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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.PopGen-module.html">Package PopGen</a> ::
<a href="Bio.PopGen.SimCoal-module.html">Package SimCoal</a> ::
Module Template
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<h1 class="epydoc">Source Code for <a href="Bio.PopGen.SimCoal.Template-module.html">Module Bio.PopGen.SimCoal.Template</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 2007 by Tiago Antao. 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"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">math</tt> <tt class="py-keyword">import</tt> <tt id="link-0" class="py-name" targets="Variable Bio.Affy.CelFile.sqrt=Bio.Affy.CelFile-module.html#sqrt,Variable Bio.LogisticRegression.sqrt=Bio.LogisticRegression-module.html#sqrt,Variable Bio.MarkovModel.sqrt=Bio.MarkovModel-module.html#sqrt,Variable Bio.MaxEntropy.sqrt=Bio.MaxEntropy-module.html#sqrt,Variable Bio.NaiveBayes.sqrt=Bio.NaiveBayes-module.html#sqrt,Variable Bio.PDB.ResidueDepth'.sqrt=Bio.PDB.ResidueDepth%27-module.html#sqrt,Variable Bio.PDB.Vector'.sqrt=Bio.PDB.Vector%27-module.html#sqrt,Variable Bio.SVDSuperimposer.SVDSuperimposer'.sqrt=Bio.SVDSuperimposer.SVDSuperimposer%27-module.html#sqrt,Variable Bio.SVDSuperimposer.sqrt=Bio.SVDSuperimposer-module.html#sqrt,Variable Bio.Statistics.lowess.sqrt=Bio.Statistics.lowess-module.html#sqrt,Variable Bio.distance.sqrt=Bio.distance-module.html#sqrt,Variable Bio.kNN.sqrt=Bio.kNN-module.html#sqrt"><a title="Bio.Affy.CelFile.sqrt
Bio.LogisticRegression.sqrt
Bio.MarkovModel.sqrt
Bio.MaxEntropy.sqrt
Bio.NaiveBayes.sqrt
Bio.PDB.ResidueDepth'.sqrt
Bio.PDB.Vector'.sqrt
Bio.SVDSuperimposer.SVDSuperimposer'.sqrt
Bio.SVDSuperimposer.sqrt
Bio.Statistics.lowess.sqrt
Bio.distance.sqrt
Bio.kNN.sqrt" class="py-name" href="#" onclick="return doclink('link-0', 'sqrt', 'link-0');">sqrt</a></tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">sys</tt> <tt class="py-keyword">import</tt> <tt class="py-name">argv</tt><tt class="py-op">,</tt><tt class="py-name">exit</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">os</tt> <tt class="py-keyword">import</tt> <tt class="py-name">sep</tt><tt class="py-op">,</tt> <tt class="py-name">mkdir</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">re</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-1" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-1', 'Bio', 'link-1');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Package Bio.PopGen=Bio.PopGen-module.html"><a title="Bio.PopGen" class="py-name" href="#" onclick="return doclink('link-2', 'PopGen', 'link-2');">PopGen</a></tt><tt class="py-op">.</tt><tt id="link-3" class="py-name" targets="Package Bio.PopGen.SimCoal=Bio.PopGen.SimCoal-module.html"><a title="Bio.PopGen.SimCoal" class="py-name" href="#" onclick="return doclink('link-3', 'SimCoal', 'link-3');">SimCoal</a></tt> <tt class="py-keyword">import</tt> <tt id="link-4" class="py-name" targets="Variable Bio.PopGen.SimCoal.builtin_tpl_dir=Bio.PopGen.SimCoal-module.html#builtin_tpl_dir"><a title="Bio.PopGen.SimCoal.builtin_tpl_dir" class="py-name" href="#" onclick="return doclink('link-4', 'builtin_tpl_dir', 'link-4');">builtin_tpl_dir</a></tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"> </tt>
<a name="exec_template"></a><div id="exec_template-def"><a name="L14"></a><tt class="py-lineno"> 14</tt> <a class="py-toggle" href="#" id="exec_template-toggle" onclick="return toggle('exec_template');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.SimCoal.Template-module.html#exec_template">exec_template</a><tt class="py-op">(</tt><tt class="py-param">template</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="exec_template-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="exec_template-expanded"><a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"> <tt class="py-name">executed_template</tt> <tt class="py-op">=</tt> <tt class="py-name">template</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"> <tt id="link-5" class="py-name" targets="Method Bio.Parsers.spark.GenericASTMatcher.match()=Bio.Parsers.spark.GenericASTMatcher-class.html#match,Method Bio.Prosite.Pattern.Prosite.match()=Bio.Prosite.Pattern.Prosite-class.html#match,Function Bio.triefind.match()=Bio.triefind-module.html#match,Method Martel.msre_parse.Tokenizer.match()=Martel.msre_parse.Tokenizer-class.html#match"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-5', 'match', 'link-5');">match</a></tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-6" class="py-name" targets="Method Bio.EUtils.DBIdsClient.DBIdsClient.search()=Bio.EUtils.DBIdsClient.DBIdsClient-class.html#search,Method