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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.Geo-module.html">Package Geo</a> ::
Module Record
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<h1 class="epydoc">Source Code for <a href="Bio.Geo.Record-module.html">Module Bio.Geo.Record</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"># 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">Hold GEO data in a straightforward format.</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 class="py-docstring">classes:</tt> </tt>
<a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"><tt class="py-docstring">o Record - All of the information in an GEO record.</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">See http://www.ncbi.nlm.nih.gov/geo/</tt> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"> </tt>
<a name="Record"></a><div id="Record-def"><a name="L16"></a><tt class="py-lineno">16</tt> <a class="py-toggle" href="#" id="Record-toggle" onclick="return toggle('Record');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Geo.Record.Record-class.html">Record</a><tt class="py-op">:</tt> </tt>
</div><div id="Record-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="Record-expanded"><a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"> <tt class="py-docstring">"""Hold GEO information in a format similar to the original record.</tt> </tt>
<a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"><tt class="py-docstring"> The Record class is meant to make data easy to get to when you are</tt> </tt>
<a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"><tt class="py-docstring"> just interested in looking at GEO data.</tt> </tt>
<a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"><tt class="py-docstring"> Attributes:</tt> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"><tt class="py-docstring"> entity_type</tt> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"><tt class="py-docstring"> entity_id</tt> </tt>
<a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"><tt class="py-docstring"> entity_attributes</tt> </tt>
<a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"><tt class="py-docstring"> col_defs</tt> </tt>
<a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"><tt class="py-docstring"> table_rows</tt> </tt>
<a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="Record.__init__"></a><div id="Record.__init__-def"><a name="L30"></a><tt class="py-lineno">30</tt> <a class="py-toggle" href="#" id="Record.__init__-toggle" onclick="return toggle('Record.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Geo.Record.Record-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="Record.__init__-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="Record.__init__-expanded"><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 class="py-name">entity_type</tt> <tt class="py-op">=</tt> <tt class="py-string">''</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 class="py-name">entity_id</tt> <tt class="py-op">=</tt> <tt class="py-string">''</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">entity_attributes</tt> <tt class="py-op">=</tt> <tt class="py-op">{</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">self</tt><tt class="py-op">.</tt><tt class="py-name">col_defs</tt> <tt class="py-op">=</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">self</tt><tt class="py-op">.</tt><tt class="py-name">table_rows</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
</div><a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"> </tt>
<a name="Record.__str__"></a><div id="Record.__str__-def"><a name="L37"></a><tt class="py-lineno">37</tt> <a class="py-toggle" href="#" id="Record.__str__-toggle" onclick="return toggle('Record.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Geo.Record.Record-class.html#__str__">__str__</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="Record.__str__-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="Record.__str__-expanded"><a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-name">output</tt> <tt class="py-op">+</tt> <tt class="py-string">'GEO Type: %s\n'</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">entity_type</tt> </tt>
<a name="L40"></a><tt class="py-lineno">40</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-name">output</tt> <tt class="py-op">+</tt> <tt class="py-string">'GEO Id: %s\n'</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">entity_id</tt> </tt>
