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<a href="Bio-module.html">Package Bio</a> ::
Package Geo
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<h1 class="epydoc">Source Code for <a href="Bio.Geo-module.html">Package Bio.Geo</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 2001 by Katharine Lindner. All rights reserved.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"># Copyright 2006 by PeterC. All rights reserved.</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"># Copyright 2007 by Michiel de Hoon. 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-docstring">"""Parser for files from NCBI's Gene Expression Omnibus (GEO).</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">http://www.ncbi.nlm.nih.gov/geo/</tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"> </tt>
<a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-0" class="py-name" targets="Class Bio.Affy.CelFile.Record=Bio.Affy.CelFile.Record-class.html,Module Bio.Blast.Record=Bio.Blast.Record-module.html,Class Bio.Cluster.Record=Bio.Cluster.Record-class.html,Class Bio.Compass.Record=Bio.Compass.Record-class.html,Class Bio.Emboss.Primer3.Record=Bio.Emboss.Primer3.Record-class.html,Class Bio.ExPASy.Enzyme.Record=Bio.ExPASy.Enzyme.Record-class.html,Class Bio.ExPASy.Prodoc.Record=Bio.ExPASy.Prodoc.Record-class.html,Class Bio.ExPASy.Prosite.Record=Bio.ExPASy.Prosite.Record-class.html,Class Bio.ExPASy.ScanProsite.Record=Bio.ExPASy.ScanProsite.Record-class.html,Module Bio.GenBank.Record=Bio.GenBank.Record-module.html,Class Bio.GenBank.Record.Record=Bio.GenBank.Record.Record-class.html,Module Bio.Geo.Record=Bio.Geo.Record-module.html,Class Bio.Geo.Record.Record=Bio.Geo.Record.Record-class.html,Class Bio.KEGG.Compound.Record=Bio.KEGG.Compound.Record-class.html,Class Bio.KEGG.Enzyme.Record=Bio.KEGG.Enzyme.Record-class.html,Class Bio.Medline.Record=Bio.Medline.Record-class.html,Class Bio.Motif.Parsers.AlignAce.Record=Bio.Motif.Parsers.AlignAce.Record-class.html,Class Bio.Motif.Parsers.MAST.Record=Bio.Motif.Parsers.MAST.Record-class.html,Class Bio.PopGen.FDist.Record=Bio.PopGen.FDist.Record-class.html,Class Bio.PopGen.GenePop.LargeFileParser.Record=Bio.PopGen.GenePop.LargeFileParser.Record-class.html,Class Bio.PopGen.GenePop.Record=Bio.PopGen.GenePop.Record-class.html,Class Bio.SCOP.Cla.Record=Bio.SCOP.Cla.Record-class.html,Class Bio.SCOP.Des.Record=Bio.SCOP.Des.Record-class.html,Class Bio.SCOP.Dom.Record=Bio.SCOP.Dom.Record-class.html,Class Bio.SCOP.Hie.Record=Bio.SCOP.Hie.Record-class.html,Class Bio.Sequencing.Phd.Record=Bio.Sequencing.Phd.Record-class.html,Class Bio.SwissProt.KeyWList.Record=Bio.SwissProt.KeyWList.Record-class.html,Class Bio.SwissProt.Record=Bio.SwissProt.Record-class.html,Class Bio.UniGene.Record=Bio.UniGene.Record-class.html"><a title="Bio.Affy.CelFile.Record
Bio.Blast.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.Emboss.Primer3.Record
Bio.ExPASy.Enzyme.Record
Bio.ExPASy.Prodoc.Record
Bio.ExPASy.Prosite.Record
Bio.ExPASy.ScanProsite.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.Medline.Record
Bio.Motif.Parsers.AlignAce.Record
Bio.Motif.Parsers.MAST.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.LargeFileParser.Record
Bio.PopGen.GenePop.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.Record
Bio.UniGene.Record" class="py-name" href="#" onclick="return doclink('link-0', 'Record', 'link-0');">Record</a></tt> </tt>
<a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"> </tt>
<a name="_read_key_value"></a><div id="_read_key_value-def"><a name="L15"></a><tt class="py-lineno">15</tt> <a class="py-toggle" href="#" id="_read_key_value-toggle" onclick="return toggle('_read_key_value');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Geo-module.html#_read_key_value">_read_key_value</a><tt class="py-op">(</tt><tt class="py-param">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_read_key_value-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="_read_key_value-expanded"><a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"> <tt class="py-name">words</tt> <tt class="py-op">=</tt> <tt class="py-name">line</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-op">.</tt><tt id="link-1" 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-1', 'split', 'link-1');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">"="</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"> <tt class="py-keyword">try</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">key</tt><tt class="py-op">,</tt> <tt id="link-2" 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-2', 'value', 'link-2');">value</a></tt> <tt class="py-op">=</tt> <tt class="py-name">words</tt> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"> <tt id="link-3" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-3', 'value', 'link-2');">value</a></tt> <tt class="py-op">=</tt> <tt id="link-4" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-4', 'value', 'link-2');">value</a></tt><tt class="py-op">.</tt><tt id="link-5" 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-5', 'strip', 'link-5');">strip</a></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-keyword">except</tt> <tt class="py-name">ValueError</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">key</tt> <tt class="py-op">=</tt> <tt class="py-name">words</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"> <tt id="link-6" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-6', 'value', 'link-2');">value</a></tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"> <tt class="py-name">key</tt> <tt class="py-op">=</tt> <tt class="py-name">key</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-7', 'strip', 'link-5');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">key</tt><tt class="py-op">,</tt> <tt id="link-8" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-8', 'value', 'link-2');">value</a></tt> </tt>
