the database."""</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</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-45" class="py-name" targets="Method BioSQL.BioSeqDatabase.Adaptor.commit()=BioSQL.BioSeqDatabase.Adaptor-class.html#commit,Method BioSQL.BioSeqDatabase.DBServer.commit()=BioSQL.BioSeqDatabase.DBServer-class.html#commit"><a title="BioSQL.BioSeqDatabase.Adaptor.commit
BioSQL.BioSeqDatabase.DBServer.commit" class="py-name" href="#" onclick="return doclink('link-45', 'commit', 'link-45');">commit</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"> </tt>
<a name="DBServer.rollback"></a><div id="DBServer.rollback-def"><a name="L258"></a><tt class="py-lineno">258</tt> <a class="py-toggle" href="#" id="DBServer.rollback-toggle" onclick="return toggle('DBServer.rollback');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.DBServer-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="DBServer.rollback-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DBServer.rollback-expanded"><a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> <tt class="py-docstring">"""Rolls backs the current transaction."""</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</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-46" class="py-name" targets="Method BioSQL.BioSeqDatabase.Adaptor.rollback()=BioSQL.BioSeqDatabase.Adaptor-class.html#rollback,Method BioSQL.BioSeqDatabase.DBServer.rollback()=BioSQL.BioSeqDatabase.DBServer-class.html#rollback"><a title="BioSQL.BioSeqDatabase.Adaptor.rollback
BioSQL.BioSeqDatabase.DBServer.rollback" class="py-name" href="#" onclick="return doclink('link-46', 'rollback', 'link-46');">rollback</a></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="DBServer.close"></a><div id="DBServer.close-def"><a name="L262"></a><tt class="py-lineno">262</tt> <a class="py-toggle" href="#" id="DBServer.close-toggle" onclick="return toggle('DBServer.close');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.DBServer-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="DBServer.close-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DBServer.close-expanded"><a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"> <tt class="py-docstring">"""Close the connection. No further activity possible."""</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</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-47" class="py-name" targets="Method Bio.SeqIO.SffIO._AddTellHandle.close()=Bio.SeqIO.SffIO._AddTellHandle-class.html#close,Method Bio.SeqIO._index._SQLiteManySeqFilesDict.close()=Bio.SeqIO._index._SQLiteManySeqFilesDict-class.html#close,Method BioSQL.BioSeqDatabase.Adaptor.close()=BioSQL.BioSeqDatabase.Adaptor-class.html#close,Method BioSQL.BioSeqDatabase.DBServer.close()=BioSQL.BioSeqDatabase.DBServer-class.html#close"><a title="Bio.SeqIO.SffIO._AddTellHandle.close
Bio.SeqIO._index._SQLiteManySeqFilesDict.close
BioSQL.BioSeqDatabase.Adaptor.close
BioSQL.BioSeqDatabase.DBServer.close" class="py-name" href="#" onclick="return doclink('link-47', 'close', 'link-47');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"> </tt>
<a name="Adaptor"></a><div id="Adaptor-def"><a name="L266"></a><tt class="py-lineno">266</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="L267"></a><tt class="py-lineno">267</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="L268"></a><tt class="py-lineno">268</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="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"> <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 class="py-name">conn</tt><tt class="py-op">.</tt><tt id="link-49" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-49', 'cursor', 'link-40');">cursor</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</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="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> </tt>
<a name="Adaptor.last_id"></a><div id="Adaptor.last_id-def"><a name="L272"></a><tt class="py-lineno">272</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="L273"></a><tt class="py-lineno">273</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-50" 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._PostgreSQL_dbutils.last_id()=BioSQL.DBUtils._PostgreSQL_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._PostgreSQL_dbutils.last_id" class="py-name" href="#" onclick="return doclink('link-50', 'last_id', 'link-50');">last_id</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-51" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-51', 'cursor', 'link-40');">cursor</a></tt><tt class="py-op">,</tt> <tt class="py-name">table</tt><tt class="py-op">)</tt> </tt>
</div><a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> </tt>
<a name="Adaptor.autocommit"></a><div id="Adaptor.autocommit-def"><a name="L275"></a><tt class="py-lineno">275</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 class="py-name">True</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="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"> <tt class="py-docstring">"""Set the autocommit mode. True values enable; False value disable."""</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</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-52" 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.Psycopg2_dbutils.autocommit()=BioSQL.DBUtils.Psycopg2_dbutils-class.html#autocommit"><a title="BioSQL.BioSeqDatabase.Adaptor.autocommit
BioSQL.DBUtils.Generic_dbutils.autocommit
BioSQL.DBUtils.Pgdb_dbutils.autocommit
BioSQL.DBUtils.Psycopg2_dbutils.autocommit" class="py-name" href="#" onclick="return doclink('link-52', 'autocommit', 'link-52');">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="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> </tt>
<a name="Adaptor.commit"></a><div id="Adaptor.commit-def"><a name="L279"></a><tt class="py-lineno">279</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="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> <tt class="py-docstring">"""Commits the current transaction."""</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</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"><a title="BioSQL.BioSeqDatabase.Adaptor.commit
BioSQL.BioSeqDatabase.DBServer.commit" class="py-name" href="#" onclick="return doclink('link-53', 'commit', 'link-45');">commit</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"> </tt>
<a name="Adaptor.rollback"></a><div id="Adaptor.rollback-def"><a name="L283"></a><tt class="py-lineno">283</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="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> <tt class="py-docstring">"""Rolls backs the current transaction."""</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</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"><a title="BioSQL.BioSeqDatabase.Adaptor.rollback
BioSQL.BioSeqDatabase.DBServer.rollback" class="py-name" href="#" onclick="return doclink('link-54', 'rollback', 'link-46');">rollback</a></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.close"></a><div id="Adaptor.close-def"><a name="L287"></a><tt class="py-lineno">287</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="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"> <tt class="py-docstring">"""Close the connection. No further activity possible."""</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 class="py-name">conn</tt><tt class="py-op">.</tt><tt id="link-55" class="py-name"><a title="Bio.SeqIO.SffIO._AddTellHandle.close
Bio.SeqIO._index._SQLiteManySeqFilesDict.close
BioSQL.BioSeqDatabase.Adaptor.close
BioSQL.BioSeqDatabase.DBServer.close" class="py-name" href="#" onclick="return doclink('link-55', 'close', 'link-47');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"> </tt>
<a name="Adaptor.fetch_dbid_by_dbname"></a><div id="Adaptor.fetch_dbid_by_dbname-def"><a name="L291"></a><tt class="py-lineno">291</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="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-56" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute
BioSQL.DBUtils.Generic_dbutils.execute
BioSQL.DBUtils.Sqlite_dbutils.execute" class="py-name" href="#" onclick="return doclink('link-56', 'execute', 'link-33');">execute</a></tt><tt class="py-op">(</tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</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="L294"></a><tt class="py-lineno">294</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="L295"></a><tt class="py-lineno">295</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="L296"></a><tt class="py-lineno">296</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="L297"></a><tt class="py-lineno">297</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="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"> <tt class="py-comment"># Cannot happen (UK)</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"><tt class="py-comment">## assert len(rv) == 1, "More than one biodatabase with name %r" % dbname</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">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="L301"></a><tt class="py-lineno">301</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="L302"></a><tt class="py-lineno">302</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="L303"></a><tt class="py-lineno">303</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="L304"></a><tt class="py-lineno">304</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.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-58', 'name', 'link-17');">name</a></tt><tt class="py-op">]</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">dbid</tt><tt class="py-op">:</tt> </tt>
<a name="L306"></a><tt class="py-lineno">306</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="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"> <tt class="py-name">fields</tt><tt class="py-op">.</tt><tt id="link-59" class="py-name" targets="Method Bio.Align.MultipleSeqAlignment.append()=Bio.Align.MultipleSeqAlignment-class.html#append,Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-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"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-59', 'append', 'link-59');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">dbid</tt><tt class="py-op">)</tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-60" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute
BioSQL.DBUtils.Generic_dbutils.execute
