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<a href="Bio-module.html">Package Bio</a> ::
Package Mindy
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<h1 class="epydoc">Source Code for <a href="Bio.Mindy-module.html">Package Bio.Mindy</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">os</tt><tt class="py-op">,</tt> <tt class="py-name">sys</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt id="link-0" class="py-name" targets="Function Bio.Entrez._open()=Bio.Entrez-module.html#_open,Function Bio.Mindy.BerkeleyDB._open()=Bio.Mindy.BerkeleyDB-module.html#_open,Function Bio.SCOP._open()=Bio.SCOP-module.html#_open,Function Bio.WWW.ExPASy._open()=Bio.WWW.ExPASy-module.html#_open,Function Bio.WWW.NCBI._open()=Bio.WWW.NCBI-module.html#_open"><a title="Bio.Entrez._open
Bio.Mindy.BerkeleyDB._open
Bio.SCOP._open
Bio.WWW.ExPASy._open
Bio.WWW.NCBI._open" class="py-name" href="#" onclick="return doclink('link-0', '_open', 'link-0');">_open</a></tt> <tt class="py-op">=</tt> <tt id="link-1" class="py-name" targets="Function Bio.Mindy.FlatDB.open()=Bio.Mindy.FlatDB-module.html#open,Function Bio.Mindy.open()=Bio.Mindy-module.html#open"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-1', 'open', 'link-1');">open</a></tt> <tt class="py-comment"># rename for internal use -- gets redefined below</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"> </tt>
<a name="open"></a><div id="open-def"><a name="L5"></a><tt class="py-lineno"> 5</tt> <a class="py-toggle" href="#" id="open-toggle" onclick="return toggle('open');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy-module.html#open">open</a><tt class="py-op">(</tt><tt class="py-param">dbname</tt><tt class="py-op">,</tt> <tt class="py-param">mode</tt> <tt class="py-op">=</tt> <tt class="py-string">"r"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="open-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="open-expanded"><a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"> <tt id="link-2" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.text()=Bio.EUtils.POM.ElementNode-class.html#text,Method Bio.Prosite.Prodoc._RecordConsumer.text()=Bio.Prosite.Prodoc._RecordConsumer-class.html#text,Variable Martel.test.test_Iterator.text=Martel.test.test_Iterator-module.html#text,Variable Martel.test.test_ParseRecords.text=Martel.test.test_ParseRecords-module.html#text"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-2', 'text', 'link-2');">text</a></tt> <tt class="py-op">=</tt> <tt id="link-3" class="py-name"><a title="Bio.Entrez._open
Bio.Mindy.BerkeleyDB._open
Bio.SCOP._open
Bio.WWW.ExPASy._open
Bio.WWW.NCBI._open" class="py-name" href="#" onclick="return doclink('link-3', '_open', 'link-0');">_open</a></tt><tt class="py-op">(</tt><tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">dbname</tt><tt class="py-op">,</tt> <tt class="py-string">"config.dat"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">"rb"</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Method Bio.AlignAce.Motif.Motif.read()=Bio.AlignAce.Motif.Motif-class.html#read,Function Bio.AlignIO.read()=Bio.AlignIO-module.html#read,Function Bio.Cluster.read()=Bio.Cluster-module.html#read,Method Bio.EUtils.ReseekFile.ReseekFile.read()=Bio.EUtils.ReseekFile.ReseekFile-class.html#read,Function Bio.Entrez.read()=Bio.Entrez-module.html#read,Method Bio.File.SGMLHandle.read()=Bio.File.SGMLHandle-class.html#read,Method Bio.File.UndoHandle.read()=Bio.File.UndoHandle-class.html#read,Method Bio.FilteredReader.FilteredReader.read()=Bio.FilteredReader.FilteredReader-class.html#read,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.read()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#read,Method Bio.Nexus.Nexus.Nexus.read()=Bio.Nexus.Nexus.Nexus-class.html#read,Function Bio.Prosite.Prodoc.read()=Bio.Prosite.Prodoc-module.html#read,Function Bio.Prosite.read()=Bio.Prosite-module.html#read,Method Bio.SGMLExtractor.SGMLExtractorHandle.read()=Bio.SGMLExtractor.SGMLExtractorHandle-class.html#read,Function Bio.SeqIO.read()=Bio.SeqIO-module.html#read,Function Bio.SwissProt.read()=Bio.SwissProt-module.html#read"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-4', 'read', 'link-4');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt id="link-5" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-5', 'text', 'link-2');">text</a></tt><tt class="py-op">.