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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.Blast-module.html">Package Blast</a> ::
Module ParseBlastTable
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<h1 class="epydoc">Source Code for <a href="Bio.Blast.ParseBlastTable-module.html">Module Bio.Blast.ParseBlastTable</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 2003 Iddo Friedberg. All rights reserved.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</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="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">"""A parser for the NCBI blastpgp version 2.2.5 output format. Currently only supports</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring">the '-m 9' option, (table w/ annotations).</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">Returns a BlastTableRec instance</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"> </tt>
<a name="BlastTableEntry"></a><div id="BlastTableEntry-def"><a name="L11"></a><tt class="py-lineno"> 11</tt> <a class="py-toggle" href="#" id="BlastTableEntry-toggle" onclick="return toggle('BlastTableEntry');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Blast.ParseBlastTable.BlastTableEntry-class.html">BlastTableEntry</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BlastTableEntry-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="BlastTableEntry-expanded"><a name="BlastTableEntry.__init__"></a><div id="BlastTableEntry.__init__-def"><a name="L12"></a><tt class="py-lineno"> 12</tt> <a class="py-toggle" href="#" id="BlastTableEntry.__init__-toggle" onclick="return toggle('BlastTableEntry.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.ParseBlastTable.BlastTableEntry-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">in_rec</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BlastTableEntry.__init__-collapsed" style="display:none;" pad="+++" indent="+++++++"></div><div id="BlastTableEntry.__init__-expanded"><a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"> <tt class="py-name">bt_fields</tt> <tt class="py-op">=</tt> <tt class="py-name">in_rec</tt><tt class="py-op">.</tt><tt id="link-0" 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-0', 'split', 'link-0');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">qid</tt> <tt class="py-op">=</tt> <tt class="py-name">bt_fields</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-1" 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-1', 'split', 'link-0');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">'|'</tt><tt class="py-op">)</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sid</tt> <tt class="py-op">=</tt> <tt class="py-name">bt_fields</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-2" 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-2', 'split', 'link-0');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">'|'</tt><tt class="py-op">)</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-3" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.pid()=Bio.GenBank._FeatureConsumer-class.html#pid,Method Bio.GenBank._RecordConsumer.pid()=Bio.GenBank._RecordConsumer-class.html#pid"><a title="Bio.GenBank._FeatureConsumer.pid
Bio.GenBank._RecordConsumer.pid" class="py-name" href="#" onclick="return doclink('link-3', 'pid', 'link-3');">pid</a></tt> <tt class="py-op">=</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">bt_fields</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ali_len</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">bt_fields</tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mis</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">bt_fields</tt><tt class="py-op">[</tt><tt class="py-number">4</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">gaps</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">bt_fields</tt><tt class="py-op">[</tt><tt class="py-number">5</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">q_bounds</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">bt_fields</tt><tt class="py-op">[</tt><tt class="py-number">6</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">bt_fields</tt><tt class="py-op">[</tt><tt class="py-number">7</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">s_bounds</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">bt_fields</tt><tt class="py-op">[</tt><tt class="py-number">8</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">bt_fields</tt><tt class="py-op">[</tt><tt class="py-number">9</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">e_value</tt> <tt class="py-op">=</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">bt_fields</tt><tt class="py-op">[</tt><tt class="py-number">10</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">bit_score</tt> <tt class="py-op">=</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">bt_fields</tt><tt class="py-op">[</tt><tt class="py-number">11</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"> </tt>