BioSQL.DBUtils.Sqlite_dbutils.execute" class="py-name" href="#" onclick="return doclink('link-60', 'execute', 'link-33');">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="L309"></a><tt class="py-lineno">309</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-61" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-61', '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="L310"></a><tt class="py-lineno">310</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="L311"></a><tt class="py-lineno">311</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-62" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-62', 'name', 'link-17');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</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="L313"></a><tt class="py-lineno">313</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-63" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-63', 'name', 'link-17');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</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="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"> </tt>
<a name="Adaptor.fetch_seqid_by_accession"></a><div id="Adaptor.fetch_seqid_by_accession-def"><a name="L316"></a><tt class="py-lineno">316</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="L317"></a><tt class="py-lineno">317</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="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"> <tt class="py-name">fields</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-64" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-64', 'name', 'link-17');">name</a></tt><tt class="py-op">]</tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">dbid</tt><tt class="py-op">:</tt> </tt>
<a name="L320"></a><tt class="py-lineno">320</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="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"> <tt class="py-name">fields</tt><tt class="py-op">.</tt><tt id="link-65" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-65', 'append', 'link-59');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">dbid</tt><tt class="py-op">)</tt> </tt>
<a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-66" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute
BioSQL.DBUtils.Generic_dbutils.execute
BioSQL.DBUtils.Sqlite_dbutils.execute" class="py-name" href="#" onclick="return doclink('link-66', 'execute', 'link-33');">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="L323"></a><tt class="py-lineno">323</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-67" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-67', '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="L324"></a><tt class="py-lineno">324</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="L325"></a><tt class="py-lineno">325</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-68" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-68', 'name', 'link-17');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L326"></a><tt class="py-lineno">326</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="L327"></a><tt class="py-lineno">327</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-69" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-69', 'name', 'link-17');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L328"></a><tt class="py-lineno">328</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="L329"></a><tt class="py-lineno">329</tt> <tt class="py-line"> </tt>
<a name="Adaptor.fetch_seqids_by_accession"></a><div id="Adaptor.fetch_seqids_by_accession-def"><a name="L330"></a><tt class="py-lineno">330</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="L331"></a><tt class="py-lineno">331</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="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"> <tt class="py-name">fields</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-70" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-70', 'name', 'link-17');">name</a></tt><tt class="py-op">]</tt> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">dbid</tt><tt class="py-op">:</tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</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="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"> <tt class="py-name">fields</tt><tt class="py-op">.</tt><tt id="link-71" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-71', 'append', 'link-59');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">dbid</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 class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-72" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute_and_fetch_col0" class="py-name" href="#" onclick="return doclink('link-72', 'execute_and_fetch_col0', 'link-18');">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="L337"></a><tt class="py-lineno">337</tt> <tt class="py-line"> </tt>
<a name="Adaptor.fetch_seqid_by_version"></a><div id="Adaptor.fetch_seqid_by_version-def"><a name="L338"></a><tt class="py-lineno">338</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="L339"></a><tt class="py-lineno">339</tt> <tt class="py-line"> <tt class="py-name">acc_version</tt> <tt class="py-op">=</tt> <tt id="link-73" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-73', 'name', 'link-17');">name</a></tt><tt class="py-op">.</tt><tt id="link-74" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.split" class="py-name" href="#" onclick="return doclink('link-74', 'split', 'link-42');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">"."</tt><tt class="py-op">)</tt> </tt>
<a name="L340"></a><tt class="py-lineno">340</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="L341"></a><tt class="py-lineno">341</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-75" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-75', 'name', 'link-17');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt> <tt class="py-line"> <tt id="link-76" 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-76', 'acc', 'link-76');">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="L343"></a><tt class="py-lineno">343</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="L344"></a><tt class="py-lineno">344</tt> <tt class="py-line"> <tt id="link-77" class="py-name" targets="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"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version" class="py-name" href="#" onclick="return doclink('link-77', 'version', 'link-77');">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="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt> <tt class="py-line"> <tt id="link-78" class="py-name"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version" class="py-name" href="#" onclick="return doclink('link-78', 'version', 'link-77');">version</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"0"</tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</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="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"> <tt class="py-string">r" AND version = %s"</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt> <tt class="py-line"> <tt class="py-name">fields</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-79" class="py-name"><a title="Bio.FSSP.fssp_rec.align.acc" class="py-name" href="#" onclick="return doclink('link-79', 'acc', 'link-76');">acc</a></tt><tt class="py-op">,</tt> <tt id="link-80" class="py-name"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version" class="py-name" href="#" onclick="return doclink('link-80', 'version', 'link-77');">version</a></tt><tt class="py-op">]</tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">dbid</tt><tt class="py-op">:</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</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="L352"></a><tt class="py-lineno">352</tt> <tt class="py-line"> <tt class="py-name">fields</tt><tt class="py-op">.</tt><tt id="link-81" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-81', 'append', 'link-59');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">dbid</tt><tt class="py-op">)</tt> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-82" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute
BioSQL.DBUtils.Generic_dbutils.execute
BioSQL.DBUtils.Sqlite_dbutils.execute" class="py-name" href="#" onclick="return doclink('link-82', 'execute', 'link-33');">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="L354"></a><tt class="py-lineno">354</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-83" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-83', '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="L355"></a><tt class="py-lineno">355</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="L356"></a><tt class="py-lineno">356</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-84" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-84', 'name', 'link-17');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L357"></a><tt class="py-lineno">357</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="L358"></a><tt class="py-lineno">358</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-85" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-85', 'name', 'link-17');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</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="L360"></a><tt class="py-lineno">360</tt> <tt class="py-line"> </tt>
<a name="Adaptor.fetch_seqid_by_identifier"></a><div id="Adaptor.fetch_seqid_by_identifier-def"><a name="L361"></a><tt class="py-lineno">361</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="L362"></a><tt class="py-lineno">362</tt> <tt class="py-line"> <tt class="py-comment"># YB: was fetch_seqid_by_seqid</tt> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt> <tt class="py-line"> <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="L364"></a><tt class="py-lineno">364</tt> <tt class="py-line"> <tt class="py-name">fields</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">identifier</tt><tt class="py-op">]</tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">dbid</tt><tt class="py-op">:</tt> </tt>
<a name="L366"></a><tt class="py-lineno">366</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="L367"></a><tt class="py-lineno">367</tt> <tt class="py-line"> <tt class="py-name">fields</tt><tt class="py-op">.</tt><tt id="link-86" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-86', 'append', 'link-59');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">dbid</tt><tt class="py-op">)</tt> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-87" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute
BioSQL.DBUtils.Generic_dbutils.execute