<a name="L41"></a><tt class="py-lineno">41</tt> <tt class="py-line"> <tt class="py-name">att_keys</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">entity_attributes</tt><tt class="py-op">.</tt><tt id="link-0" class="py-name" targets="Method Bio.Crystal.Crystal.keys()=Bio.Crystal.Crystal-class.html#keys,Method Bio.EUtils.MultiDict._BaseMultiDict.keys()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#keys,Method Bio.GenBank.NCBIDictionary.keys()=Bio.GenBank.NCBIDictionary-class.html#keys,Method Bio.Mindy.BaseDB.DictLookup.keys()=Bio.Mindy.BaseDB.DictLookup-class.html#keys,Method Bio.Mindy.BaseDB.OpenDB.keys()=Bio.Mindy.BaseDB.OpenDB-class.html#keys,Method Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys()=Bio.Mindy.BerkeleyDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys()=Bio.Mindy.BerkeleyDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryNamespace.keys()=Bio.Mindy.FlatDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryTable.keys()=Bio.Mindy.FlatDB.PrimaryTable-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryNamespace.keys()=Bio.Mindy.FlatDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryTable.keys()=Bio.Mindy.FlatDB.SecondaryTable-class.html#keys,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#keys,Method Bio.Prosite.ExPASyDictionary.keys()=Bio.Prosite.ExPASyDictionary-class.html#keys,Method Bio.Prosite.Prodoc.ExPASyDictionary.keys()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#keys,Method Bio.PubMed.Dictionary.keys()=Bio.PubMed.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.Dictionary.keys()=Bio.SwissProt.SProt.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.ExPASyDictionary.keys()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#keys,Method Bio.config.Registry.Registry.keys()=Bio.config.Registry.Registry-class.html#keys,Method BioSQL.BioSeqDatabase.BioSeqDatabase.keys()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#keys,Method BioSQL.BioSeqDatabase.DBServer.keys()=BioSQL.BioSeqDatabase.DBServer-class.html#keys,Method Martel.Parser.MartelAttributeList.keys()=Martel.Parser.MartelAttributeList-class.html#keys"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-0', 'keys', 'link-0');">keys</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-name">att_keys</tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Method Bio.PDB.Residue.DisorderedResidue.sort()=Bio.PDB.Residue.DisorderedResidue-class.html#sort,Method Bio.PDB.Residue.Residue.sort()=Bio.PDB.Residue.Residue-class.html#sort,Method Bio.Sequencing.Ace.ACEFileRecord.sort()=Bio.Sequencing.Ace.ACEFileRecord-class.html#sort"><a title="Bio.PDB.Residue.DisorderedResidue.sort
Bio.PDB.Residue.Residue.sort
Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-1', 'sort', 'link-1');">sort</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L43"></a><tt class="py-lineno">43</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <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-keyword">in</tt> <tt class="py-name">att_keys</tt><tt class="py-op">:</tt> </tt>
<a name="L44"></a><tt class="py-lineno">44</tt> <tt class="py-line"> <tt id="link-3" class="py-name" targets="Function Bio.listfns.contents()=Bio.listfns-module.html#contents"><a title="Bio.listfns.contents" class="py-name" href="#" onclick="return doclink('link-3', 'contents', 'link-3');">contents</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">entity_attributes</tt><tt class="py-op">[</tt> <tt id="link-4" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-4', 'key', 'link-2');">key</a></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 class="py-op">(</tt> <tt id="link-5" 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-5', 'type', 'link-5');">type</a></tt><tt class="py-op">(</tt> <tt id="link-6" class="py-name"><a title="Bio.listfns.contents" class="py-name" href="#" onclick="return doclink('link-6', 'contents', 'link-3');">contents</a></tt> <tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt id="link-7" class="py-name"><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-7', 'type', 'link-5');">type</a></tt><tt class="py-op">(</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> <tt class="py-op">)</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-keyword">for</tt> <tt id="link-8" class="py-name" targets="Method Bio.EUtils.Datatypes.DBIds.item()=Bio.EUtils.Datatypes.DBIds-class.html#item"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-8', 'item', 'link-8');">item</a></tt> <tt class="py-keyword">in</tt> <tt id="link-9" class="py-name"><a title="Bio.listfns.contents" class="py-name" href="#" onclick="return doclink('link-9', 'contents', 'link-3');">contents</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">try</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">output</tt> <tt class="py-op">=</tt> <tt class="py-name">output</tt> <tt class="py-op">+</tt> <tt class="py-string">'%s: %s\n'</tt> <tt class="py-op">%</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.