</tt><tt id="link-6" class="py-name" targets="Method Bio.Nexus.Trees.Tree.split()=Bio.Nexus.Trees.Tree-class.html#split,Method Bio.Restriction.Restriction.RestrictionBatch.split()=Bio.Restriction.Restriction.RestrictionBatch-class.html#split"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-6', 'split', 'link-6');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">"\n"</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="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt> <tt class="py-op">==</tt> <tt class="py-string">"index\tBerkeleyDB/1"</tt><tt class="py-op">:</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt id="link-7" class="py-name" targets="Module Bio.Mindy.BerkeleyDB=Bio.Mindy.BerkeleyDB-module.html,Class Bio.Mindy.BerkeleyDB.BerkeleyDB=Bio.Mindy.BerkeleyDB.BerkeleyDB-class.html"><a title="Bio.Mindy.BerkeleyDB
Bio.Mindy.BerkeleyDB.BerkeleyDB" class="py-name" href="#" onclick="return doclink('link-7', 'BerkeleyDB', 'link-7');">BerkeleyDB</a></tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-8" class="py-name"><a title="Bio.Mindy.BerkeleyDB
Bio.Mindy.BerkeleyDB.BerkeleyDB" class="py-name" href="#" onclick="return doclink('link-8', 'BerkeleyDB', 'link-7');">BerkeleyDB</a></tt><tt class="py-op">.</tt><tt id="link-9" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-9', 'open', 'link-1');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">dbname</tt><tt class="py-op">,</tt> <tt class="py-name">mode</tt><tt class="py-op">)</tt> </tt>
<a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">line</tt> <tt class="py-op">==</tt> <tt class="py-string">"index\tflat/1"</tt><tt class="py-op">:</tt> </tt>
<a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt id="link-10" class="py-name" targets="Module Bio.Mindy.FlatDB=Bio.Mindy.FlatDB-module.html"><a title="Bio.Mindy.FlatDB" class="py-name" href="#" onclick="return doclink('link-10', 'FlatDB', 'link-10');">FlatDB</a></tt> </tt>
<a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-11" class="py-name"><a title="Bio.Mindy.FlatDB" class="py-name" href="#" onclick="return doclink('link-11', 'FlatDB', 'link-10');">FlatDB</a></tt><tt class="py-op">.</tt><tt id="link-12" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-12', 'open', 'link-1');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">dbname</tt><tt class="py-op">,</tt> <tt class="py-name">mode</tt><tt class="py-op">)</tt> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"> </tt>
<a name="L15"></a><tt class="py-lineno">15</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">"Unknown index type: %r"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"> </tt>
<a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"> </tt>
<a name="main"></a><div id="main-def"><a name="L18"></a><tt class="py-lineno">18</tt> <a class="py-toggle" href="#" id="main-toggle" onclick="return toggle('main');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy-module.html#main">main</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="main-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="main-expanded"><a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt id="link-13" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-13', 'Bio', 'link-13');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-14" class="py-name" targets="Module Bio.Std=Bio.Std-module.html"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-14', 'Std', 'link-14');">Std</a></tt> </tt>
<a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt id="link-15" class="py-name" targets="Module Bio.Mindy.XPath=Bio.Mindy.XPath-module.html"><a title="Bio.Mindy.XPath" class="py-name" href="#" onclick="return doclink('link-15', 'XPath', 'link-15');">XPath</a></tt> </tt>
