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biopython-doc-1.47-2mdv2008.1.x86_64.rpm

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        <a href="Bio-module.html">Package&nbsp;Bio</a> ::
        Package&nbsp;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"></tt><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"></tt><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"></tt><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"></tt><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"></tt><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 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="Module Bio.Blast.Record=Bio.Blast.Record-module.html,Module Bio.CDD.Record=Bio.CDD.Record-module.html,Class Bio.CDD.Record.Record=Bio.CDD.Record.Record-class.html,Class Bio.Cluster.Record=Bio.Cluster.Record-class.html,Class Bio.Compass.Record=Bio.Compass.Record-class.html,Module Bio.ECell.Record=Bio.ECell.Record-module.html,Class Bio.ECell.Record.Record=Bio.ECell.Record.Record-class.html,Class Bio.Fasta.Record=Bio.Fasta.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.Gobase.Record=Bio.Gobase.Record-class.html,Module Bio.IntelliGenetics.Record=Bio.IntelliGenetics.Record-module.html,Class Bio.IntelliGenetics.Record.Record=Bio.IntelliGenetics.Record.Record-class.html,Class Bio.InterPro.Record=Bio.InterPro.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.LocusLink.Record=Bio.LocusLink.Record-class.html,Class Bio.LocusLink.web_parse.Record=Bio.LocusLink.web_parse.Record-class.html,Class Bio.Medline.Record=Bio.Medline.Record-class.html,Module Bio.MetaTool.Record=Bio.MetaTool.Record-module.html,Class Bio.MetaTool.Record.Record=Bio.MetaTool.Record.Record-class.html,Module Bio.NBRF.Record=Bio.NBRF.Record-module.html,Class Bio.NBRF.Record.Record=Bio.NBRF.Record.Record-class.html,Class Bio.Ndb.Record=Bio.Ndb.Record-class.html,Class Bio.PopGen.FDist.Record=Bio.PopGen.FDist.Record-class.html,Class Bio.PopGen.GenePop.Record=Bio.PopGen.GenePop.Record-class.html,Class Bio.Prosite.Prodoc.Record=Bio.Prosite.Prodoc.Record-class.html,Class Bio.Prosite.Record=Bio.Prosite.Record-class.html,Class Bio.Rebase.Record=Bio.Rebase.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,Module Bio.Saf.Record=Bio.Saf.Record-module.html,Class Bio.Saf.Record.Record=Bio.Saf.Record.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.SProt.Record=Bio.SwissProt.SProt.Record-class.html"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.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.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-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 id="link-2" class="py-name" targets="Variable Bio.Translate.key=Bio.Translate-module.html#key"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-2', 'key', 'link-2');">key</a></tt><tt class="py-op">,</tt> <tt id="link-3" class="py-name" targets="Variable Bio.Translate.value=Bio.Translate-module.html#value"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-3', 'value', 'link-3');">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-4" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-4', 'value', 'link-3');">value</a></tt> <tt class="py-op">=</tt> <tt id="link-5" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-5', 'value', 'link-3');">value</a></tt><tt class="py-op">.</tt><tt id="link-6" class="py-name" targets="Class Bio.EUtils.DTDs.LinkOut.strip=Bio.EUtils.DTDs.LinkOut.strip-class.html,Method Bio.File.SGMLStripper.strip()=Bio.File.SGMLStripper-class.html#strip,Method Bio.SGMLExtractor.SGMLExtractor.strip()=Bio.SGMLExtractor.SGMLExtractor-class.html#strip"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-6', 'strip', 'link-6');">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 id="link-7" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-7', 'key', 'link-2');">key</a></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-8" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-8', 'value', 'link-3');">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 id="link-9" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-9', 'key', 'link-2');">key</a></tt> <tt class="py-op">=</tt> <tt id="link-10" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-10', 'key', 'link-2');">key</a></tt><tt class="py-op">.