<a name="BlastTableRec"></a><div id="BlastTableRec-def"><a name="L25"></a><tt class="py-lineno"> 25</tt> <a class="py-toggle" href="#" id="BlastTableRec-toggle" onclick="return toggle('BlastTableRec');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Blast.ParseBlastTable.BlastTableRec-class.html">BlastTableRec</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BlastTableRec-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="BlastTableRec-expanded"><a name="BlastTableRec.__init__"></a><div id="BlastTableRec.__init__-def"><a name="L26"></a><tt class="py-lineno"> 26</tt> <a class="py-toggle" href="#" id="BlastTableRec.__init__-toggle" onclick="return toggle('BlastTableRec.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.ParseBlastTable.BlastTableRec-class.html#__init__">__init__</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="BlastTableRec.__init__-collapsed" style="display:none;" pad="+++" indent="+++++++"></div><div id="BlastTableRec.__init__-expanded"><a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">program</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-4" 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-4', 'version', 'link-4');">version</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.date()=Bio.GenBank._FeatureConsumer-class.html#date,Method Bio.GenBank._RecordConsumer.date()=Bio.GenBank._RecordConsumer-class.html#date,Method Bio.Phylo.PhyloXMLIO.Parser.date()=Bio.Phylo.PhyloXMLIO.Parser-class.html#date,Method Bio.Phylo.PhyloXMLIO.Writer.date()=Bio.Phylo.PhyloXMLIO.Writer-class.html#date"><a title="Bio.GenBank._FeatureConsumer.date
Bio.GenBank._RecordConsumer.date
Bio.Phylo.PhyloXMLIO.Parser.date
Bio.Phylo.PhyloXMLIO.Writer.date" class="py-name" href="#" onclick="return doclink('link-5', 'date', 'link-5');">date</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">iteration</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-6" class="py-name" targets="Method Bio.Blast.NCBIStandalone._HSPConsumer.query()=Bio.Blast.NCBIStandalone._HSPConsumer-class.html#query"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.query" class="py-name" href="#" onclick="return doclink('link-6', 'query', 'link-6');">query</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name" targets="Method Bio.Blast.NCBIStandalone._DatabaseReportConsumer.database()=Bio.Blast.NCBIStandalone._DatabaseReportConsumer-class.html#database"><a title="Bio.Blast.NCBIStandalone._DatabaseReportConsumer.database" class="py-name" href="#" onclick="return doclink('link-7', 'database', 'link-7');">database</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">entries</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
</div><a name="BlastTableRec.add_entry"></a><div id="BlastTableRec.add_entry-def"><a name="L34"></a><tt class="py-lineno"> 34</tt> <a class="py-toggle" href="#" id="BlastTableRec.add_entry-toggle" onclick="return toggle('BlastTableRec.add_entry');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.ParseBlastTable.BlastTableRec-class.html#add_entry">add_entry</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">entry</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BlastTableRec.add_entry-collapsed" style="display:none;" pad="+++" indent="+++++++"></div><div id="BlastTableRec.add_entry-expanded"><a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">entries</tt><tt class="py-op">.</tt><tt id="link-8" 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-8', 'append', 'link-8');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">entry</tt><tt class="py-op">)</tt> </tt>
</div></div><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 id="link-9" class="py-name" targets="Variable Bio.Blast.ParseBlastTable.reader_keywords=Bio.Blast.ParseBlastTable-module.html#reader_keywords"><a title="Bio.Blast.ParseBlastTable.reader_keywords" class="py-name" href="#" onclick="return doclink('link-9', 'reader_keywords', 'link-9');">reader_keywords</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">'BLASTP'</tt><tt class="py-op">:</tt> <tt class="py-string">'version'</tt><tt class="py-op">,</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt class="py-string">'Iteration'</tt><tt class="py-op">:</tt> <tt class="py-string">'iteration'</tt><tt class="py-op">,</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt class="py-string">'Query'</tt><tt class="py-op">:</tt> <tt class="py-string">'query'</tt><tt class="py-op">,</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> <tt class="py-string">'Database'</tt><tt class="py-op">:</tt> <tt class="py-string">'database'</tt><tt class="py-op">,</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-string">'Fields'</tt><tt class="py-op">:</tt> <tt class="py-string">'fields'</tt><tt class="py-op">}</tt> </tt>
<a name="BlastTableReader"></a><div id="BlastTableReader-def"><a name="L42"></a><tt class="py-lineno"> 42</tt> <a class="py-toggle" href="#" id="BlastTableReader-toggle" onclick="return toggle('BlastTableReader');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Blast.ParseBlastTable.BlastTableReader-class.html">BlastTableReader</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BlastTableReader-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="BlastTableReader-expanded"><a name="BlastTableReader.__init__"></a><div id="BlastTableReader.__init__-def"><a name="L43"></a><tt class="py-lineno"> 43</tt> <a class="py-toggle" href="#" id="BlastTableReader.__init__-toggle" onclick="return toggle('BlastTableReader.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.ParseBlastTable.BlastTableReader-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">handle</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BlastTableReader.__init__-collapsed" style="display:none;" pad="+++" indent="+++++++"></div><div id="BlastTableReader.__init__-expanded"><a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-10" class="py-name" targets="Variable Bio.UniGene.UniGene.handle=Bio.UniGene.UniGene-module.html#handle"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-10', 'handle', 'link-10');">handle</a></tt> <tt class="py-op">=</tt> <tt id="link-11" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-11', 'handle', 'link-10');">handle</a></tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> <tt class="py-name">inline</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-12" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-12', 'handle', 'link-10');">handle</a></tt><tt class="py-op">.