</div><a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"> </tt>
<a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"> </tt>
<a name="parse"></a><div id="parse-def"><a name="L27"></a><tt class="py-lineno">27</tt> <a class="py-toggle" href="#" id="parse-toggle" onclick="return toggle('parse');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Geo-module.html#parse">parse</a><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="parse-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="parse-expanded"><a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"> <tt class="py-name">record</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-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt id="link-9" 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-9', 'handle', 'link-9');">handle</a></tt><tt class="py-op">:</tt> </tt>
<a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-10" class="py-name"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-10', 'strip', 'link-5');">strip</a></tt><tt class="py-op">(</tt><tt class="py-string">'\n'</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-11" class="py-name"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-11', 'strip', 'link-5');">strip</a></tt><tt class="py-op">(</tt><tt class="py-string">'\r'</tt><tt class="py-op">)</tt> </tt>
<a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">line</tt><tt class="py-op">:</tt> <tt class="py-keyword">continue</tt> <tt class="py-comment"># Ignore empty lines</tt> </tt>
<a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"> <tt class="py-name">c</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">c</tt><tt class="py-op">==</tt><tt class="py-string">'^'</tt><tt class="py-op">:</tt> </tt>
<a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">record</tt><tt class="py-op">:</tt> <tt class="py-keyword">yield</tt> <tt class="py-name">record</tt> </tt>
<a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"> <tt class="py-name">record</tt> <tt class="py-op">=</tt> <tt id="link-12" class="py-name"><a title="Bio.Affy.CelFile.Record
Bio.Blast.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.Emboss.Primer3.Record
Bio.ExPASy.Enzyme.Record
Bio.ExPASy.Prodoc.Record
Bio.ExPASy.Prosite.Record
Bio.ExPASy.ScanProsite.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.Medline.Record
Bio.Motif.Parsers.AlignAce.Record
Bio.Motif.Parsers.MAST.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.LargeFileParser.Record
Bio.PopGen.GenePop.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.Record
Bio.UniGene.Record" class="py-name" href="#" onclick="return doclink('link-12', 'Record', 'link-0');">Record</a></tt><tt class="py-op">.</tt><tt id="link-13" class="py-name"><a title="Bio.Affy.CelFile.Record
Bio.Blast.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.Emboss.Primer3.Record
Bio.ExPASy.Enzyme.Record
Bio.ExPASy.Prodoc.Record
Bio.ExPASy.Prosite.Record
Bio.ExPASy.ScanProsite.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.Medline.Record
Bio.Motif.Parsers.AlignAce.Record
Bio.Motif.Parsers.MAST.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.LargeFileParser.Record
Bio.PopGen.GenePop.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.Record
Bio.UniGene.Record" class="py-name" href="#" onclick="return doclink('link-13', 'Record', 'link-0');">Record</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt class="py-name">entity_type</tt><tt class="py-op">,</tt> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt class="py-name">entity_id</tt> <tt class="py-op">=</tt> <tt id="link-14" class="py-name" targets="Function Bio.Geo._read_key_value()=Bio.Geo-module.html#_read_key_value"><a title="Bio.Geo._read_key_value" class="py-name" href="#" onclick="return doclink('link-14', '_read_key_value', 'link-14');">_read_key_value</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">c</tt><tt class="py-op">==</tt><tt class="py-string">'!'</tt><tt class="py-op">:</tt> </tt>
<a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">'!Sample_table_begin'</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">'!Sample_table_end'</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">'!Platform_table_begin'</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">'!Platform_table_end'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L42"></a><tt class="py-lineno">42</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L43"></a><tt class="py-lineno">43</tt> <tt class="py-line"> <tt class="py-name">key</tt><tt class="py-op">,</tt> <tt id="link-15" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-15', 'value', 'link-2');">value</a></tt> <tt class="py-op">=</tt> <tt id="link-16" class="py-name"><a title="Bio.Geo._read_key_value" class="py-name" href="#" onclick="return doclink('link-16', '_read_key_value', 'link-14');">_read_key_value</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L44"></a><tt class="py-lineno">44</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">key</tt> <tt class="py-keyword">in</tt> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt class="py-name">entity_attributes</tt><tt class="py-op">:</tt> </tt>