BioSQL.DBUtils.Sqlite_dbutils.execute" class="py-name" href="#" onclick="return doclink('link-87', 'execute', 'link-33');">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="L369"></a><tt class="py-lineno">369</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-88" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-88', '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="L370"></a><tt class="py-lineno">370</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="L371"></a><tt class="py-lineno">371</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 class="py-name">identifier</tt><tt class="py-op">)</tt> </tt>
<a name="L372"></a><tt class="py-lineno">372</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="L373"></a><tt class="py-lineno">373</tt> <tt class="py-line"> </tt>
<a name="Adaptor.list_biodatabase_names"></a><div id="Adaptor.list_biodatabase_names-def"><a name="L374"></a><tt class="py-lineno">374</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="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-89" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute_and_fetch_col0" class="py-name" href="#" onclick="return doclink('link-89', 'execute_and_fetch_col0', 'link-18');">execute_and_fetch_col0</a></tt><tt class="py-op">(</tt> </tt>
<a name="L376"></a><tt class="py-lineno">376</tt> <tt class="py-line"> <tt class="py-string">"SELECT name FROM biodatabase"</tt><tt class="py-op">)</tt> </tt>
</div><a name="L377"></a><tt class="py-lineno">377</tt> <tt class="py-line"> </tt>
<a name="Adaptor.list_bioentry_ids"></a><div id="Adaptor.list_bioentry_ids-def"><a name="L378"></a><tt class="py-lineno">378</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="L379"></a><tt class="py-lineno">379</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-90" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute_and_fetch_col0" class="py-name" href="#" onclick="return doclink('link-90', 'execute_and_fetch_col0', 'link-18');">execute_and_fetch_col0</a></tt><tt class="py-op">(</tt> </tt>
<a name="L380"></a><tt class="py-lineno">380</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="L381"></a><tt class="py-lineno">381</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">dbid</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L382"></a><tt class="py-lineno">382</tt> <tt class="py-line"> </tt>
<a name="Adaptor.list_bioentry_display_ids"></a><div id="Adaptor.list_bioentry_display_ids-def"><a name="L383"></a><tt class="py-lineno">383</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="L384"></a><tt class="py-lineno">384</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-91" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute_and_fetch_col0" class="py-name" href="#" onclick="return doclink('link-91', 'execute_and_fetch_col0', 'link-18');">execute_and_fetch_col0</a></tt><tt class="py-op">(</tt> </tt>
<a name="L385"></a><tt class="py-lineno">385</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="L386"></a><tt class="py-lineno">386</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">dbid</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L387"></a><tt class="py-lineno">387</tt> <tt class="py-line"> </tt>
<a name="Adaptor.list_any_ids"></a><div id="Adaptor.list_any_ids-def"><a name="L388"></a><tt class="py-lineno">388</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="L389"></a><tt class="py-lineno">389</tt> <tt class="py-line"> <tt class="py-docstring">"""Return ids given a SQL statement to select for them.</tt> </tt>
<a name="L390"></a><tt class="py-lineno">390</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L391"></a><tt class="py-lineno">391</tt> <tt class="py-line"><tt class="py-docstring"> This assumes that the given SQL does a SELECT statement that</tt> </tt>
<a name="L392"></a><tt class="py-lineno">392</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="L393"></a><tt class="py-lineno">393</tt> <tt class="py-line"><tt class="py-docstring"> they come as and just returns them in a list.</tt> </tt>
<a name="L394"></a><tt class="py-lineno">394</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L395"></a><tt class="py-lineno">395</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-92" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute_and_fetch_col0" class="py-name" href="#" onclick="return doclink('link-92', 'execute_and_fetch_col0', 'link-18');">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="L396"></a><tt class="py-lineno">396</tt> <tt class="py-line"> </tt>
<a name="Adaptor.execute_one"></a><div id="Adaptor.execute_one-def"><a name="L397"></a><tt class="py-lineno">397</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="L398"></a><tt class="py-lineno">398</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-93" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute
BioSQL.DBUtils.Generic_dbutils.execute
BioSQL.DBUtils.Sqlite_dbutils.execute" class="py-name" href="#" onclick="return doclink('link-93', 'execute', 'link-33');">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="L399"></a><tt class="py-lineno">399</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="L400"></a><tt class="py-lineno">400</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="L401"></a><tt class="py-lineno">401</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="L402"></a><tt class="py-lineno">402</tt> <tt class="py-line"> </tt>
<a name="Adaptor.execute"></a><div id="Adaptor.execute-def"><a name="L403"></a><tt class="py-lineno">403</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="L404"></a><tt class="py-lineno">404</tt> <tt class="py-line"> <tt class="py-docstring">"""Just execute an sql command.</tt> </tt>
<a name="L405"></a><tt class="py-lineno">405</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L406"></a><tt class="py-lineno">406</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 id="link-95" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute
BioSQL.DBUtils.Generic_dbutils.execute
BioSQL.DBUtils.Sqlite_dbutils.execute" class="py-name" href="#" onclick="return doclink('link-95', 'execute', 'link-33');">execute</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-96" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-96', 'cursor', 'link-40');">cursor</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="L407"></a><tt class="py-lineno">407</tt> <tt class="py-line"> </tt>
<a name="Adaptor.get_subseq_as_string"></a><div id="Adaptor.get_subseq_as_string-def"><a name="L408"></a><tt class="py-lineno">408</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="L409"></a><tt class="py-lineno">409</tt> <tt class="py-line"> <tt id="link-97" class="py-name" targets="Method Bio.Blast.NCBIStandalone._AlignmentConsumer.length()=Bio.Blast.NCBIStandalone._AlignmentConsumer-class.html#length"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-97', 'length', 'link-97');">length</a></tt> <tt class="py-op">=</tt> <tt id="link-98" class="py-name" targets="Variable Bio.SeqFeature.FeatureLocation.end=Bio.SeqFeature.FeatureLocation-class.html#end"><a title="Bio.SeqFeature.FeatureLocation.end" class="py-name" href="#" onclick="return doclink('link-98', 'end', 'link-98');">end</a></tt> <tt class="py-op">-</tt> <tt id="link-99" class="py-name" targets="Variable Bio.Restriction._Update.RestrictionCompiler.start=Bio.Restriction._Update.RestrictionCompiler-module.html#start,Variable Bio.SeqFeature.FeatureLocation.start=Bio.SeqFeature.FeatureLocation-class.html#start"><a title="Bio.Restriction._Update.RestrictionCompiler.start
Bio.SeqFeature.FeatureLocation.start" class="py-name" href="#" onclick="return doclink('link-99', 'start', 'link-99');">start</a></tt> </tt>
<a name="L410"></a><tt class="py-lineno">410</tt> <tt class="py-line"> <tt class="py-comment"># XXX Check this on MySQL and PostgreSQL. substr should be general,</tt> </tt>
<a name="L411"></a><tt class="py-lineno">411</tt> <tt class="py-line"> <tt class="py-comment"># does it need dbutils?</tt> </tt>
<a name="L412"></a><tt class="py-lineno">412</tt> <tt class="py-line"> <tt class="py-comment">#return self.execute_one(</tt> </tt>
<a name="L413"></a><tt class="py-lineno">413</tt> <tt class="py-line"> <tt class="py-comment"># """select SUBSTRING(seq FROM %s FOR %s)</tt> </tt>
<a name="L414"></a><tt class="py-lineno">414</tt> <tt class="py-line"> <tt class="py-comment"># from biosequence where bioentry_id = %s""",</tt> </tt>
<a name="L415"></a><tt class="py-lineno">415</tt> <tt class="py-line"> <tt class="py-comment"># (start+1, length, seqid))[0]</tt> </tt>
<a name="L416"></a><tt class="py-lineno">416</tt> <tt class="py-line"> <tt class="py-comment"># </tt> </tt>
<a name="L417"></a><tt class="py-lineno">417</tt> <tt class="py-line"> <tt class="py-comment"># Convert to a string on returning for databases that give back</tt> </tt>
<a name="L418"></a><tt class="py-lineno">418</tt> <tt class="py-line"> <tt class="py-comment"># unicode. Shouldn't need unicode for sequences so this seems safe.</tt> </tt>
<a name="L419"></a><tt class="py-lineno">419</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-100" 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-100', 'execute_one', 'link-100');">execute_one</a></tt><tt class="py-op">(</tt> </tt>
<a name="L420"></a><tt class="py-lineno">420</tt> <tt class="py-line"> <tt class="py-string">"""select SUBSTR(seq, %s, %s)</tt> </tt>
<a name="L421"></a><tt class="py-lineno">421</tt> <tt class="py-line"><tt class="py-string"> from biosequence where bioentry_id = %s"""</tt><tt class="py-op">,</tt> </tt>
<a name="L422"></a><tt class="py-lineno">422</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt id="link-101" class="py-name"><a title="Bio.Restriction._Update.RestrictionCompiler.start
Bio.SeqFeature.FeatureLocation.start" class="py-name" href="#" onclick="return doclink('link-101', 'start', 'link-99');">start</a></tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt id="link-102" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-102', 'length', 'link-97');">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 class="py-op">)</tt> </tt>
</div><a name="L423"></a><tt class="py-lineno">423</tt> <tt class="py-line"> </tt>
<a name="Adaptor.execute_and_fetch_col0"></a><div id="Adaptor.execute_and_fetch_col0-def"><a name="L424"></a><tt class="py-lineno">424</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="L425"></a><tt class="py-lineno">425</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-103" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute
BioSQL.DBUtils.Generic_dbutils.execute
BioSQL.DBUtils.Sqlite_dbutils.execute" class="py-name" href="#" onclick="return doclink('link-103', 'execute', 'link-33');">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="L426"></a><tt class="py-lineno">426</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-104" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-104', '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="L427"></a><tt class="py-lineno">427</tt> <tt class="py-line"> </tt>