</tt><tt id="link-11" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-11', 'strip', 'link-6');">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 id="link-12" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-12', 'key', 'link-2');">key</a></tt><tt class="py-op">,</tt> <tt id="link-13" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-13', 'value', 'link-3');">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 id="link-14" class="py-name" targets="Variable Bio.Emboss.primer3_format.record=Bio.Emboss.primer3_format-module.html#record,Variable Bio.Emboss.primersearch_format.record=Bio.Emboss.primersearch_format-module.html#record,Method Bio.GFF.Feature.record()=Bio.GFF.Feature-class.html#record,Variable Bio.LocusLink.web_parse.record=Bio.LocusLink.web_parse-module.html#record,Variable Bio.Ndb.record=Bio.Ndb-module.html#record,Function Bio.Std.record()=Bio.Std-module.html#record,Variable Bio.expressions.blocks.record=Bio.expressions.blocks-module.html#record,Variable Bio.expressions.embl.embl65.record=Bio.expressions.embl.embl65-module.html#record,Variable Bio.expressions.fasta.record=Bio.expressions.fasta-module.html#record,Variable Bio.expressions.genbank.record=Bio.expressions.genbank-module.html#record,Variable Bio.expressions.hmmpfam.record=Bio.expressions.hmmpfam-module.html#record,Variable Bio.expressions.swissprot.ipi.record=Bio.expressions.swissprot.ipi-module.html#record,Variable Bio.expressions.swissprot.speclist.record=Bio.expressions.swissprot.speclist-module.html#record,Variable Bio.expressions.swissprot.sprot38.record=Bio.expressions.swissprot.sprot38-module.html#record,Variable Bio.expressions.swissprot.sprot40.record=Bio.expressions.swissprot.sprot40-module.html#record,Variable Martel.test.test_swissprot38.record=Martel.test.test_swissprot38-module.html#record,Variable Martel.test.testformats.swissprot38.record=Martel.test.testformats.swissprot38-module.html#record"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-14', 'record', 'link-14');">record</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-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt id="link-15" class="py-name" targets="Variable Bio.LocusLink.web_parse.handle=Bio.LocusLink.web_parse-module.html#handle,Variable Bio.Ndb.handle=Bio.Ndb-module.html#handle"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-15', 'handle', 'link-15');">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-16" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-16', 'strip', 'link-6');">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-17" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-17', 'strip', 'link-6');">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 id="link-18" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-18', 'record', 'link-14');">record</a></tt><tt class="py-op">:</tt> <tt class="py-keyword">yield</tt> <tt id="link-19" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-19', 'record', 'link-14');">record</a></tt> </tt>
<a name="L35"></a><tt class="py-lineno">35</tt>  <tt class="py-line">            <tt id="link-20" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-20', 'record', 'link-14');">record</a></tt> <tt class="py-op">=</tt> <tt id="link-21" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-21', 'Record', 'link-0');">Record</a></tt><tt class="py-op">.</tt><tt id="link-22" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-22', '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 id="link-23" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-23', 'record', 'link-14');">record</a></tt><tt class="py-op">.</tt><tt class="py-name">entity_type</tt><tt class="py-op">,</tt> <tt id="link-24" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-24', 'record', 'link-14');">record</a></tt><tt class="py-op">.</tt><tt class="py-name">entity_id</tt> <tt class="py-op">=</tt> <tt id="link-25" 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-25', '_read_key_value', 'link-25');">_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 id="link-26" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-26', 'key', 'link-2');">key</a></tt><tt class="py-op">,</tt> <tt id="link-27" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-27', 'value', 'link-3');">value</a></tt> <tt class="py-op">=</tt> <tt id="link-28" class="py-name"><a title="Bio.Geo._read_key_value" class="py-name" href="#" onclick="return doclink('link-28', '_read_key_value', 'link-25');">_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 id="link-29" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-29', 'key', 'link-2');">key</a></tt> <tt class="py-keyword">in</tt> <tt id="link-30" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-30', 'record', 'link-14');">record</a></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-31" 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"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-31', 'type', 'link-31');">type</a></tt><tt class="py-op">(</tt><tt id="link-32" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-32', 'record', 'link-14');">record</a></tt><tt class="py-op">.</tt><tt class="py-name">entity_attributes</tt><tt class="py-op">[</tt><tt id="link-33" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-33', 'key', 'link-2');">key</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt id="link-34" 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-34', 'list', 'link-34');">list</a></tt><tt class="py-op">:</tt> </tt>