<a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt id="link-16" class="py-name"><a title="Bio.Mindy.FlatDB" class="py-name" href="#" onclick="return doclink('link-16', 'FlatDB', 'link-10');">FlatDB</a></tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"> <tt id="link-17" class="py-name"><a title="Bio.Mindy.XPath" class="py-name" href="#" onclick="return doclink('link-17', 'XPath', 'link-15');">XPath</a></tt><tt class="py-op">.</tt><tt id="link-18" class="py-name" targets="Function Bio.Mindy.XPath.xpath_index()=Bio.Mindy.XPath-module.html#xpath_index"><a title="Bio.Mindy.XPath.xpath_index" class="py-name" href="#" onclick="return doclink('link-18', 'xpath_index', 'link-18');">xpath_index</a></tt><tt class="py-op">(</tt> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"> <tt class="py-comment">#dbname = "sprot_flat",</tt> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"> <tt class="py-name">dbname</tt> <tt class="py-op">=</tt> <tt class="py-string">"sprot_small"</tt><tt class="py-op">,</tt> </tt>
<a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"> <tt class="py-name">filenames</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-string">"/home/dalke/ftps/swissprot/smaller_sprot38.dat"</tt><tt class="py-op">,</tt> </tt>
<a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"> <tt class="py-comment">#filenames = ["/home/dalke/ftps/swissprot/sprot38.dat",</tt> </tt>
<a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"> <tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"> <tt class="py-name">primary_namespace</tt> <tt class="py-op">=</tt> <tt class="py-string">"entry"</tt><tt class="py-op">,</tt> </tt>
<a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"> <tt class="py-name">extract_info</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> </tt>
<a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"entry"</tt><tt class="py-op">,</tt> <tt class="py-string">"//entry_name"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"accession"</tt><tt class="py-op">,</tt> <tt class="py-string">"//%s[@type='accession']"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-19" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-19', 'Std', 'link-14');">Std</a></tt><tt class="py-op">.</tt><tt id="link-20" class="py-name" targets="Function Bio.Std.dbid()=Bio.Std-module.html#dbid"><a title="Bio.Std.dbid" class="py-name" href="#" onclick="return doclink('link-20', 'dbid', 'link-20');">dbid</a></tt><tt class="py-op">.</tt><tt id="link-21" class="py-name" targets="Variable Martel.Time.tag=Martel.Time-module.html#tag"><a title="Martel.Time.tag" class="py-name" href="#" onclick="return doclink('link-21', 'tag', 'link-21');">tag</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="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"> <tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"> <tt class="py-comment">#creator_factory = FlatDB.CreateFlatDB,</tt> </tt>
<a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
</div><a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"> </tt>
<a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"> </tt>
<a name="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"><tt class="py-keyword">if</tt> <tt class="py-name">__name__</tt> <tt class="py-op">==</tt> <tt class="py-string">"__main__"</tt><tt class="py-op">:</tt> </tt>
<a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"> <tt id="link-22" class="py-name" targets="Function Bio.EUtils.dtd2py.main()=Bio.EUtils.dtd2py-module.html#main,Function Bio.Mindy.main()=Bio.Mindy-module.html#main,Function Bio.Wise.dnal.main()=Bio.Wise.dnal-module.html#main,Function Bio.Wise.main()=Bio.Wise-module.html#main,Function Bio.Wise.psw.main()=Bio.Wise.psw-module.html#main,Function Bio.biblio.main()=Bio.biblio-module.html#main,Function Bio.expressions.blast.wublast.main()=Bio.expressions.blast.wublast-module.html#main,Function Martel.test.run_tests.main()=Martel.test.run_tests-module.html#main"><a title="Bio.EUtils.dtd2py.main
Bio.Mindy.main
Bio.Wise.dnal.main
Bio.Wise.main
Bio.Wise.psw.main
Bio.biblio.main
Bio.expressions.blast.wublast.main
Martel.test.run_tests.main" class="py-name" href="#" onclick="return doclink('link-22', 'main', 'link-22');">main</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"> </tt><script type="text/javascript">
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