</tt><tt id="link-13" class="py-name" targets="Method Bio.File.UndoHandle.readline()=Bio.File.UndoHandle-class.html#readline"><a title="Bio.File.UndoHandle.readline" class="py-name" href="#" onclick="return doclink('link-13', 'readline', 'link-13');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt class="py-comment"># zip forward to start of record</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-name">inline</tt> <tt class="py-keyword">and</tt> <tt class="py-name">inline</tt><tt class="py-op">.</tt><tt id="link-14" 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-14', 'find', 'link-14');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">'BLASTP'</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>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-name">inline</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-15', 'handle', 'link-10');">handle</a></tt><tt class="py-op">.</tt><tt id="link-16" class="py-name"><a title="Bio.File.UndoHandle.readline" class="py-name" href="#" onclick="return doclink('link-16', 'readline', 'link-13');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_lookahead</tt> <tt class="py-op">=</tt> <tt class="py-name">inline</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_n</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_in_header</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
</div><a name="BlastTableReader.next"></a><div id="BlastTableReader.next-def"><a name="L52"></a><tt class="py-lineno"> 52</tt> <a class="py-toggle" href="#" id="BlastTableReader.next-toggle" onclick="return toggle('BlastTableReader.next');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.ParseBlastTable.BlastTableReader-class.html#next">next</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="BlastTableReader.next-collapsed" style="display:none;" pad="+++" indent="+++++++"></div><div id="BlastTableReader.next-expanded"><a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">table_record</tt> <tt class="py-op">=</tt> <tt id="link-17" class="py-name" targets="Class Bio.Blast.ParseBlastTable.BlastTableRec=Bio.Blast.ParseBlastTable.BlastTableRec-class.html"><a title="Bio.Blast.ParseBlastTable.BlastTableRec" class="py-name" href="#" onclick="return doclink('link-17', 'BlastTableRec', 'link-17');">BlastTableRec</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_n</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-name">inline</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_lookahead</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">inline</tt><tt class="py-op">:</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-name">inline</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">if</tt> <tt class="py-name">inline</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-string">'#'</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-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_in_header</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">self</tt><tt class="py-op">.</tt><tt class="py-name">_in_header</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name" targets="Method Bio.Blast.ParseBlastTable.BlastTableReader._consume_header()=Bio.Blast.ParseBlastTable.BlastTableReader-class.html#_consume_header"><a title="Bio.Blast.ParseBlastTable.BlastTableReader._consume_header" class="py-name" href="#" onclick="return doclink('link-18', '_consume_header', 'link-18');">_consume_header</a></tt><tt class="py-op">(</tt><tt class="py-name">inline</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">else</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">break</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name" targets="Method Bio.Blast.ParseBlastTable.BlastTableReader._consume_entry()=Bio.Blast.ParseBlastTable.BlastTableReader-class.html#_consume_entry"><a title="Bio.Blast.ParseBlastTable.BlastTableReader._consume_entry" class="py-name" href="#" onclick="return doclink('link-19', '_consume_entry', 'link-19');">_consume_entry</a></tt><tt class="py-op">(</tt><tt class="py-name">inline</tt><tt class="py-op">)</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_in_header</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-name">inline</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-20', 'handle', 'link-10');">handle</a></tt><tt class="py-op">.</tt><tt id="link-21" class="py-name"><a title="Bio.File.UndoHandle.readline" class="py-name" href="#" onclick="return doclink('link-21', 'readline', 'link-13');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_lookahead</tt> <tt class="py-op">=</tt> <tt class="py-name">inline</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_in_header</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</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">table_record</tt> </tt>
</div><a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> </tt>