Bio.EUtils.HistoryClient.HistoryClient.search()=Bio.EUtils.HistoryClient.HistoryClient-class.html#search,Method Bio.KDTree.KDTree.KDTree.search()=Bio.KDTree.KDTree.KDTree-class.html#search,Method Bio.PDB.NeighborSearch.NeighborSearch.search()=Bio.PDB.NeighborSearch.NeighborSearch-class.html#search,Method Bio.Prosite.Pattern.Prosite.search()=Bio.Prosite.Pattern.Prosite-class.html#search,Class Method Bio.Restriction.Restriction.AbstractCut.search()=Bio.Restriction.Restriction.AbstractCut-class.html#search,Method Bio.Restriction.Restriction.RestrictionBatch.search()=Bio.Restriction.Restriction.RestrictionBatch-class.html#search,Function Bio.SCOP.search()=Bio.SCOP-module.html#search,Module Bio.builders.Search.search=Bio.builders.Search.search-module.html,Module Bio.formatdefs.search=Bio.formatdefs.search-module.html,Variable Bio.formatdefs.search.search=Bio.formatdefs.search-module.html#search"><a title="Bio.EUtils.DBIdsClient.DBIdsClient.search
Bio.EUtils.HistoryClient.HistoryClient.search
Bio.KDTree.KDTree.KDTree.search
Bio.PDB.NeighborSearch.NeighborSearch.search
Bio.Prosite.Pattern.Prosite.search
Bio.Restriction.Restriction.AbstractCut.search
Bio.Restriction.Restriction.RestrictionBatch.search
Bio.SCOP.search
Bio.builders.Search.search
Bio.formatdefs.search
Bio.formatdefs.search.search" class="py-name" href="#" onclick="return doclink('link-6', 'search', 'link-6');">search</a></tt><tt class="py-op">(</tt><tt class="py-string">'!!!(.*?)!!!'</tt><tt class="py-op">,</tt> <tt class="py-name">executed_template</tt><tt class="py-op">,</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">MULTILINE</tt><tt class="py-op">)</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"> <tt class="py-comment">#while len(match.groups())>0 :</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">while</tt> <tt id="link-7" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-7', 'match', 'link-5');">match</a></tt> <tt class="py-op">:</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"> <tt class="py-name">exec_result</tt> <tt class="py-op">=</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">eval</tt><tt class="py-op">(</tt><tt id="link-8" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-8', 'match', 'link-5');">match</a></tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Method Bio.Prosite.Pattern.PrositeMatch.groups()=Bio.Prosite.Pattern.PrositeMatch-class.html#groups"><a title="Bio.Prosite.Pattern.PrositeMatch.groups" class="py-name" href="#" onclick="return doclink('link-9', 'groups', 'link-9');">groups</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"> <tt class="py-name">executed_template</tt> <tt class="py-op">=</tt> <tt class="py-name">executed_template</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"> <tt class="py-string">'!!!'</tt> <tt class="py-op">+</tt> <tt id="link-10" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-10', 'match', 'link-5');">match</a></tt><tt class="py-op">.</tt><tt id="link-11" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.groups" class="py-name" href="#" onclick="return doclink('link-11', 'groups', 'link-9');">groups</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-string">'!!!'</tt><tt class="py-op">,</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"> <tt class="py-name">exec_result</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"> <tt id="link-12" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-12', 'match', 'link-5');">match</a></tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-13" class="py-name"><a title="Bio.EUtils.DBIdsClient.DBIdsClient.search
Bio.EUtils.HistoryClient.HistoryClient.search
Bio.KDTree.KDTree.KDTree.search
Bio.PDB.NeighborSearch.NeighborSearch.search
Bio.Prosite.Pattern.Prosite.search
Bio.Restriction.Restriction.AbstractCut.search
Bio.Restriction.Restriction.RestrictionBatch.search
Bio.SCOP.search
Bio.builders.Search.search
Bio.formatdefs.search
Bio.formatdefs.search.search" class="py-name" href="#" onclick="return doclink('link-13', 'search', 'link-6');">search</a></tt><tt class="py-op">(</tt><tt class="py-string">'!!!(.*?)!!!'</tt><tt class="py-op">,</tt> <tt class="py-name">executed_template</tt><tt class="py-op">,</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">MULTILINE</tt><tt class="py-op">)</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"> <tt class="py-comment">#match = patt.matcher(String(executed_template))</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt class="py-name">executed_template</tt> </tt>
</div><a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"> </tt>