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-11', 'item', 'link-8');">item</a></tt><tt class="py-op">[</tt> <tt class="py-op">:</tt><tt class="py-number">40</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">output</tt> <tt class="py-op">=</tt> <tt class="py-name">output</tt> <tt class="py-op">+</tt> <tt id="link-12" class="py-name" targets="Function Bio.Geo.Record.out_block()=Bio.Geo.Record-module.html#out_block"><a title="Bio.Geo.Record.out_block" class="py-name" href="#" onclick="return doclink('link-12', 'out_block', 'link-12');">out_block</a></tt><tt class="py-op">(</tt> <tt id="link-13" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-13', 'item', 'link-8');">item</a></tt><tt class="py-op">[</tt> <tt class="py-number">40</tt><tt class="py-op">:</tt> <tt class="py-op">]</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">except</tt><tt class="py-op">:</tt> </tt>
<a name="L51"></a><tt class="py-lineno">51</tt> <tt class="py-line"> <tt class="py-keyword">pass</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-op">(</tt> <tt id="link-14" class="py-name"><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-14', 'type', 'link-5');">type</a></tt><tt class="py-op">(</tt> <tt id="link-15" class="py-name"><a title="Bio.listfns.contents" class="py-name" href="#" onclick="return doclink('link-15', 'contents', 'link-3');">contents</a></tt> <tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt id="link-16" class="py-name"><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-16', 'type', 'link-5');">type</a></tt><tt class="py-op">(</tt> <tt class="py-string">''</tt> <tt class="py-op">)</tt> <tt class="py-op">)</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">output</tt> <tt class="py-op">=</tt> <tt class="py-name">output</tt> <tt class="py-op">+</tt> <tt class="py-string">'%s: %s\n'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt> <tt id="link-17" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-17', 'key', 'link-2');">key</a></tt><tt class="py-op">,</tt> <tt id="link-18" class="py-name"><a title="Bio.listfns.contents" class="py-name" href="#" onclick="return doclink('link-18', 'contents', 'link-3');">contents</a></tt><tt class="py-op">[</tt> <tt class="py-op">:</tt><tt class="py-number">40</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">output</tt> <tt class="py-op">=</tt> <tt class="py-name">output</tt> <tt class="py-op">+</tt> <tt id="link-19" class="py-name"><a title="Bio.Geo.Record.out_block" class="py-name" href="#" onclick="return doclink('link-19', 'out_block', 'link-12');">out_block</a></tt><tt class="py-op">(</tt> <tt id="link-20" class="py-name"><a title="Bio.listfns.contents" class="py-name" href="#" onclick="return doclink('link-20', 'contents', 'link-3');">contents</a></tt><tt class="py-op">[</tt> <tt class="py-number">40</tt><tt class="py-op">:</tt> <tt class="py-op">]</tt> <tt class="py-op">)</tt> </tt>
<a name="L55"></a><tt class="py-lineno">55</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L56"></a><tt class="py-lineno">56</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt id="link-21" class="py-name"><a title="Bio.listfns.contents" class="py-name" href="#" onclick="return doclink('link-21', 'contents', 'link-3');">contents</a></tt> </tt>
<a name="L57"></a><tt class="py-lineno">57</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-name">output</tt> <tt class="py-op">+</tt> <tt class="py-string">'%s: %s\n'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt> <tt id="link-22" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-22', 'key', 'link-2');">key</a></tt><tt class="py-op">,</tt> <tt class="py-name">val</tt><tt class="py-op">[</tt> <tt class="py-op">:</tt><tt class="py-number">40</tt> <tt class="py-op">]</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">output</tt> <tt class="py-op">=</tt> <tt class="py-name">output</tt> <tt class="py-op">+</tt> <tt id="link-23" class="py-name"><a title="Bio.Geo.Record.out_block" class="py-name" href="#" onclick="return doclink('link-23', 'out_block', 'link-12');">out_block</a></tt><tt class="py-op">(</tt> <tt class="py-name">val</tt><tt class="py-op">[</tt> <tt class="py-number">40</tt><tt class="py-op">:</tt> <tt class="py-op">]</tt> <tt class="py-op">)</tt> </tt>
