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<h1 class="epydoc">Source Code for <a href="Bio.KEGG.Map-module.html">Package Bio.KEGG.Map</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 Tarjei Mikkelsen. 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 2007 by Michiel de Hoon. 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"># This code is part of the Biopython distribution and governed by its</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"># license. Please see the LICENSE file that should have been included</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"># as part of this package.</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">This module provides code to import KEGG Pathway maps for use with</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">the Biopython Pathway module.</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 class="py-docstring">The pathway maps are in the format:</tt> </tt>
<a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"><tt class="py-docstring">RXXXXX:[X.X.X.X:] A + 2 B <=> C</tt> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"><tt class="py-docstring">RXXXXX:[X.X.X.X:] 3C <=> 2 D + E</tt> </tt>
<a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"><tt class="py-docstring">...</tt> </tt>
<a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"><tt class="py-docstring">where RXXXXX is a five-digit reaction id, and X.X.X.X is the optional</tt> </tt>
<a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"><tt class="py-docstring">EC number of the enzyme that catalyze the reaction.</tt> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"> </tt>
<a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Package Bio.Pathway=Bio.Pathway-module.html"><a title="Bio.Pathway" class="py-name" href="#" onclick="return doclink('link-1', 'Pathway', 'link-1');">Pathway</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name" targets="Class Bio.Pathway.Reaction=Bio.Pathway.Reaction-class.html"><a title="Bio.Pathway.Reaction" class="py-name" href="#" onclick="return doclink('link-2', 'Reaction', 'link-2');">Reaction</a></tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"> </tt>
<a name="parse"></a><div id="parse-def"><a name="L24"></a><tt class="py-lineno">24</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.KEGG.Map-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="L25"></a><tt class="py-lineno">25</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-3" 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-3', 'handle', 'link-3');">handle</a></tt><tt class="py-op">:</tt> </tt>
<a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"> <tt id="link-4" class="py-name" targets="Variable BioSQL.BioSeq.DBSeq.data=BioSQL.BioSeq.DBSeq-class.html#data"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-4', 'data', 'link-4');">data</a></tt><tt class="py-op">,</tt> <tt class="py-name">catalysts</tt><tt class="py-op">,</tt> <tt id="link-5" class="py-name" targets="Method Bio.MetaTool._RecordConsumer.reaction()=Bio.MetaTool._RecordConsumer-class.html#reaction,Variable Bio.MetaTool.metatool_format.reaction=Bio.MetaTool.metatool_format-module.html#reaction"><a title="Bio.MetaTool._RecordConsumer.reaction
Bio.MetaTool.metatool_format.reaction" class="py-name" href="#" onclick="return doclink('link-5', 'reaction', 'link-5');">reaction</a></tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-6" class="py-name" targets="Method Bio.Nexus.Trees.Tree.split()=Bio.Nexus.Trees.Tree-class.html#split,Method Bio.Restriction.Restriction.RestrictionBatch.split()=Bio.Restriction.Restriction.RestrictionBatch-class.html#split"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-6', 'split', 'link-6');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">":"</tt><tt class="py-op">)</tt> </tt>
<a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"> <tt class="py-name">catalysts</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">catalysts</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"> <tt class="py-name">reactants</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"> <tt class="py-name">before</tt><tt class="py-op">,</tt> <tt class="py-name">after</tt> <tt class="py-op">=</tt> <tt id="link-7" class="py-name"><a title="Bio.MetaTool._RecordConsumer.reaction
Bio.MetaTool.metatool_format.reaction" class="py-name" href="#" onclick="return doclink('link-7', 'reaction', 'link-5');">reaction</a></tt><tt class="py-op">.</tt><tt id="link-8" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-8', 'split', 'link-6');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">"<=>"</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">compounds</tt> <tt class="py-op">=</tt> <tt class="py-name">before</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-9', 'split', 'link-6');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">" + "</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">for</tt> <tt class="py-name">compound</tt> <tt class="py-keyword">in</tt> <tt class="py-name">compounds</tt><tt class="py-op">:</tt> </tt>
<a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"> <tt class="py-name">compound</tt> <tt class="py-op">=</tt> <tt class="py-name">compound</tt><tt class="py-op">.</tt><tt id="link-10" 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-10', 'strip', 'link-10');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"> <tt class="py-name">number</tt><tt class="py-op">,</tt> <tt class="py-name">compound</tt> <tt class="py-op">=</tt> <tt class="py-name">compound</tt><tt class="py-op">.</tt><tt id="link-11" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-11', 'split', 'link-6');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"> <tt class="py-name">number</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">number</tt><tt class="py-op">)</tt> </tt>
<a name="L36"></a><tt class="py-lineno">36</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="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"> <tt class="py-name">number</tt> <tt class="py-op">=</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt> </tt>
<a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"> <tt class="py-name">reactants</tt><tt class="py-op">[</tt><tt class="py-name">compound</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">number</tt> </tt>
<a name="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"> <tt class="py-name">compounds</tt> <tt class="py-op">=</tt> <tt class="py-name">after</tt><tt class="py-op">.</tt><tt id="link-12" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-12', 'split', 'link-6');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">" + "</tt><tt class="py-op">)</tt> </tt>
<a name="L40"></a><tt class="py-lineno">40</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">compound</tt> <tt class="py-keyword">in</tt> <tt class="py-name">compounds</tt><tt class="py-op">:</tt> </tt>
<a name="L41"></a><tt class="py-lineno">41</tt> <tt class="py-line"> <tt class="py-name">compound</tt> <tt class="py-op">=</tt> <tt class="py-name">compound</tt><tt class="py-op">.</tt><tt id="link-13" 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-13', 'strip', 'link-10');">strip</a></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">try</tt><tt class="py-op">:</tt> </tt>
<a name="L43"></a><tt class="py-lineno">43</tt> <tt class="py-line"> <tt class="py-name">number</tt><tt class="py-op">,</tt> <tt class="py-name">compound</tt> <tt class="py-op">=</tt> <tt class="py-name">compound</tt><tt class="py-op">.</tt><tt id="link-14" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-14', 'split', 'link-6');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L44"></a><tt class="py-lineno">44</tt> <tt class="py-line"> <tt class="py-name">number</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">number</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">except</tt> <tt class="py-name">ValueError</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">number</tt> <tt class="py-op">=</tt> <tt class="py-op">+</tt><tt class="py-number">1</tt> </tt>
<a name="L47"></a><tt class="py-lineno">47</tt> <tt class="py-line"> <tt class="py-name">reactants</tt><tt class="py-op">[</tt><tt class="py-name">compound</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">number</tt> </tt>
<a name="L48"></a><tt class="py-lineno">48</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt id="link-15" class="py-name"><a title="Bio.Pathway.Reaction" class="py-name" href="#" onclick="return doclink('link-15', 'Reaction', 'link-2');">Reaction</a></tt><tt class="py-op">(</tt><tt class="py-name">reactants</tt><tt class="py-op">,</tt> <tt class="py-name">catalysts</tt><tt class="py-op">,</tt> <tt id="link-16" class="py-name" targets="Variable Bio.EUtils.POM.True=Bio.EUtils.POM-module.html#True"><a title="Bio.EUtils.POM.True" class="py-name" href="#" onclick="return doclink('link-16', 'True', 'link-16');">True</a></tt><tt class="py-op">,</tt> <tt id="link-17" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-17', 'data', 'link-4');">data</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L49"></a><tt class="py-lineno">49</tt> <tt class="py-line"> </tt><script type="text/javascript">
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