<a name="process_para"></a><div id="process_para-def"><a name="L28"></a><tt class="py-lineno"> 28</tt> <a class="py-toggle" href="#" id="process_para-toggle" onclick="return toggle('process_para');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.SimCoal.Template-module.html#process_para">process_para</a><tt class="py-op">(</tt><tt class="py-param">in_string</tt><tt class="py-op">,</tt> <tt class="py-param">out_file_prefix</tt><tt class="py-op">,</tt> <tt class="py-param">para_list</tt><tt class="py-op">,</tt> <tt class="py-param">curr_values</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="process_para-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="process_para-expanded"><a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt class="py-name">para_list</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="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"> <tt class="py-name">template</tt> <tt class="py-op">=</tt> <tt class="py-name">in_string</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"> <tt class="py-name">f_name</tt> <tt class="py-op">=</tt> <tt class="py-name">out_file_prefix</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> <tt class="py-comment">#f_name += '_' + str(total_size)</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt class="py-name">tup</tt> <tt class="py-keyword">in</tt> <tt class="py-name">curr_values</tt><tt class="py-op">:</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"> <tt id="link-14" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.name=Bio.Encodings.IUPACEncoding-module.html#name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-14', 'name', 'link-14');">name</a></tt><tt class="py-op">,</tt> <tt class="py-name">val</tt> <tt class="py-op">=</tt> <tt class="py-name">tup</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> <tt class="py-name">f_name</tt> <tt class="py-op">+=</tt> <tt class="py-string">'_'</tt> <tt class="py-op">+</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">val</tt><tt class="py-op">)</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-comment">#reg = re.compile('\?' + name, re.MULTILINE)</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#template = re.sub(reg, str(val), template)</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">template</tt> <tt class="py-op">=</tt> <tt class="py-name">template</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">'?'</tt><tt class="py-op">+</tt><tt id="link-15" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-15', 'name', 'link-14');">name</a></tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">val</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt id="link-16" class="py-name" targets="Function Bio.Mindy.FlatDB.open()=Bio.Mindy.FlatDB-module.html#open,Function Bio.Mindy.open()=Bio.Mindy-module.html#open"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-16', 'open', 'link-16');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">f_name</tt> <tt class="py-op">+</tt> <tt class="py-string">'.par'</tt><tt class="py-op">,</tt> <tt class="py-string">'w'</tt><tt class="py-op">)</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> <tt class="py-comment">#executed_template = template</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">executed_template</tt> <tt class="py-op">=</tt> <tt id="link-17" class="py-name" targets="Function Bio.PopGen.SimCoal.Template.exec_template()=Bio.PopGen.SimCoal.Template-module.html#exec_template"><a title="Bio.PopGen.SimCoal.Template.exec_template" class="py-name" href="#" onclick="return doclink('link-17', 'exec_template', 'link-17');">exec_template</a></tt><tt class="py-op">(</tt><tt class="py-name">template</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">clean_template</tt> <tt class="py-op">=</tt> <tt class="py-name">executed_template</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">'\r\n'</tt><tt class="py-op">,</tt><tt class="py-string">'\n'</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">'\n\n'</tt><tt class="py-op">,</tt><tt class="py-string">'\n'</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">'\n'</tt><tt class="py-op">,</tt><tt class="py-string">'\r\n'</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">f</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name" targets="Method Bio.AlignAce.Motif.Motif.write()=Bio.AlignAce.Motif.Motif-class.html#write,Function Bio.AlignIO.write()=Bio.AlignIO-module.html#write,Method Bio.EUtils.sourcegen.SourceFile.write()=Bio.EUtils.sourcegen.SourceFile-class.html#write,Method Bio.EUtils.sourcegen.SourceGen.write()=Bio.EUtils.sourcegen.SourceGen-class.html#write,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.write()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#write,Function