<a name="L46"></a><tt class="py-lineno">46</tt>  <tt class="py-line">                    <tt id="link-35" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-35', 'record', 'link-14');">record</a></tt><tt class="py-op">.</tt><tt class="py-name">entity_attributes</tt><tt class="py-op">[</tt><tt id="link-36" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-36', 'key', 'link-2');">key</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name" targets="Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-class.html#append,Method Bio.EUtils.POM.ElementNode.append()=Bio.EUtils.POM.ElementNode-class.html#append,Method Bio.EUtils.sourcegen.SourceFile.append()=Bio.EUtils.sourcegen.SourceFile-class.html#append,Method Bio.SCOP.Raf.SeqMap.append()=Bio.SCOP.Raf.SeqMap-class.html#append,Method Bio.Seq.MutableSeq.append()=Bio.Seq.MutableSeq-class.html#append,Method Bio.Wise.psw.Alignment.append()=Bio.Wise.psw.Alignment-class.html#append,Method Bio.Wise.psw.AlignmentColumn.append()=Bio.Wise.psw.AlignmentColumn-class.html#append,Method Martel.msre_parse.SubPattern.append()=Martel.msre_parse.SubPattern-class.html#append"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-37', 'append', 'link-37');">append</a></tt><tt class="py-op">(</tt><tt id="link-38" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-38', 'value', 'link-3');">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 id="link-39" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-39', 'record', 'link-14');">record</a></tt><tt class="py-op">.</tt><tt class="py-name">entity_attributes</tt><tt class="py-op">[</tt><tt id="link-40" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-40', 'key', 'link-2');">key</a></tt><tt class="py-op">]</tt> </tt>
<a name="L49"></a><tt class="py-lineno">49</tt>  <tt class="py-line">                    <tt id="link-41" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-41', 'record', 'link-14');">record</a></tt><tt class="py-op">.</tt><tt class="py-name">entity_attributes</tt><tt class="py-op">[</tt><tt id="link-42" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-42', 'key', 'link-2');">key</a></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-43" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-43', 'value', 'link-3');">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 id="link-44" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-44', 'record', 'link-14');">record</a></tt><tt class="py-op">.</tt><tt class="py-name">entity_attributes</tt><tt class="py-op">[</tt><tt id="link-45" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-45', 'key', 'link-2');">key</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-46" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-46', 'value', 'link-3');">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 id="link-47" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-47', 'key', 'link-2');">key</a></tt><tt class="py-op">,</tt> <tt id="link-48" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-48', 'value', 'link-3');">value</a></tt> <tt class="py-op">=</tt> <tt id="link-49" class="py-name"><a title="Bio.Geo._read_key_value" class="py-name" href="#" onclick="return doclink('link-49', '_read_key_value', 'link-25');">_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 id="link-50" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-50', 'key', 'link-2');">key</a></tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt id="link-51" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-51', 'record', 'link-14');">record</a></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 id="link-52" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-52', 'record', 'link-14');">record</a></tt><tt class="py-op">.</tt><tt class="py-name">col_defs</tt><tt class="py-op">[</tt><tt id="link-53" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-53', 'key', 'link-2');">key</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-54" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-54', 'value', 'link-3');">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-55" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-55', '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 id="link-56" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-56', 'record', 'link-14');">record</a></tt><tt class="py-op">.</tt><tt class="py-name">table_rows</tt><tt class="py-op">.</tt><tt id="link-57" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-57', 'append', 'link-37');">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 id="link-58" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-58', 'record', 'link-14');">record</a></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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