<a name="Adaptor.execute_and_fetchall"></a><div id="Adaptor.execute_and_fetchall-def"><a name="L428"></a><tt class="py-lineno">428</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="L429"></a><tt class="py-lineno">429</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-105" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute
BioSQL.DBUtils.Generic_dbutils.execute
BioSQL.DBUtils.Sqlite_dbutils.execute" class="py-name" href="#" onclick="return doclink('link-105', 'execute', 'link-33');">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="L430"></a><tt class="py-lineno">430</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="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-106', '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="L431"></a><tt class="py-lineno">431</tt> <tt class="py-line"> </tt>
<a name="L432"></a><tt class="py-lineno">432</tt> <tt class="py-line"><tt id="link-107" 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-107', '_allowed_lookups', 'link-107');">_allowed_lookups</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt> </tt>
<a name="L433"></a><tt class="py-lineno">433</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="L434"></a><tt class="py-lineno">434</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="L435"></a><tt class="py-lineno">435</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="L436"></a><tt class="py-lineno">436</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="L437"></a><tt class="py-lineno">437</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="L438"></a><tt class="py-lineno">438</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="L439"></a><tt class="py-lineno">439</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="L440"></a><tt class="py-lineno">440</tt> <tt class="py-line"> <tt class="py-op">}</tt> </tt>
<a name="L441"></a><tt class="py-lineno">441</tt> <tt class="py-line"> </tt>
<a name="BioSeqDatabase"></a><div id="BioSeqDatabase-def"><a name="L442"></a><tt class="py-lineno">442</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="L443"></a><tt class="py-lineno">443</tt> <tt class="py-line"> <tt class="py-docstring">"""Represents a namespace (sub-database) within the BioSQL database.</tt> </tt>
<a name="L444"></a><tt class="py-lineno">444</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L445"></a><tt class="py-lineno">445</tt> <tt class="py-line"><tt class="py-docstring"> i.e. One row in the biodatabase table, and all all rows in the bioentry</tt> </tt>
<a name="L446"></a><tt class="py-lineno">446</tt> <tt class="py-line"><tt class="py-docstring"> table associated with it.</tt> </tt>
<a name="L447"></a><tt class="py-lineno">447</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="BioSeqDatabase.__init__"></a><div id="BioSeqDatabase.__init__-def"><a name="L448"></a><tt class="py-lineno">448</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="L449"></a><tt class="py-lineno">449</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="L450"></a><tt class="py-lineno">450</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-108" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-108', 'name', 'link-17');">name</a></tt> <tt class="py-op">=</tt> <tt id="link-109" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-109', 'name', 'link-17');">name</a></tt> </tt>
<a name="L451"></a><tt class="py-lineno">451</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dbid</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-110" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.fetch_dbid_by_dbname" class="py-name" href="#" onclick="return doclink('link-110', 'fetch_dbid_by_dbname', 'link-29');">fetch_dbid_by_dbname</a></tt><tt class="py-op">(</tt><tt id="link-111" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-111', 'name', 'link-17');">name</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L452"></a><tt class="py-lineno">452</tt> <tt class="py-line"> </tt>
<a name="BioSeqDatabase.__repr__"></a><div id="BioSeqDatabase.__repr__-def"><a name="L453"></a><tt class="py-lineno">453</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="L454"></a><tt class="py-lineno">454</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-112" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-112', 'name', 'link-17');">name</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L455"></a><tt class="py-lineno">455</tt> <tt class="py-line"> </tt>
<a name="BioSeqDatabase.get_Seq_by_id"></a><div id="BioSeqDatabase.get_Seq_by_id-def"><a name="L456"></a><tt class="py-lineno">456</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="L457"></a><tt class="py-lineno">457</tt> <tt class="py-line"> <tt class="py-docstring">"""Gets a DBSeqRecord object by its name</tt> </tt>
<a name="L458"></a><tt class="py-lineno">458</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L459"></a><tt class="py-lineno">459</tt> <tt class="py-line"><tt class="py-docstring"> Example: seq_rec = db.get_Seq_by_id('ROA1_HUMAN')</tt> </tt>
<a name="L460"></a><tt class="py-lineno">460</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L461"></a><tt class="py-lineno">461</tt> <tt class="py-line"><tt class="py-docstring"> The name of this method is misleading since it returns a DBSeqRecord</tt> </tt>
<a name="L462"></a><tt class="py-lineno">462</tt> <tt class="py-line"><tt class="py-docstring"> rather than a DBSeq ojbect, and presumably was to mirror BioPerl.</tt> </tt>
<a name="L463"></a><tt class="py-lineno">463</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L464"></a><tt class="py-lineno">464</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-113" 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-113', 'fetch_seqid_by_display_id', 'link-113');">fetch_seqid_by_display_id</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dbid</tt><tt class="py-op">,</tt> <tt id="link-114" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-114', 'name', 'link-17');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L465"></a><tt class="py-lineno">465</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-115" class="py-name"><a title="BioSQL.BioSeq" class="py-name" href="#" onclick="return doclink('link-115', 'BioSeq', 'link-0');">BioSeq</a></tt><tt class="py-op">.</tt><tt id="link-116" 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-116', 'DBSeqRecord', 'link-116');">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="L466"></a><tt class="py-lineno">466</tt> <tt class="py-line"> </tt>
<a name="BioSeqDatabase.get_Seq_by_acc"></a><div id="BioSeqDatabase.get_Seq_by_acc-def"><a name="L467"></a><tt class="py-lineno">467</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="L468"></a><tt class="py-lineno">468</tt> <tt class="py-line"> <tt class="py-docstring">"""Gets a DBSeqRecord object by accession number</tt> </tt>
<a name="L469"></a><tt class="py-lineno">469</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L470"></a><tt class="py-lineno">470</tt> <tt class="py-line"><tt class="py-docstring"> Example: seq_rec = db.get_Seq_by_acc('X77802')</tt> </tt>
<a name="L471"></a><tt class="py-lineno">471</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L472"></a><tt class="py-lineno">472</tt> <tt class="py-line"><tt class="py-docstring"> The name of this method is misleading since it returns a DBSeqRecord</tt> </tt>
<a name="L473"></a><tt class="py-lineno">473</tt> <tt class="py-line"><tt class="py-docstring"> rather than a DBSeq ojbect, and presumably was to mirror BioPerl.</tt> </tt>
<a name="L474"></a><tt class="py-lineno">474</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L475"></a><tt class="py-lineno">475</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-117" 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-117', 'fetch_seqid_by_accession', 'link-117');">fetch_seqid_by_accession</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dbid</tt><tt class="py-op">,</tt> <tt id="link-118" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-118', 'name', 'link-17');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L476"></a><tt class="py-lineno">476</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-119" class="py-name"><a title="BioSQL.BioSeq" class="py-name" href="#" onclick="return doclink('link-119', 'BioSeq', 'link-0');">BioSeq</a></tt><tt class="py-op">.</tt><tt id="link-120" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord" class="py-name" href="#" onclick="return doclink('link-120', 'DBSeqRecord', 'link-116');">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="L477"></a><tt class="py-lineno">477</tt> <tt class="py-line"> </tt>
<a name="BioSeqDatabase.get_Seq_by_ver"></a><div id="BioSeqDatabase.get_Seq_by_ver-def"><a name="L478"></a><tt class="py-lineno">478</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="L479"></a><tt class="py-lineno">479</tt> <tt class="py-line"> <tt class="py-docstring">"""Gets a DBSeqRecord object by version number</tt> </tt>
<a name="L480"></a><tt class="py-lineno">480</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L481"></a><tt class="py-lineno">481</tt> <tt class="py-line"><tt class="py-docstring"> Example: seq_rec = db.get_Seq_by_ver('X77802.1')</tt> </tt>
<a name="L482"></a><tt class="py-lineno">482</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L483"></a><tt class="py-lineno">483</tt> <tt class="py-line"><tt class="py-docstring"> The name of this method is misleading since it returns a DBSeqRecord</tt> </tt>
<a name="L484"></a><tt class="py-lineno">484</tt> <tt class="py-line"><tt class="py-docstring"> rather than a DBSeq ojbect, and presumably was to mirror BioPerl.</tt> </tt>
<a name="L485"></a><tt class="py-lineno">485</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L486"></a><tt class="py-lineno">486</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-121" 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-121', 'fetch_seqid_by_version', 'link-121');">fetch_seqid_by_version</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dbid</tt><tt class="py-op">,</tt> <tt id="link-122" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-122', 'name', 'link-17');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L487"></a><tt class="py-lineno">487</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-123" class="py-name"><a title="BioSQL.BioSeq" class="py-name" href="#" onclick="return doclink('link-123', 'BioSeq', 'link-0');">BioSeq</a></tt><tt class="py-op">.</tt><tt id="link-124" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord" class="py-name" href="#" onclick="return doclink('link-124', 'DBSeqRecord', 'link-116');">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="L488"></a><tt class="py-lineno">488</tt> <tt class="py-line"> </tt>