<a name="BlastTableReader._consume_entry"></a><div id="BlastTableReader._consume_entry-def"><a name="L73"></a><tt class="py-lineno"> 73</tt> <a class="py-toggle" href="#" id="BlastTableReader._consume_entry-toggle" onclick="return toggle('BlastTableReader._consume_entry');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.ParseBlastTable.BlastTableReader-class.html#_consume_entry">_consume_entry</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">inline</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BlastTableReader._consume_entry-collapsed" style="display:none;" pad="+++" indent="+++++++"></div><div id="BlastTableReader._consume_entry-expanded"><a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-name">current_entry</tt> <tt class="py-op">=</tt> <tt id="link-22" class="py-name" targets="Class Bio.Blast.ParseBlastTable.BlastTableEntry=Bio.Blast.ParseBlastTable.BlastTableEntry-class.html"><a title="Bio.Blast.ParseBlastTable.BlastTableEntry" class="py-name" href="#" onclick="return doclink('link-22', 'BlastTableEntry', 'link-22');">BlastTableEntry</a></tt><tt class="py-op">(</tt><tt class="py-name">inline</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">self</tt><tt class="py-op">.</tt><tt class="py-name">table_record</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name" targets="Method Bio.Blast.ParseBlastTable.BlastTableRec.add_entry()=Bio.Blast.ParseBlastTable.BlastTableRec-class.html#add_entry"><a title="Bio.Blast.ParseBlastTable.BlastTableRec.add_entry" class="py-name" href="#" onclick="return doclink('link-23', 'add_entry', 'link-23');">add_entry</a></tt><tt class="py-op">(</tt><tt class="py-name">current_entry</tt><tt class="py-op">)</tt> </tt>
</div><a name="BlastTableReader._consume_header"></a><div id="BlastTableReader._consume_header-def"><a name="L76"></a><tt class="py-lineno"> 76</tt> <a class="py-toggle" href="#" id="BlastTableReader._consume_header-toggle" onclick="return toggle('BlastTableReader._consume_header');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.ParseBlastTable.BlastTableReader-class.html#_consume_header">_consume_header</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">inline</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BlastTableReader._consume_header-collapsed" style="display:none;" pad="+++" indent="+++++++"></div><div id="BlastTableReader._consume_header-expanded"><a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">keyword</tt> <tt class="py-keyword">in</tt> <tt id="link-24" class="py-name"><a title="Bio.Blast.ParseBlastTable.reader_keywords" class="py-name" href="#" onclick="return doclink('link-24', 'reader_keywords', 'link-9');">reader_keywords</a></tt><tt class="py-op">:</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">inline</tt><tt class="py-op">.</tt><tt id="link-25" 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-25', 'find', 'link-14');">find</a></tt><tt class="py-op">(</tt><tt class="py-name">keyword</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>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-name">in_header</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name" targets="Method Bio.Blast.ParseBlastTable.BlastTableReader._Parse()=Bio.Blast.ParseBlastTable.BlastTableReader-class.html#_Parse"><a title="Bio.Blast.ParseBlastTable.BlastTableReader._Parse" class="py-name" href="#" onclick="return doclink('link-26', '_Parse', 'link-26');">_Parse</a></tt><tt class="py-op">(</tt><tt class="py-string">'_parse_%s'</tt> <tt class="py-op">%</tt> <tt id="link-27" class="py-name"><a title="Bio.Blast.ParseBlastTable.reader_keywords" class="py-name" href="#" onclick="return doclink('link-27', 'reader_keywords', 'link-9');">reader_keywords</a></tt><tt class="py-op">[</tt><tt class="py-name">keyword</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">inline</tt><tt class="py-op">)</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">in_header</tt> </tt>
</div><a name="BlastTableReader._parse_version"></a><div id="BlastTableReader._parse_version-def"><a name="L82"></a><tt class="py-lineno"> 82</tt> <a class="py-toggle" href="#" id="BlastTableReader._parse_version-toggle" onclick="return toggle('BlastTableReader._parse_version');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.ParseBlastTable.BlastTableReader-class.html#_parse_version">_parse_version</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">inline</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BlastTableReader._parse_version-collapsed" style="display:none;" pad="+++" indent="+++++++"></div><div id="BlastTableReader._parse_version-expanded"><a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-name">program</tt><tt class="py-op">,</tt> <tt id="link-28" 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-28', 'version', 'link-4');">version</a></tt><tt class="py-op">,</tt> <tt id="link-29" class="py-name"><a title="Bio.GenBank._FeatureConsumer.date
Bio.GenBank._RecordConsumer.date
Bio.Phylo.PhyloXMLIO.Parser.date
Bio.Phylo.PhyloXMLIO.Writer.date" class="py-name" href="#" onclick="return doclink('link-29', 'date', 'link-5');">date</a></tt> <tt class="py-op">=</tt> <tt class="py-name">inline</tt><tt class="py-op">.</tt><tt id="link-30" 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-30', 'split', 'link-0');">split</a></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>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">table_record</tt><tt class="py-op">.</tt><tt class="py-name">program</tt> <tt class="py-op">=</tt> <tt class="py-name">program</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">table_record</tt><tt class="py-op">.</tt><tt id="link-31" 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-31', 'version', 'link-4');">version</a></tt> <tt class="py-op">=</tt> <tt id="link-32" 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-32', 'version', 'link-4');">version</a></tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">table_record</tt><tt class="py-op">.</tt><tt id="link-33" class="py-name"><a title="Bio.GenBank._FeatureConsumer.date
Bio.GenBank._RecordConsumer.date
Bio.Phylo.PhyloXMLIO.Parser.date