<a name="L59"></a><tt class="py-lineno">59</tt> <tt class="py-line"> <tt class="py-name">col_keys</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">col_defs</tt><tt class="py-op">.</tt><tt id="link-24" class="py-name"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-24', 'keys', 'link-0');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L60"></a><tt class="py-lineno">60</tt> <tt class="py-line"> <tt class="py-name">col_keys</tt><tt class="py-op">.</tt><tt id="link-25" class="py-name"><a title="Bio.PDB.Residue.DisorderedResidue.sort
Bio.PDB.Residue.Residue.sort
Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-25', 'sort', 'link-1');">sort</a></tt><tt class="py-op">(</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">output</tt> <tt class="py-op">=</tt> <tt class="py-name">output</tt> <tt class="py-op">+</tt> <tt class="py-string">'Column Header Definitions\n'</tt> </tt>
<a name="L62"></a><tt class="py-lineno">62</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <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-keyword">in</tt> <tt class="py-name">col_keys</tt><tt class="py-op">:</tt> </tt>
<a name="L63"></a><tt class="py-lineno">63</tt> <tt class="py-line"> <tt class="py-name">val</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">col_defs</tt><tt class="py-op">[</tt> <tt id="link-27" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-27', 'key', 'link-2');">key</a></tt> <tt class="py-op">]</tt> </tt>
<a name="L64"></a><tt class="py-lineno">64</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-name">output</tt> <tt class="py-op">+</tt> <tt class="py-string">' %s: %s\n'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt> <tt id="link-28" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-28', 'key', 'link-2');">key</a></tt><tt class="py-op">,</tt> <tt class="py-name">val</tt><tt class="py-op">[</tt> <tt class="py-op">:</tt><tt class="py-number">40</tt> <tt class="py-op">]</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">output</tt> <tt class="py-op">=</tt> <tt class="py-name">output</tt> <tt class="py-op">+</tt> <tt id="link-29" class="py-name"><a title="Bio.Geo.Record.out_block" class="py-name" href="#" onclick="return doclink('link-29', 'out_block', 'link-12');">out_block</a></tt><tt class="py-op">(</tt> <tt class="py-name">val</tt><tt class="py-op">[</tt> <tt class="py-number">40</tt><tt class="py-op">:</tt> <tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">' '</tt> <tt class="py-op">)</tt> </tt>
<a name="L66"></a><tt class="py-lineno">66</tt> <tt class="py-line"> <tt class="py-comment">#May have to display VERY large tables,</tt> </tt>
<a name="L67"></a><tt class="py-lineno">67</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#so only show the first 20 lines of data</tt> </tt>
<a name="L68"></a><tt class="py-lineno">68</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">MAX_ROWS</tt> <tt class="py-op">=</tt> <tt class="py-number">20</tt><tt class="py-op">+</tt><tt class="py-number">1</tt> <tt class="py-comment"># include header in count</tt> </tt>
<a name="L69"></a><tt class="py-lineno">69</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">row</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">table_rows</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-name">MAX_ROWS</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L70"></a><tt class="py-lineno">70</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-name">output</tt> <tt class="py-op">+</tt> <tt class="py-string">'%s: '</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">table_rows</tt><tt class="py-op">.</tt><tt id="link-30" class="py-name" targets="Method Bio.Crystal.Chain.index()=Bio.Crystal.Chain-class.html#index,Method Bio.EUtils.POM.ElementNode.index()=Bio.EUtils.POM.ElementNode-class.html#index,Method Bio.SCOP.Raf.SeqMap.index()=Bio.SCOP.Raf.SeqMap-class.html#index,Method Bio.Seq.MutableSeq.index()=Bio.Seq.MutableSeq-class.html#index"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-30', 'index', 'link-30');">index</a></tt><tt class="py-op">(</tt> <tt class="py-name">row</tt> <tt class="py-op">)</tt> </tt>
<a name="L71"></a><tt class="py-lineno">71</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">col</tt> <tt class="py-keyword">in</tt> <tt class="py-name">row</tt><tt class="py-op">:</tt> </tt>
<a name="L72"></a><tt class="py-lineno">72</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-name">output</tt> <tt class="py-op">+</tt> <tt class="py-string">'%s\t'</tt> <tt class="py-op">%</tt> <tt class="py-name">col</tt> </tt>
<a name="L73"></a><tt class="py-lineno">73</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-name">output</tt> <tt class="py-op">+</tt> <tt class="py-string">'\n'</tt> </tt>