<a name="BioSeqDatabase.get_Seqs_by_acc"></a><div id="BioSeqDatabase.get_Seqs_by_acc-def"><a name="L489"></a><tt class="py-lineno">489</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="L490"></a><tt class="py-lineno">490</tt> <tt class="py-line"> <tt class="py-docstring">"""Gets a list of DBSeqRecord objects by accession number</tt> </tt>
<a name="L491"></a><tt class="py-lineno">491</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L492"></a><tt class="py-lineno">492</tt> <tt class="py-line"><tt class="py-docstring"> Example: seq_recs = db.get_Seq_by_acc('X77802')</tt> </tt>
<a name="L493"></a><tt class="py-lineno">493</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L494"></a><tt class="py-lineno">494</tt> <tt class="py-line"><tt class="py-docstring"> The name of this method is misleading since it returns a list of</tt> </tt>
<a name="L495"></a><tt class="py-lineno">495</tt> <tt class="py-line"><tt class="py-docstring"> DBSeqRecord objects rather than a list of DBSeq ojbects, and presumably</tt> </tt>
<a name="L496"></a><tt class="py-lineno">496</tt> <tt class="py-line"><tt class="py-docstring"> was to mirror BioPerl.</tt> </tt>
<a name="L497"></a><tt class="py-lineno">497</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L498"></a><tt class="py-lineno">498</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-125" 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-125', 'fetch_seqids_by_accession', 'link-125');">fetch_seqids_by_accession</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dbid</tt><tt class="py-op">,</tt> <tt id="link-126" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-126', 'name', 'link-17');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L499"></a><tt class="py-lineno">499</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">[</tt><tt id="link-127" class="py-name"><a title="BioSQL.BioSeq" class="py-name" href="#" onclick="return doclink('link-127', 'BioSeq', 'link-0');">BioSeq</a></tt><tt class="py-op">.</tt><tt id="link-128" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord" class="py-name" href="#" onclick="return doclink('link-128', 'DBSeqRecord', 'link-116');">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="L500"></a><tt class="py-lineno">500</tt> <tt class="py-line"> </tt>
<a name="BioSeqDatabase.get_all_primary_ids"></a><div id="BioSeqDatabase.get_all_primary_ids-def"><a name="L501"></a><tt class="py-lineno">501</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="L502"></a><tt class="py-lineno">502</tt> <tt class="py-line"> <tt class="py-docstring">"""All the primary_ids of the sequences in the database (OBSOLETE).</tt> </tt>
<a name="L503"></a><tt class="py-lineno">503</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L504"></a><tt class="py-lineno">504</tt> <tt class="py-line"><tt class="py-docstring"> These maybe ids (display style) or accession numbers or</tt> </tt>
<a name="L505"></a><tt class="py-lineno">505</tt> <tt class="py-line"><tt class="py-docstring"> something else completely different - they *are not*</tt> </tt>
<a name="L506"></a><tt class="py-lineno">506</tt> <tt class="py-line"><tt class="py-docstring"> meaningful outside of this database implementation.</tt> </tt>
<a name="L507"></a><tt class="py-lineno">507</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L508"></a><tt class="py-lineno">508</tt> <tt class="py-line"><tt class="py-docstring"> Please use .keys() instead of .get_all_primary_ids()</tt> </tt>
<a name="L509"></a><tt class="py-lineno">509</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L510"></a><tt class="py-lineno">510</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">warnings</tt> </tt>
<a name="L511"></a><tt class="py-lineno">511</tt> <tt class="py-line"> <tt class="py-name">warnings</tt><tt class="py-op">.</tt><tt class="py-name">warn</tt><tt class="py-op">(</tt><tt class="py-string">"Use bio_seq_database.keys() instead of "</tt> </tt>
<a name="L512"></a><tt class="py-lineno">512</tt> <tt class="py-line"> <tt class="py-string">"bio_seq_database.get_all_primary_ids()"</tt><tt class="py-op">,</tt> </tt>
<a name="L513"></a><tt class="py-lineno">513</tt> <tt class="py-line"> <tt class="py-name">PendingDeprecationWarning</tt><tt class="py-op">)</tt> </tt>
<a name="L514"></a><tt class="py-lineno">514</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-129" class="py-name"><a title="Bio.Crystal.Crystal.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Phylo.PhyloXML.Events.keys
Bio.SeqIO._index._IndexedSeqFileDict.keys
Bio.SeqIO._index._SQLiteManySeqFilesDict.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys" class="py-name" href="#" onclick="return doclink('link-129', 'keys', 'link-23');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L515"></a><tt class="py-lineno">515</tt> <tt class="py-line"> </tt>
<a name="BioSeqDatabase.__getitem__"></a><div id="BioSeqDatabase.__getitem__-def"><a name="L516"></a><tt class="py-lineno">516</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="L517"></a><tt class="py-lineno">517</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-130" class="py-name"><a title="BioSQL.BioSeq" class="py-name" href="#" onclick="return doclink('link-130', 'BioSeq', 'link-0');">BioSeq</a></tt><tt class="py-op">.</tt><tt id="link-131" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord" class="py-name" href="#" onclick="return doclink('link-131', 'DBSeqRecord', 'link-116');">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">key</tt><tt class="py-op">)</tt> </tt>
</div><a name="L518"></a><tt class="py-lineno">518</tt> <tt class="py-line"> </tt>
<a name="BioSeqDatabase.__delitem__"></a><div id="BioSeqDatabase.__delitem__-def"><a name="L519"></a><tt class="py-lineno">519</tt> <a class="py-toggle" href="#" id="BioSeqDatabase.__delitem__-toggle" onclick="return toggle('BioSeqDatabase.__delitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#__delitem__">__delitem__</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.__delitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSeqDatabase.__delitem__-expanded"><a name="L520"></a><tt class="py-lineno">520</tt> <tt class="py-line"> <tt class="py-docstring">"""Remove an entry and all its annotation."""</tt> </tt>
<a name="L521"></a><tt class="py-lineno">521</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">key</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">:</tt> </tt>
<a name="L522"></a><tt class="py-lineno">522</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-name">key</tt><tt class="py-op">)</tt> </tt>
<a name="L523"></a><tt class="py-lineno">523</tt> <tt class="py-line"> <tt class="py-comment">#Assuming this will automatically cascade to the other tables...</tt> </tt>
<a name="L524"></a><tt class="py-lineno">524</tt> <tt class="py-line"> <tt class="py-name">sql</tt> <tt class="py-op">=</tt> <tt class="py-string">"DELETE FROM bioentry "</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L525"></a><tt class="py-lineno">525</tt> <tt class="py-line"> <tt class="py-string">"WHERE biodatabase_id=%s AND bioentry_id=%s;"</tt> </tt>
<a name="L526"></a><tt class="py-lineno">526</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-132" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute
BioSQL.DBUtils.Generic_dbutils.execute
BioSQL.DBUtils.Sqlite_dbutils.execute" class="py-name" href="#" onclick="return doclink('link-132', 'execute', 'link-33');">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">self</tt><tt class="py-op">.</tt><tt class="py-name">dbid</tt><tt class="py-op">,</tt><tt class="py-name">key</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L527"></a><tt class="py-lineno">527</tt> <tt class="py-line"> </tt>
<a name="BioSeqDatabase.__len__"></a><div id="BioSeqDatabase.__len__-def"><a name="L528"></a><tt class="py-lineno">528</tt> <a class="py-toggle" href="#" id="BioSeqDatabase.__len__-toggle" onclick="return toggle('BioSeqDatabase.__len__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#__len__">__len__</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.__len__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSeqDatabase.__len__-expanded"><a name="L529"></a><tt class="py-lineno">529</tt> <tt class="py-line"> <tt class="py-docstring">"""Number of records in this namespace (sub database)."""</tt> </tt>
<a name="L530"></a><tt class="py-lineno">530</tt> <tt class="py-line"> <tt class="py-name">sql</tt> <tt class="py-op">=</tt> <tt class="py-string">"SELECT COUNT(bioentry_id) FROM bioentry "</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L531"></a><tt class="py-lineno">531</tt> <tt class="py-line"> <tt class="py-string">"WHERE biodatabase_id=%s;"</tt> </tt>
<a name="L532"></a><tt class="py-lineno">532</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">int</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.execute_and_fetch_col0" class="py-name" href="#" onclick="return doclink('link-133', 'execute_and_fetch_col0', 'link-18');">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-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dbid</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">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
</div><a name="L533"></a><tt class="py-lineno">533</tt> <tt class="py-line"> </tt>
<a name="BioSeqDatabase.__contains__"></a><div id="BioSeqDatabase.__contains__-def"><a name="L534"></a><tt class="py-lineno">534</tt> <a class="py-toggle" href="#" id="BioSeqDatabase.__contains__-toggle" onclick="return toggle('BioSeqDatabase.__contains__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#__contains__">__contains__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">value</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BioSeqDatabase.__contains__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSeqDatabase.__contains__-expanded"><a name="L535"></a><tt class="py-lineno">535</tt> <tt class="py-line"> <tt class="py-docstring">"""Check if a primary (internal) id is this namespace (sub database)."""</tt> </tt>
<a name="L536"></a><tt class="py-lineno">536</tt> <tt class="py-line"> <tt class="py-name">sql</tt> <tt class="py-op">=</tt> <tt class="py-string">"SELECT COUNT(bioentry_id) FROM bioentry "</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L537"></a><tt class="py-lineno">537</tt> <tt class="py-line"> <tt class="py-string">"WHERE biodatabase_id=%s AND bioentry_id=%s;"</tt> </tt>
<a name="L538"></a><tt class="py-lineno">538</tt> <tt class="py-line"> <tt class="py-comment">#The bioentry_id field is an integer in the schema.</tt> </tt>
<a name="L539"></a><tt class="py-lineno">539</tt> <tt class="py-line"> <tt class="py-comment">#PostgreSQL will throw an error if we use a non integer in the query.</tt> </tt>