Bio.Phylo.PhyloXMLIO.Writer.date" class="py-name" href="#" onclick="return doclink('link-33', 'date', 'link-5');">date</a></tt> <tt class="py-op">=</tt> <tt id="link-34" class="py-name"><a title="Bio.GenBank._FeatureConsumer.date
Bio.GenBank._RecordConsumer.date
Bio.Phylo.PhyloXMLIO.Parser.date
Bio.Phylo.PhyloXMLIO.Writer.date" class="py-name" href="#" onclick="return doclink('link-34', 'date', 'link-5');">date</a></tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
</div><a name="BlastTableReader._parse_iteration"></a><div id="BlastTableReader._parse_iteration-def"><a name="L88"></a><tt class="py-lineno"> 88</tt> <a class="py-toggle" href="#" id="BlastTableReader._parse_iteration-toggle" onclick="return toggle('BlastTableReader._parse_iteration');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.ParseBlastTable.BlastTableReader-class.html#_parse_iteration">_parse_iteration</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">inline</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BlastTableReader._parse_iteration-collapsed" style="display:none;" pad="+++" indent="+++++++"></div><div id="BlastTableReader._parse_iteration-expanded"><a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">table_record</tt><tt class="py-op">.</tt><tt class="py-name">iteration</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">inline</tt><tt class="py-op">.</tt><tt id="link-35" 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-35', 'split', 'link-0');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
</div><a name="BlastTableReader._parse_query"></a><div id="BlastTableReader._parse_query-def"><a name="L91"></a><tt class="py-lineno"> 91</tt> <a class="py-toggle" href="#" id="BlastTableReader._parse_query-toggle" onclick="return toggle('BlastTableReader._parse_query');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.ParseBlastTable.BlastTableReader-class.html#_parse_query">_parse_query</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">inline</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BlastTableReader._parse_query-collapsed" style="display:none;" pad="+++" indent="+++++++"></div><div id="BlastTableReader._parse_query-expanded"><a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">table_record</tt><tt class="py-op">.</tt><tt id="link-36" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.query" class="py-name" href="#" onclick="return doclink('link-36', 'query', 'link-6');">query</a></tt> <tt class="py-op">=</tt> <tt class="py-name">inline</tt><tt class="py-op">.</tt><tt id="link-37" 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-37', 'split', 'link-0');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
</div><a name="BlastTableReader._parse_database"></a><div id="BlastTableReader._parse_database-def"><a name="L94"></a><tt class="py-lineno"> 94</tt> <a class="py-toggle" href="#" id="BlastTableReader._parse_database-toggle" onclick="return toggle('BlastTableReader._parse_database');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.ParseBlastTable.BlastTableReader-class.html#_parse_database">_parse_database</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">inline</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BlastTableReader._parse_database-collapsed" style="display:none;" pad="+++" indent="+++++++"></div><div id="BlastTableReader._parse_database-expanded"><a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">table_record</tt><tt class="py-op">.</tt><tt id="link-38" class="py-name"><a title="Bio.Blast.NCBIStandalone._DatabaseReportConsumer.database" class="py-name" href="#" onclick="return doclink('link-38', 'database', 'link-7');">database</a></tt> <tt class="py-op">=</tt> <tt class="py-name">inline</tt><tt class="py-op">.</tt><tt id="link-39" 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-39', 'split', 'link-0');">split</a></tt><tt class="py-op">(</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="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
</div><a name="BlastTableReader._parse_fields"></a><div id="BlastTableReader._parse_fields-def"><a name="L97"></a><tt class="py-lineno"> 97</tt> <a class="py-toggle" href="#" id="BlastTableReader._parse_fields-toggle" onclick="return toggle('BlastTableReader._parse_fields');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.ParseBlastTable.BlastTableReader-class.html#_parse_fields">_parse_fields</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">inline</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BlastTableReader._parse_fields-collapsed" style="display:none;" pad="+++" indent="+++++++"></div><div id="BlastTableReader._parse_fields-expanded"><a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
</div><a name="BlastTableReader._Parse"></a><div id="BlastTableReader._Parse-def"><a name="L99"></a><tt class="py-lineno"> 99</tt> <a class="py-toggle" href="#" id="BlastTableReader._Parse-toggle" onclick="return toggle('BlastTableReader._Parse');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Blast.ParseBlastTable.BlastTableReader-class.html#_Parse">_Parse</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">method_name</tt><tt class="py-op">,</tt> <tt class="py-param">inline</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BlastTableReader._Parse-collapsed" style="display:none;" pad="+++" indent="+++++++"></div><div id="BlastTableReader._Parse-expanded"><a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-keyword">return</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">method_name</tt><tt class="py-op">)</tt><tt class="py-op">(</tt><tt class="py-name">inline</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> </tt><script type="text/javascript">
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