Bio.SeqIO.write()=Bio.SeqIO-module.html#write,Method Bio.Writer.Writer.write()=Bio.Writer.Writer-class.html#write,Method Bio.writers.SeqRecord.embl.WriteEmbl.write()=Bio.writers.SeqRecord.embl.WriteEmbl-class.html#write,Method Bio.writers.SeqRecord.fasta.WriteFasta.write()=Bio.writers.SeqRecord.fasta.WriteFasta-class.html#write"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-18', 'write', 'link-18');">write</a></tt><tt class="py-op">(</tt><tt class="py-name">clean_template</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">f</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name" targets="Method Bio.FilteredReader.FilteredReader.close()=Bio.FilteredReader.FilteredReader-class.html#close,Method Bio.Mindy.BerkeleyDB.BerkeleyDB.close()=Bio.Mindy.BerkeleyDB.BerkeleyDB-class.html#close,Method Bio.Mindy.FlatDB.MemoryFlatDB.close()=Bio.Mindy.FlatDB.MemoryFlatDB-class.html#close,Method BioSQL.BioSeqDatabase.Adaptor.close()=BioSQL.BioSeqDatabase.Adaptor-class.html#close,Method Martel.Parser.Parser.close()=Martel.Parser.Parser-class.html#close,Method Martel.Parser.RecordParser.close()=Martel.Parser.RecordParser-class.html#close"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-19', 'close', 'link-19');">close</a></tt><tt class="py-op">(</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">return</tt> <tt class="py-op">[</tt><tt class="py-name">f_name</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">else</tt><tt class="py-op">:</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt id="link-20" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-20', 'name', 'link-14');">name</a></tt><tt class="py-op">,</tt> <tt class="py-name">rng</tt> <tt class="py-op">=</tt> <tt class="py-name">para_list</tt><tt class="py-op">[</tt><tt class="py-number">0</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">fnames</tt> <tt class="py-op">=</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-keyword">for</tt> <tt class="py-name">val</tt> <tt class="py-keyword">in</tt> <tt class="py-name">rng</tt><tt class="py-op">:</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt class="py-name">new_values</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">(</tt><tt id="link-21" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-21', 'name', 'link-14');">name</a></tt><tt class="py-op">,</tt> <tt class="py-name">val</tt><tt class="py-op">)</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">new_values</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.extend()=Bio.EUtils.POM.ElementNode-class.html#extend,Method Bio.SCOP.Raf.SeqMap.extend()=Bio.SCOP.Raf.SeqMap-class.html#extend,Method Bio.Seq.MutableSeq.extend()=Bio.Seq.MutableSeq-class.html#extend"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-22', 'extend', 'link-22');">extend</a></tt><tt class="py-op">(</tt><tt class="py-name">curr_values</tt><tt class="py-op">)</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> <tt class="py-name">more_names</tt> <tt class="py-op">=</tt> <tt id="link-23" class="py-name" targets="Function Bio.PopGen.SimCoal.Template.process_para()=Bio.PopGen.SimCoal.Template-module.html#process_para"><a title="Bio.PopGen.SimCoal.Template.process_para" class="py-name" href="#" onclick="return doclink('link-23', 'process_para', 'link-23');">process_para</a></tt><tt class="py-op">(</tt><tt class="py-name">in_string</tt><tt class="py-op">,</tt> <tt class="py-name">out_file_prefix</tt><tt class="py-op">,</tt> <tt class="py-name">para_list</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 class="py-name">new_values</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">fnames</tt><tt class="py-op">.</tt><tt id="link-24" class="py-name"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-24', 'extend', 'link-22');">extend</a></tt><tt class="py-op">(</tt><tt class="py-name">more_names</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">return</tt> <tt class="py-name">fnames</tt> </tt>
</div><a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> </tt>