<a name="L540"></a><tt class="py-lineno">540</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L541"></a><tt class="py-lineno">541</tt> <tt class="py-line"> <tt class="py-name">bioentry_id</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-134" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-134', 'value', 'link-20');">value</a></tt><tt class="py-op">)</tt> </tt>
<a name="L542"></a><tt class="py-lineno">542</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">ValueError</tt><tt class="py-op">:</tt> </tt>
<a name="L543"></a><tt class="py-lineno">543</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">False</tt> </tt>
<a name="L544"></a><tt class="py-lineno">544</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">bool</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-135" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute_and_fetch_col0" class="py-name" href="#" onclick="return doclink('link-135', 'execute_and_fetch_col0', 'link-18');">execute_and_fetch_col0</a></tt><tt class="py-op">(</tt><tt class="py-name">sql</tt><tt class="py-op">,</tt> </tt>
<a name="L545"></a><tt class="py-lineno">545</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">dbid</tt><tt class="py-op">,</tt> <tt class="py-name">bioentry_id</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 class="py-op">)</tt> </tt>
</div><a name="L546"></a><tt class="py-lineno">546</tt> <tt class="py-line"> </tt>
<a name="BioSeqDatabase.__iter__"></a><div id="BioSeqDatabase.__iter__-def"><a name="L547"></a><tt class="py-lineno">547</tt> <a class="py-toggle" href="#" id="BioSeqDatabase.__iter__-toggle" onclick="return toggle('BioSeqDatabase.__iter__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#__iter__">__iter__</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.__iter__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSeqDatabase.__iter__-expanded"><a name="L548"></a><tt class="py-lineno">548</tt> <tt class="py-line"> <tt class="py-docstring">"""Iterate over ids (which may not be meaningful outside this database)."""</tt> </tt>
<a name="L549"></a><tt class="py-lineno">549</tt> <tt class="py-line"> <tt class="py-comment">#TODO - Iterate over the cursor, much more efficient</tt> </tt>
<a name="L550"></a><tt class="py-lineno">550</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">iter</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.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-136', 'list_bioentry_ids', 'link-136');">list_bioentry_ids</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dbid</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L551"></a><tt class="py-lineno">551</tt> <tt class="py-line"> </tt>
<a name="L552"></a><tt class="py-lineno">552</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">hasattr</tt><tt class="py-op">(</tt><tt class="py-name">dict</tt><tt class="py-op">,</tt> <tt class="py-string">"iteritems"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L553"></a><tt class="py-lineno">553</tt> <tt class="py-line"> <tt class="py-comment">#Python 2, use iteritems etc </tt> </tt>
<a name="BioSeqDatabase.keys"></a><div id="BioSeqDatabase.keys-def"><a name="L554"></a><tt class="py-lineno">554</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="L555"></a><tt class="py-lineno">555</tt> <tt class="py-line"> <tt class="py-docstring">"""List of ids which may not be meaningful outside this database."""</tt> </tt>
<a name="L556"></a><tt class="py-lineno">556</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-137" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.list_bioentry_ids" class="py-name" href="#" onclick="return doclink('link-137', 'list_bioentry_ids', 'link-136');">list_bioentry_ids</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dbid</tt><tt class="py-op">)</tt> </tt>
</div><a name="L557"></a><tt class="py-lineno">557</tt> <tt class="py-line"> </tt>
<a name="BioSeqDatabase.values"></a><div id="BioSeqDatabase.values-def"><a name="L558"></a><tt class="py-lineno">558</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="L559"></a><tt class="py-lineno">559</tt> <tt class="py-line"> <tt class="py-docstring">"""List of DBSeqRecord objects in the namespace (sub database)."""</tt> </tt>
<a name="L560"></a><tt class="py-lineno">560</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 class="py-name">key</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">key</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-138" class="py-name"><a title="Bio.Crystal.Crystal.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Phylo.PhyloXML.Events.keys
Bio.SeqIO._index._IndexedSeqFileDict.keys
Bio.SeqIO._index._SQLiteManySeqFilesDict.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys" class="py-name" href="#" onclick="return doclink('link-138', '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="L561"></a><tt class="py-lineno">561</tt> <tt class="py-line"> </tt>
<a name="BioSeqDatabase.items"></a><div id="BioSeqDatabase.items-def"><a name="L562"></a><tt class="py-lineno">562</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="L563"></a><tt class="py-lineno">563</tt> <tt class="py-line"> <tt class="py-docstring">"""List of (id, DBSeqRecord) for the namespace (sub database)."""</tt> </tt>
<a name="L564"></a><tt class="py-lineno">564</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">key</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">[</tt><tt class="py-name">key</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">key</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-139" class="py-name"><a title="Bio.Crystal.Crystal.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Phylo.PhyloXML.Events.keys
Bio.SeqIO._index._IndexedSeqFileDict.keys
Bio.SeqIO._index._SQLiteManySeqFilesDict.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys" class="py-name" href="#" onclick="return doclink('link-139', '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="L565"></a><tt class="py-lineno">565</tt> <tt class="py-line"> </tt>
<a name="BioSeqDatabase.iterkeys"></a><div id="BioSeqDatabase.iterkeys-def"><a name="L566"></a><tt class="py-lineno">566</tt> <a class="py-toggle" href="#" id="BioSeqDatabase.iterkeys-toggle" onclick="return toggle('BioSeqDatabase.iterkeys');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#iterkeys">iterkeys</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.iterkeys-collapsed" style="display:none;" pad="+++" indent="++++++++++++++++"></div><div id="BioSeqDatabase.iterkeys-expanded"><a name="L567"></a><tt class="py-lineno">567</tt> <tt class="py-line"> <tt class="py-docstring">"""Iterate over ids (which may not be meaningful outside this database)."""</tt> </tt>
<a name="L568"></a><tt class="py-lineno">568</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">iter</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> </tt>
</div><a name="L569"></a><tt class="py-lineno">569</tt> <tt class="py-line"> </tt>
<a name="BioSeqDatabase.itervalues"></a><div id="BioSeqDatabase.itervalues-def"><a name="L570"></a><tt class="py-lineno">570</tt> <a class="py-toggle" href="#" id="BioSeqDatabase.itervalues-toggle" onclick="return toggle('BioSeqDatabase.itervalues');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#itervalues">itervalues</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.itervalues-collapsed" style="display:none;" pad="+++" indent="++++++++++++++++"></div><div id="BioSeqDatabase.itervalues-expanded"><a name="L571"></a><tt class="py-lineno">571</tt> <tt class="py-line"> <tt class="py-docstring">"""Iterate over DBSeqRecord objects in the namespace (sub database)."""</tt> </tt>
<a name="L572"></a><tt class="py-lineno">572</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">key</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">:</tt> </tt>
<a name="L573"></a><tt class="py-lineno">573</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-name">self</tt><tt class="py-op">[</tt><tt class="py-name">key</tt><tt class="py-op">]</tt> </tt>
</div><a name="L574"></a><tt class="py-lineno">574</tt> <tt class="py-line"> </tt>
<a name="BioSeqDatabase.iteritems"></a><div id="BioSeqDatabase.iteritems-def"><a name="L575"></a><tt class="py-lineno">575</tt> <a class="py-toggle" href="#" id="BioSeqDatabase.iteritems-toggle" onclick="return toggle('BioSeqDatabase.iteritems');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#iteritems">iteritems</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.iteritems-collapsed" style="display:none;" pad="+++" indent="++++++++++++++++"></div><div id="BioSeqDatabase.iteritems-expanded"><a name="L576"></a><tt class="py-lineno">576</tt> <tt class="py-line"> <tt class="py-docstring">"""Iterate over (id, DBSeqRecord) for the namespace (sub database)."""</tt> </tt>
<a name="L577"></a><tt class="py-lineno">577</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">key</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">:</tt> </tt>
<a name="L578"></a><tt class="py-lineno">578</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-name">key</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">[</tt><tt class="py-name">key</tt><tt class="py-op">]</tt> </tt>
</div><a name="L579"></a><tt class="py-lineno">579</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L580"></a><tt class="py-lineno">580</tt> <tt class="py-line"> <tt class="py-comment">#Python 3, items etc are all iterators</tt> </tt>
<a name="BioSeqDatabase.keys"></a><div id="BioSeqDatabase.keys-def"><a name="L581"></a><tt class="py-lineno">581</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="L582"></a><tt class="py-lineno">582</tt> <tt class="py-line"> <tt class="py-docstring">"""Iterate over ids (which may not be meaningful outside this database)."""</tt> </tt>
<a name="L583"></a><tt class="py-lineno">583</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">iter</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> </tt>
</div><a name="L584"></a><tt class="py-lineno">584</tt> <tt class="py-line"> </tt>
<a name="BioSeqDatabase.values"></a><div id="BioSeqDatabase.values-def"><a name="L585"></a><tt class="py-lineno">585</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="L586"></a><tt class="py-lineno">586</tt> <tt class="py-line"> <tt class="py-docstring">"""Iterate over DBSeqRecord objects in the namespace (sub database)."""</tt> </tt>
<a name="L587"></a><tt class="py-lineno">587</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">key</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">:</tt> </tt>
<a name="L588"></a><tt class="py-lineno">588</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-name">self</tt><tt class="py-op">[</tt><tt class="py-name">key</tt><tt class="py-op">]</tt> </tt>