<a name="L74"></a><tt class="py-lineno">74</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">table_rows</tt><tt class="py-op">)</tt> <tt class="py-op">></tt> <tt class="py-name">MAX_ROWS</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">output</tt> <tt class="py-op">=</tt> <tt class="py-name">output</tt> <tt class="py-op">+</tt> <tt class="py-string">'...\n'</tt> </tt>
<a name="L76"></a><tt class="py-lineno">76</tt> <tt class="py-line"> <tt class="py-name">row</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">table_rows</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="L77"></a><tt class="py-lineno">77</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-name">output</tt> <tt class="py-op">+</tt> <tt class="py-string">'%s: '</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">table_rows</tt><tt class="py-op">.</tt><tt id="link-31" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-31', 'index', 'link-30');">index</a></tt><tt class="py-op">(</tt> <tt class="py-name">row</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">for</tt> <tt class="py-name">col</tt> <tt class="py-keyword">in</tt> <tt class="py-name">row</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">output</tt> <tt class="py-op">=</tt> <tt class="py-name">output</tt> <tt class="py-op">+</tt> <tt class="py-string">'%s\t'</tt> <tt class="py-op">%</tt> <tt class="py-name">col</tt> </tt>
<a name="L80"></a><tt class="py-lineno">80</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-name">output</tt> <tt class="py-op">+</tt> <tt class="py-string">'\n'</tt> </tt>
<a name="L81"></a><tt class="py-lineno">81</tt> <tt class="py-line"> </tt>
<a name="L82"></a><tt class="py-lineno">82</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">output</tt> </tt>
</div></div><a name="L83"></a><tt class="py-lineno">83</tt> <tt class="py-line"> </tt>
<a name="out_block"></a><div id="out_block-def"><a name="L84"></a><tt class="py-lineno">84</tt> <a class="py-toggle" href="#" id="out_block-toggle" onclick="return toggle('out_block');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Geo.Record-module.html#out_block">out_block</a><tt class="py-op">(</tt> <tt class="py-param">text</tt><tt class="py-op">,</tt> <tt class="py-param">prefix</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="out_block-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="out_block-expanded"><a name="L85"></a><tt class="py-lineno">85</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L86"></a><tt class="py-lineno">86</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">j</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt> <tt id="link-32" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.text()=Bio.EUtils.POM.ElementNode-class.html#text,Method Bio.Prosite.Prodoc._RecordConsumer.text()=Bio.Prosite.Prodoc._RecordConsumer-class.html#text,Variable Martel.test.test_Iterator.text=Martel.test.test_Iterator-module.html#text,Variable Martel.test.test_ParseRecords.text=Martel.test.test_ParseRecords-module.html#text"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-32', 'text', 'link-32');">text</a></tt> <tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-number">80</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L87"></a><tt class="py-lineno">87</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-name">output</tt> <tt class="py-op">+</tt> <tt class="py-string">'%s%s\n'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt> <tt id="link-33" class="py-name" targets="Variable Bio.DocSQL.Query.prefix=Bio.DocSQL.Query-class.html#prefix"><a title="Bio.DocSQL.Query.prefix" class="py-name" href="#" onclick="return doclink('link-33', 'prefix', 'link-33');">prefix</a></tt><tt class="py-op">,</tt> <tt id="link-34" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-34', 'text', 'link-32');">text</a></tt><tt class="py-op">[</tt> <tt class="py-name">j</tt><tt class="py-op">:</tt> <tt class="py-name">j</tt> <tt class="py-op">+</tt> <tt class="py-number">80</tt> <tt class="py-op">]</tt> <tt class="py-op">)</tt> </tt>
<a name="L88"></a><tt class="py-lineno">88</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-name">output</tt> <tt class="py-op">+</tt> <tt class="py-string">'\n'</tt> </tt>
<a name="L89"></a><tt class="py-lineno">89</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">output</tt> </tt>
</div><a name="L90"></a><tt class="py-lineno">90</tt> <tt class="py-line"> </tt><script type="text/javascript">
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