<a name="L45"></a><tt class="py-lineno">45</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-17" class="py-name" targets="Variable Bio.GenBank.LocationParser.Integer.type=Bio.GenBank.LocationParser.Integer-class.html#type,Variable Bio.GenBank.LocationParser.Symbol.type=Bio.GenBank.LocationParser.Symbol-class.html#type,Variable Bio.GenBank.LocationParser.UnsignedInteger.type=Bio.GenBank.LocationParser.UnsignedInteger-class.html#type,Method Bio.Phylo.PhyloXMLIO.Writer.type()=Bio.Phylo.PhyloXMLIO.Writer-class.html#type"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type
Bio.Phylo.PhyloXMLIO.Writer.type" class="py-name" href="#" onclick="return doclink('link-17', 'type', 'link-17');">type</a></tt><tt class="py-op">(</tt><tt class="py-name">record</tt><tt class="py-op">.</tt><tt class="py-name">entity_attributes</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-op">==</tt><tt id="link-18" class="py-name" targets="Method Bio.Pathway.Rep.HashSet.HashSet.list()=Bio.Pathway.Rep.HashSet.HashSet-class.html#list"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-18', 'list', 'link-18');">list</a></tt><tt class="py-op">:</tt> </tt>
<a name="L46"></a><tt class="py-lineno">46</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt class="py-name">entity_attributes</tt><tt class="py-op">[</tt><tt class="py-name">key</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-19" 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-19', 'append', 'link-19');">append</a></tt><tt class="py-op">(</tt><tt id="link-20" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-20', 'value', 'link-2');">value</a></tt><tt class="py-op">)</tt> </tt>
<a name="L47"></a><tt class="py-lineno">47</tt> <tt class="py-line"> <tt class="py-keyword">else</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">existing</tt> <tt class="py-op">=</tt> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt class="py-name">entity_attributes</tt><tt class="py-op">[</tt><tt class="py-name">key</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">record</tt><tt class="py-op">.</tt><tt class="py-name">entity_attributes</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-op">[</tt><tt class="py-name">existing</tt><tt class="py-op">,</tt> <tt id="link-21" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-21', 'value', 'link-2');">value</a></tt><tt class="py-op">]</tt> </tt>
<a name="L50"></a><tt class="py-lineno">50</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L51"></a><tt class="py-lineno">51</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt class="py-name">entity_attributes</tt><tt class="py-op">[</tt><tt class="py-name">key</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-22" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-22', 'value', 'link-2');">value</a></tt> </tt>
<a name="L52"></a><tt class="py-lineno">52</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">c</tt><tt class="py-op">==</tt><tt class="py-string">'#'</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">key</tt><tt class="py-op">,</tt> <tt id="link-23" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-23', 'value', 'link-2');">value</a></tt> <tt class="py-op">=</tt> <tt id="link-24" class="py-name"><a title="Bio.Geo._read_key_value" class="py-name" href="#" onclick="return doclink('link-24', '_read_key_value', 'link-14');">_read_key_value</a></tt><tt class="py-op">(</tt><tt class="py-name">line</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">assert</tt> <tt class="py-name">key</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt class="py-name">col_defs</tt> </tt>
<a name="L55"></a><tt class="py-lineno">55</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt class="py-name">col_defs</tt><tt class="py-op">[</tt><tt class="py-name">key</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-25" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-25', 'value', 'link-2');">value</a></tt> </tt>
<a name="L56"></a><tt class="py-lineno">56</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L57"></a><tt class="py-lineno">57</tt> <tt class="py-line"> <tt class="py-name">row</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-26" 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-26', 'split', 'link-1');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">"\t"</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">record</tt><tt class="py-op">.</tt><tt class="py-name">table_rows</tt><tt class="py-op">.</tt><tt id="link-27" 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-27', 'append', 'link-19');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">row</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">yield</tt> <tt class="py-name">record</tt> </tt>
</div><a name="L60"></a><tt class="py-lineno">60</tt> <tt class="py-line"> </tt><script type="text/javascript">
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