</div><a name="L589"></a><tt class="py-lineno">589</tt> <tt class="py-line"> </tt>
<a name="BioSeqDatabase.items"></a><div id="BioSeqDatabase.items-def"><a name="L590"></a><tt class="py-lineno">590</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="L591"></a><tt class="py-lineno">591</tt> <tt class="py-line"> <tt class="py-docstring">"""Iterate over (id, DBSeqRecord) for the namespace (sub database)."""</tt> </tt>
<a name="L592"></a><tt class="py-lineno">592</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">key</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">:</tt> </tt>
<a name="L593"></a><tt class="py-lineno">593</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-name">key</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">[</tt><tt class="py-name">key</tt><tt class="py-op">]</tt> </tt>
</div><a name="L594"></a><tt class="py-lineno">594</tt> <tt class="py-line"> </tt>
<a name="BioSeqDatabase.lookup"></a><div id="BioSeqDatabase.lookup-def"><a name="L595"></a><tt class="py-lineno">595</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="L596"></a><tt class="py-lineno">596</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="L597"></a><tt class="py-lineno">597</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="L598"></a><tt class="py-lineno">598</tt> <tt class="py-line"> <tt class="py-name">k</tt><tt class="py-op">,</tt> <tt class="py-name">v</tt> <tt class="py-op">=</tt> <tt class="py-name">kwargs</tt><tt class="py-op">.</tt><tt id="link-140" class="py-name"><a title="Bio.Crystal.Crystal.items
Bio.Phylo.PhyloXML.Events.items
Bio.SeqIO._index._IndexedSeqFileDict.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items" class="py-name" href="#" onclick="return doclink('link-140', 'items', 'link-8');">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="L599"></a><tt class="py-lineno">599</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">k</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt id="link-141" class="py-name"><a title="BioSQL.BioSeqDatabase._allowed_lookups" class="py-name" href="#" onclick="return doclink('link-141', '_allowed_lookups', 'link-107');">_allowed_lookups</a></tt><tt class="py-op">:</tt> </tt>
<a name="L600"></a><tt class="py-lineno">600</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="L601"></a><tt class="py-lineno">601</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">repr</tt><tt class="py-op">(</tt><tt id="link-142" class="py-name"><a title="BioSQL.BioSeqDatabase._allowed_lookups" class="py-name" href="#" onclick="return doclink('link-142', '_allowed_lookups', 'link-107');">_allowed_lookups</a></tt><tt class="py-op">.</tt><tt id="link-143" class="py-name"><a title="Bio.Crystal.Crystal.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Phylo.PhyloXML.Events.keys
Bio.SeqIO._index._IndexedSeqFileDict.keys
Bio.SeqIO._index._SQLiteManySeqFilesDict.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys" class="py-name" href="#" onclick="return doclink('link-143', '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="L602"></a><tt class="py-lineno">602</tt> <tt class="py-line"> <tt class="py-name">lookup_name</tt> <tt class="py-op">=</tt> <tt id="link-144" class="py-name"><a title="BioSQL.BioSeqDatabase._allowed_lookups" class="py-name" href="#" onclick="return doclink('link-144', '_allowed_lookups', 'link-107');">_allowed_lookups</a></tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt> </tt>
<a name="L603"></a><tt class="py-lineno">603</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="L604"></a><tt class="py-lineno">604</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 class="py-name">dbid</tt><tt class="py-op">,</tt> <tt class="py-name">v</tt><tt class="py-op">)</tt> </tt>
<a name="L605"></a><tt class="py-lineno">605</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-145" class="py-name"><a title="BioSQL.BioSeq" class="py-name" href="#" onclick="return doclink('link-145', 'BioSeq', 'link-0');">BioSeq</a></tt><tt class="py-op">.</tt><tt id="link-146" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord" class="py-name" href="#" onclick="return doclink('link-146', 'DBSeqRecord', 'link-116');">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="L606"></a><tt class="py-lineno">606</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="L607"></a><tt class="py-lineno">607</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="L608"></a><tt class="py-lineno">608</tt> <tt class="py-line"> <tt class="py-docstring">"""Get a DBSeqRecord by the primary (internal) id (OBSOLETE).</tt> </tt>
<a name="L609"></a><tt class="py-lineno">609</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L610"></a><tt class="py-lineno">610</tt> <tt class="py-line"><tt class="py-docstring"> Rather than db.get_Seq_by_primary_id(my_id) use db[my_id]</tt> </tt>
<a name="L611"></a><tt class="py-lineno">611</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L612"></a><tt class="py-lineno">612</tt> <tt class="py-line"><tt class="py-docstring"> The name of this method is misleading since it returns a DBSeqRecord</tt> </tt>
<a name="L613"></a><tt class="py-lineno">613</tt> <tt class="py-line"><tt class="py-docstring"> rather than a DBSeq ojbect, and presumably was to mirror BioPerl.</tt> </tt>
<a name="L614"></a><tt class="py-lineno">614</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L615"></a><tt class="py-lineno">615</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">warnings</tt> </tt>
<a name="L616"></a><tt class="py-lineno">616</tt> <tt class="py-line"> <tt class="py-name">warnings</tt><tt class="py-op">.</tt><tt class="py-name">warn</tt><tt class="py-op">(</tt><tt class="py-string">"Use bio_seq_database[my_id] instead of "</tt> </tt>
<a name="L617"></a><tt class="py-lineno">617</tt> <tt class="py-line"> <tt class="py-string">"bio_seq_database.get_Seq_by_primary_id(my_id)"</tt><tt class="py-op">,</tt> </tt>
<a name="L618"></a><tt class="py-lineno">618</tt> <tt class="py-line"> <tt class="py-name">PendingDeprecationWarning</tt><tt class="py-op">)</tt> </tt>
<a name="L619"></a><tt class="py-lineno">619</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="L620"></a><tt class="py-lineno">620</tt> <tt class="py-line"> </tt>
<a name="BioSeqDatabase.load"></a><div id="BioSeqDatabase.load-def"><a name="L621"></a><tt class="py-lineno">621</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-param">fetch_NCBI_taxonomy</tt><tt class="py-op">=</tt><tt class="py-name">False</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="L622"></a><tt class="py-lineno">622</tt> <tt class="py-line"> <tt class="py-docstring">"""Load a set of SeqRecords into the BioSQL database.</tt> </tt>
<a name="L623"></a><tt class="py-lineno">623</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L624"></a><tt class="py-lineno">624</tt> <tt class="py-line"><tt class="py-docstring"> record_iterator is either a list of SeqRecord objects, or an</tt> </tt>
<a name="L625"></a><tt class="py-lineno">625</tt> <tt class="py-line"><tt class="py-docstring"> Iterator object that returns SeqRecord objects (such as the</tt> </tt>
<a name="L626"></a><tt class="py-lineno">626</tt> <tt class="py-line"><tt class="py-docstring"> output from the Bio.SeqIO.parse() function), which will be</tt> </tt>
<a name="L627"></a><tt class="py-lineno">627</tt> <tt class="py-line"><tt class="py-docstring"> used to populate the database.</tt> </tt>
<a name="L628"></a><tt class="py-lineno">628</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L629"></a><tt class="py-lineno">629</tt> <tt class="py-line"><tt class="py-docstring"> fetch_NCBI_taxonomy is boolean flag allowing or preventing</tt> </tt>
<a name="L630"></a><tt class="py-lineno">630</tt> <tt class="py-line"><tt class="py-docstring"> connection to the taxonomic database on the NCBI server</tt> </tt>
<a name="L631"></a><tt class="py-lineno">631</tt> <tt class="py-line"><tt class="py-docstring"> (via Bio.Entrez) to fetch a detailed taxonomy for each</tt> </tt>
<a name="L632"></a><tt class="py-lineno">632</tt> <tt class="py-line"><tt class="py-docstring"> SeqRecord.</tt> </tt>
<a name="L633"></a><tt class="py-lineno">633</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L634"></a><tt class="py-lineno">634</tt> <tt class="py-line"><tt class="py-docstring"> Example:</tt> </tt>
<a name="L635"></a><tt class="py-lineno">635</tt> <tt class="py-line"><tt class="py-docstring"> from Bio import SeqIO</tt> </tt>
<a name="L636"></a><tt class="py-lineno">636</tt> <tt class="py-line"><tt class="py-docstring"> count = db.load(SeqIO.parse(open(filename), format))</tt> </tt>
<a name="L637"></a><tt class="py-lineno">637</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L638"></a><tt class="py-lineno">638</tt> <tt class="py-line"><tt class="py-docstring"> Returns the number of records loaded.</tt> </tt>
<a name="L639"></a><tt class="py-lineno">639</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L640"></a><tt class="py-lineno">640</tt> <tt class="py-line"> <tt class="py-name">db_loader</tt> <tt class="py-op">=</tt> <tt id="link-147" class="py-name"><a title="BioSQL.Loader" class="py-name" href="#" onclick="return doclink('link-147', 'Loader', 'link-1');">Loader</a></tt><tt class="py-op">.</tt><tt id="link-148" 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-148', 'DatabaseLoader', 'link-148');">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 class="py-name">dbid</tt><tt class="py-op">,</tt> \ </tt>
<a name="L641"></a><tt class="py-lineno">641</tt> <tt class="py-line"> <tt class="py-name">fetch_NCBI_taxonomy</tt><tt class="py-op">)</tt> </tt>
<a name="L642"></a><tt class="py-lineno">642</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="L643"></a><tt class="py-lineno">643</tt> <tt class="py-line"> <tt class="py-keyword">global</tt> <tt id="link-149" class="py-name"><a title="BioSQL.BioSeqDatabase._POSTGRES_RULES_PRESENT" class="py-name" href="#" onclick="return doclink('link-149', '_POSTGRES_RULES_PRESENT', 'link-3');">_POSTGRES_RULES_PRESENT</a></tt> </tt>
<a name="L644"></a><tt class="py-lineno">644</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="L645"></a><tt class="py-lineno">645</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="L646"></a><tt class="py-lineno">646</tt> <tt class="py-line"> <tt class="py-comment">#Hack to work arround BioSQL Bug 2839 - If using PostgreSQL and</tt> </tt>
<a name="L647"></a><tt class="py-lineno">647</tt> <tt class="py-line"> <tt class="py-comment">#the RULES are present check for a duplicate record before loading</tt> </tt>