<a name="dupe"></a><div id="dupe-def"><a name="L57"></a><tt class="py-lineno"> 57</tt> <a class="py-toggle" href="#" id="dupe-toggle" onclick="return toggle('dupe');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.SimCoal.Template-module.html#dupe">dupe</a><tt class="py-op">(</tt><tt class="py-param">motif</tt><tt class="py-op">,</tt> <tt class="py-param">times</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="dupe-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="dupe-expanded"><a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt class="py-name">ret_str</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-25" class="py-name" targets="Variable Bio.PDB.Polypeptide.i=Bio.PDB.Polypeptide-module.html#i"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-25', 'i', 'link-25');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">times</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-name">ret_str</tt> <tt class="py-op">+=</tt> <tt id="link-26" class="py-name" targets="Method Bio.AlignAce.Parser.AlignAceConsumer.motif()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#motif"><a title="Bio.AlignAce.Parser.AlignAceConsumer.motif" class="py-name" href="#" onclick="return doclink('link-26', 'motif', 'link-26');">motif</a></tt> <tt class="py-op">+</tt> <tt class="py-string">'\r\n'</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">ret_str</tt> </tt>
</div><a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> </tt>
<a name="get_xy_from_matrix"></a><div id="get_xy_from_matrix-def"><a name="L63"></a><tt class="py-lineno"> 63</tt> <a class="py-toggle" href="#" id="get_xy_from_matrix-toggle" onclick="return toggle('get_xy_from_matrix');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.SimCoal.Template-module.html#get_xy_from_matrix">get_xy_from_matrix</a><tt class="py-op">(</tt><tt class="py-param">x_max</tt><tt class="py-op">,</tt> <tt class="py-param">y_max</tt><tt class="py-op">,</tt> <tt class="py-param">pos</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="get_xy_from_matrix-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="get_xy_from_matrix-expanded"><a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-name">y</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">pos</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-name">x_max</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt id="link-27" class="py-name" targets="Variable Bio.MarkovModel.x=Bio.MarkovModel-module.html#x,Variable Bio.Statistics.lowess.x=Bio.Statistics.lowess-module.html#x"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-27', 'x', 'link-27');">x</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">pos</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-name">x_max</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-28" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-28', 'x', 'link-27');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">y</tt> </tt>
</div><a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> </tt>
<a name="get_step_2d"></a><div id="get_step_2d-def"><a name="L68"></a><tt class="py-lineno"> 68</tt> <a class="py-toggle" href="#" id="get_step_2d-toggle" onclick="return toggle('get_step_2d');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.SimCoal.Template-module.html#get_step_2d">get_step_2d</a><tt class="py-op">(</tt><tt class="py-param">x_max</tt><tt class="py-op">,</tt> <tt class="py-param">y_max</tt><tt class="py-op">,</tt> <tt class="py-param">x</tt><tt class="py-op">,</tt> <tt class="py-param">y</tt><tt class="py-op">,</tt> <tt class="py-param">mig</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="get_step_2d-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="get_step_2d-expanded"><a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt class="py-name">my_x</tt><tt class="py-op">,</tt> <tt class="py-name">my_y</tt> <tt class="py-op">=</tt> <tt id="link-29" class="py-name" targets="Function Bio.PopGen.SimCoal.Template.get_xy_from_matrix()=Bio.PopGen.SimCoal.Template-module.html#get_xy_from_matrix"><a title="Bio.PopGen.SimCoal.Template.get_xy_from_matrix" class="py-name" href="#" onclick="return doclink('link-29', 'get_xy_from_matrix', 'link-29');">get_xy_from_matrix</a></tt><tt class="py-op">(</tt><tt class="py-name">x_max</tt><tt class="py-op">,</tt> <tt class="py-name">y_max</tt><tt class="py-op">,</tt> <tt class="py-name">y</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">other_x</tt><tt class="py-op">,</tt> <tt class="py-name">other_y</tt> <tt class="py-op">=</tt> <tt id="link-30" class="py-name"><a title="Bio.PopGen.SimCoal.Template.get_xy_from_matrix" class="py-name" href="#" onclick="return doclink('link-30', 'get_xy_from_matrix', 'link-29');">get_xy_from_matrix</a></tt><tt class="py-op">(</tt><tt class="py-name">x_max</tt><tt class="py-op">,</tt> <tt class="py-name">y_max</tt><tt class="py-op">,</tt> <tt id="link-31" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-31', 'x', 'link-27');">x</a></tt><tt class="py-op">)</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt class="py-name">my_x</tt><tt class="py-op">-</tt><tt class="py-name">other_x</tt><tt class="py-op">)</tt><tt class="py-op">**</tt><tt class="py-number">2</tt> <tt class="py-op">+</tt> <tt class="py-op">(</tt><tt class="py-name">my_y</tt><tt class="py-op">-</tt><tt class="py-name">other_y</tt><tt class="py-op">)</tt><tt class="py-op">**</tt><tt class="py-number">2</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">mig</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">' '</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">'0 '</tt> </tt>
</div><a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> </tt>
<a name="generate_ssm2d_mat"></a><div id="generate_ssm2d_mat-def"><a name="L77"></a><tt class="py-lineno"> 77</tt> <a class="py-toggle" href="#" id="generate_ssm2d_mat-toggle" onclick="return toggle('generate_ssm2d_mat');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.SimCoal.Template-module.html#generate_ssm2d_mat">generate_ssm2d_mat</a><tt class="py-op">(</tt><tt class="py-param">x_max</tt><tt class="py-op">,</tt> <tt class="py-param">y_max</tt><tt class="py-op">,</tt> <tt class="py-param">mig</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="generate_ssm2d_mat-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="generate_ssm2d_mat-expanded"><a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-name">mig_mat</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-32" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-32', 'x', 'link-27');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">x_max</tt><tt class="py-op">*</tt><tt class="py-name">y_max</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">y</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">x_max</tt><tt class="py-op">*</tt><tt class="py-name">y_max</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-name">mig_mat</tt> <tt class="py-op">+=</tt> <tt id="link-33" class="py-name" targets="Function Bio.PopGen.SimCoal.Template.get_step_2d()=Bio.PopGen.SimCoal.Template-module.html#get_step_2d"><a title="Bio.PopGen.SimCoal.Template.get_step_2d" class="py-name" href="#" onclick="return doclink('link-33', 'get_step_2d', 'link-33');">get_step_2d</a></tt><tt class="py-op">(</tt><tt class="py-name">x_max</tt><tt class="py-op">,</tt> <tt class="py-name">y_max</tt><tt class="py-op">,</tt> <tt id="link-34" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-34', 'x', 'link-27');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">y</tt><tt class="py-op">,</tt> <tt class="py-name">mig</tt><tt class="py-op">)</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-name">mig_mat</tt> <tt class="py-op">+=</tt> <tt class="py-string">"\r\n"</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">mig_mat</tt> </tt>
</div><a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> </tt>
<a name="generate_island_mat"></a><div id="generate_island_mat-def"><a name="L85"></a><tt class="py-lineno"> 85</tt> <a class="py-toggle" href="#" id="generate_island_mat-toggle" onclick="return toggle('generate_island_mat');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.SimCoal.Template-module.html#generate_island_mat">generate_island_mat</a><tt class="py-op">(</tt><tt class="py-param">total_size</tt><tt class="py-op">,</tt> <tt class="py-param">mig</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="generate_island_mat-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="generate_island_mat-expanded"><a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-name">mig_mat</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-35" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-35', 'x', 'link-27');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">total_size</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">y</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">total_size</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt id="link-36" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-36', 'x', 'link-27');">x</a></tt> <tt class="py-op">==</tt> <tt class="py-name">y</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-name">mig_mat</tt> <tt class="py-op">+=</tt> <tt class="py-string">'0 '</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-name">mig_mat</tt> <tt class="py-op">+=</tt> <tt class="py-string">'!!!'</tt> <tt class="py-op">+</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">mig</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">'!!! '</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-name">mig_mat</tt> <tt class="py-op">+=</tt> <tt class="py-string">"\r\n"</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">mig_mat</tt> </tt>
</div><a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> </tt>