<a name="L648"></a><tt class="py-lineno">648</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-150" class="py-name"><a title="BioSQL.BioSeqDatabase._POSTGRES_RULES_PRESENT" class="py-name" href="#" onclick="return doclink('link-150', '_POSTGRES_RULES_PRESENT', 'link-3');">_POSTGRES_RULES_PRESENT</a></tt><tt class="py-op">:</tt> </tt>
<a name="L649"></a><tt class="py-lineno">649</tt> <tt class="py-line"> <tt class="py-comment">#Recreate what the Loader's _load_bioentry_table will do:</tt> </tt>
<a name="L650"></a><tt class="py-lineno">650</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">cur_record</tt><tt class="py-op">.</tt><tt id="link-151" class="py-name" targets="Method Bio.Phylo.PhyloXMLIO.Parser.id()=Bio.Phylo.PhyloXMLIO.Parser-class.html#id,Method Bio.Phylo.PhyloXMLIO.Writer.id()=Bio.Phylo.PhyloXMLIO.Writer-class.html#id"><a title="Bio.Phylo.PhyloXMLIO.Parser.id
Bio.Phylo.PhyloXMLIO.Writer.id" class="py-name" href="#" onclick="return doclink('link-151', 'id', 'link-151');">id</a></tt><tt class="py-op">.</tt><tt id="link-152" class="py-name" targets="Method Bio.Crystal.Chain.count()=Bio.Crystal.Chain-class.html#count,Method Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count()=Bio.NeuralNetwork.Gene.Pattern.PatternRepository-class.html#count,Method Bio.Seq.MutableSeq.count()=Bio.Seq.MutableSeq-class.html#count,Method Bio.Seq.Seq.count()=Bio.Seq.Seq-class.html#count,Method Bio.Seq.UnknownSeq.count()=Bio.Seq.UnknownSeq-class.html#count"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.Seq.UnknownSeq.count" class="py-name" href="#" onclick="return doclink('link-152', 'count', 'link-152');">count</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">1</tt><tt class="py-op">:</tt> </tt>
<a name="L651"></a><tt class="py-lineno">651</tt> <tt class="py-line"> <tt id="link-153" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.accession()=Bio.GenBank._FeatureConsumer-class.html#accession,Method Bio.GenBank._RecordConsumer.accession()=Bio.GenBank._RecordConsumer-class.html#accession,Method Bio.Phylo.PhyloXMLIO.Parser.accession()=Bio.Phylo.PhyloXMLIO.Parser-class.html#accession,Method Bio.Phylo.PhyloXMLIO.Writer.accession()=Bio.Phylo.PhyloXMLIO.Writer-class.html#accession"><a title="Bio.GenBank._FeatureConsumer.accession
Bio.GenBank._RecordConsumer.accession
Bio.Phylo.PhyloXMLIO.Parser.accession
Bio.Phylo.PhyloXMLIO.Writer.accession" class="py-name" href="#" onclick="return doclink('link-153', 'accession', 'link-153');">accession</a></tt><tt class="py-op">,</tt> <tt id="link-154" class="py-name"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version" class="py-name" href="#" onclick="return doclink('link-154', 'version', 'link-77');">version</a></tt> <tt class="py-op">=</tt> <tt class="py-name">cur_record</tt><tt class="py-op">.</tt><tt id="link-155" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Parser.id
Bio.Phylo.PhyloXMLIO.Writer.id" class="py-name" href="#" onclick="return doclink('link-155', 'id', 'link-151');">id</a></tt><tt class="py-op">.</tt><tt id="link-156" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.split" class="py-name" href="#" onclick="return doclink('link-156', 'split', 'link-42');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">'.'</tt><tt class="py-op">)</tt> </tt>
<a name="L652"></a><tt class="py-lineno">652</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L653"></a><tt class="py-lineno">653</tt> <tt class="py-line"> <tt id="link-157" class="py-name"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version" class="py-name" href="#" onclick="return doclink('link-157', 'version', 'link-77');">version</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-158" class="py-name"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version" class="py-name" href="#" onclick="return doclink('link-158', 'version', 'link-77');">version</a></tt><tt class="py-op">)</tt> </tt>
<a name="L654"></a><tt class="py-lineno">654</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">ValueError</tt><tt class="py-op">:</tt> </tt>
<a name="L655"></a><tt class="py-lineno">655</tt> <tt class="py-line"> <tt id="link-159" class="py-name"><a title="Bio.GenBank._FeatureConsumer.accession
Bio.GenBank._RecordConsumer.accession
Bio.Phylo.PhyloXMLIO.Parser.accession
Bio.Phylo.PhyloXMLIO.Writer.accession" class="py-name" href="#" onclick="return doclink('link-159', 'accession', 'link-153');">accession</a></tt> <tt class="py-op">=</tt> <tt class="py-name">cur_record</tt><tt class="py-op">.</tt><tt id="link-160" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Parser.id
Bio.Phylo.PhyloXMLIO.Writer.id" class="py-name" href="#" onclick="return doclink('link-160', 'id', 'link-151');">id</a></tt> </tt>
<a name="L656"></a><tt class="py-lineno">656</tt> <tt class="py-line"> <tt id="link-161" class="py-name"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version" class="py-name" href="#" onclick="return doclink('link-161', 'version', 'link-77');">version</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L657"></a><tt class="py-lineno">657</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L658"></a><tt class="py-lineno">658</tt> <tt class="py-line"> <tt id="link-162" class="py-name"><a title="Bio.GenBank._FeatureConsumer.accession
Bio.GenBank._RecordConsumer.accession
Bio.Phylo.PhyloXMLIO.Parser.accession
Bio.Phylo.PhyloXMLIO.Writer.accession" class="py-name" href="#" onclick="return doclink('link-162', 'accession', 'link-153');">accession</a></tt> <tt class="py-op">=</tt> <tt class="py-name">cur_record</tt><tt class="py-op">.</tt><tt id="link-163" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Parser.id
Bio.Phylo.PhyloXMLIO.Writer.id" class="py-name" href="#" onclick="return doclink('link-163', 'id', 'link-151');">id</a></tt> </tt>
<a name="L659"></a><tt class="py-lineno">659</tt> <tt class="py-line"> <tt id="link-164" class="py-name"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version" class="py-name" href="#" onclick="return doclink('link-164', 'version', 'link-77');">version</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L660"></a><tt class="py-lineno">660</tt> <tt class="py-line"> <tt id="link-165" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.gi()=Bio.GenBank._FeatureConsumer-class.html#gi,Method Bio.GenBank._RecordConsumer.gi()=Bio.GenBank._RecordConsumer-class.html#gi"><a title="Bio.GenBank._FeatureConsumer.gi
Bio.GenBank._RecordConsumer.gi" class="py-name" href="#" onclick="return doclink('link-165', 'gi', 'link-165');">gi</a></tt> <tt class="py-op">=</tt> <tt class="py-name">cur_record</tt><tt class="py-op">.</tt><tt id="link-166" class="py-name" targets="Variable BioSQL.BioSeq.DBSeqRecord.annotations=BioSQL.BioSeq.DBSeqRecord-class.html#annotations"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-166', 'annotations', 'link-166');">annotations</a></tt><tt class="py-op">.</tt><tt id="link-167" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqIO._index.SeqFileRandomAccess.get
Bio.SeqIO._index.SffRandomAccess.get
Bio.SeqIO._index.SffTrimedRandomAccess.get
Bio.SeqIO._index.UniprotRandomAccess.get
Bio.SeqIO._index._IndexedSeqFileDict.get
Bio.SeqIO._index._SQLiteManySeqFilesDict.get" class="py-name" href="#" onclick="return doclink('link-167', 'get', 'link-5');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">"gi"</tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
<a name="L661"></a><tt class="py-lineno">661</tt> <tt class="py-line"> <tt class="py-name">sql</tt> <tt class="py-op">=</tt> <tt class="py-string">"SELECT bioentry_id FROM bioentry WHERE (identifier "</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L662"></a><tt class="py-lineno">662</tt> <tt class="py-line"> <tt class="py-string">"= '%s' AND biodatabase_id = '%s') OR (accession = "</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L663"></a><tt class="py-lineno">663</tt> <tt class="py-line"> <tt class="py-string">"'%s' AND version = '%s' AND biodatabase_id = '%s')"</tt> </tt>
<a name="L664"></a><tt class="py-lineno">664</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-168" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute
BioSQL.DBUtils.Generic_dbutils.execute
BioSQL.DBUtils.Sqlite_dbutils.execute" class="py-name" href="#" onclick="return doclink('link-168', 'execute', 'link-33');">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 id="link-169" class="py-name"><a title="Bio.GenBank._FeatureConsumer.gi
Bio.GenBank._RecordConsumer.gi" class="py-name" href="#" onclick="return doclink('link-169', 'gi', 'link-165');">gi</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dbid</tt><tt class="py-op">,</tt> <tt id="link-170" class="py-name"><a title="Bio.GenBank._FeatureConsumer.accession
Bio.GenBank._RecordConsumer.accession
Bio.Phylo.PhyloXMLIO.Parser.accession
Bio.Phylo.PhyloXMLIO.Writer.accession" class="py-name" href="#" onclick="return doclink('link-170', 'accession', 'link-153');">accession</a></tt><tt class="py-op">,</tt> <tt id="link-171" class="py-name"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version" class="py-name" href="#" onclick="return doclink('link-171', 'version', 'link-77');">version</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dbid</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L665"></a><tt class="py-lineno">665</tt> <tt class="py-line"> <tt class="py-keyword">if</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-172" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-172', 'cursor', 'link-40');">cursor</a></tt><tt class="py-op">.</tt><tt class="py-name">fetchone</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L666"></a><tt class="py-lineno">666</tt> <tt class="py-line"> <tt class="py-keyword">raise</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 class="py-op">.</tt><tt class="py-name">IntegrityError</tt><tt class="py-op">(</tt><tt class="py-string">"Duplicate record "</tt> </tt>
<a name="L667"></a><tt class="py-lineno">667</tt> <tt class="py-line"> <tt class="py-string">"detected: record has not been inserted"</tt><tt class="py-op">)</tt> </tt>
<a name="L668"></a><tt class="py-lineno">668</tt> <tt class="py-line"> <tt class="py-comment">#End of hack</tt> </tt>
<a name="L669"></a><tt class="py-lineno">669</tt> <tt class="py-line"> <tt class="py-name">db_loader</tt><tt class="py-op">.</tt><tt id="link-173" 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-173', 'load_seqrecord', 'link-173');">load_seqrecord</a></tt><tt class="py-op">(</tt><tt class="py-name">cur_record</tt><tt class="py-op">)</tt> </tt>
<a name="L670"></a><tt class="py-lineno">670</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">num_records</tt> </tt>
</div></div><a name="L671"></a><tt class="py-lineno">671</tt> <tt class="py-line"> </tt><script type="text/javascript">
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