<a name="generate_null_mat"></a><div id="generate_null_mat-def"><a name="L96"></a><tt class="py-lineno"> 96</tt> <a class="py-toggle" href="#" id="generate_null_mat-toggle" onclick="return toggle('generate_null_mat');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.SimCoal.Template-module.html#generate_null_mat">generate_null_mat</a><tt class="py-op">(</tt><tt class="py-param">total_size</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="generate_null_mat-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="generate_null_mat-expanded"><a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-name">null_mat</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-37" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-37', 'x', 'link-27');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">total_size</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">y</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">total_size</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-name">null_mat</tt> <tt class="py-op">+=</tt> <tt class="py-string">'0 '</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-name">null_mat</tt> <tt class="py-op">+=</tt> <tt class="py-string">'\r\n'</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">null_mat</tt> </tt>
</div><a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> </tt>
<a name="generate_join_events"></a><div id="generate_join_events-def"><a name="L104"></a><tt class="py-lineno">104</tt> <a class="py-toggle" href="#" id="generate_join_events-toggle" onclick="return toggle('generate_join_events');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.SimCoal.Template-module.html#generate_join_events">generate_join_events</a><tt class="py-op">(</tt><tt class="py-param">t</tt><tt class="py-op">,</tt> <tt class="py-param">total_size</tt><tt class="py-op">,</tt> <tt class="py-param">join_size</tt><tt class="py-op">,</tt> <tt class="py-param">orig_size</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="generate_join_events-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="generate_join_events-expanded"><a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-name">events</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-38" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-38', 'i', 'link-25');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">total_size</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-name">events</tt> <tt class="py-op">+=</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">' '</tt> <tt class="py-op">+</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-39" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-39', 'i', 'link-25');">i</a></tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">' 0 1 1 0 1\r\n'</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-name">events</tt> <tt class="py-op">+=</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">' '</tt> <tt class="py-op">+</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">total_size</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-string">' 0 1 '</tt> <tt class="py-op">+</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-number">1.0</tt><tt class="py-op">*</tt><tt class="py-name">total_size</tt><tt class="py-op">*</tt><tt class="py-name">join_size</tt><tt class="py-op">/</tt><tt class="py-name">orig_size</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">' 0 1\r\n'</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">events</tt> </tt>
</div><a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> </tt>
<a name="no_processor"></a><div id="no_processor-def"><a name="L111"></a><tt class="py-lineno">111</tt> <a class="py-toggle" href="#" id="no_processor-toggle" onclick="return toggle('no_processor');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.SimCoal.Template-module.html#no_processor">no_processor</a><tt class="py-op">(</tt><tt class="py-param">in_string</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="no_processor-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="no_processor-expanded"><a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">in_string</tt> </tt>
</div><a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> </tt>
<a name="process_text"></a><div id="process_text-def"><a name="L114"></a><tt class="py-lineno">114</tt> <a class="py-toggle" href="#" id="process_text-toggle" onclick="return toggle('process_text');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.SimCoal.Template-module.html#process_text">process_text</a><tt class="py-op">(</tt><tt class="py-param">in_string</tt><tt class="py-op">,</tt> <tt class="py-param">out_file_prefix</tt><tt class="py-op">,</tt> <tt class="py-param">para_list</tt><tt class="py-op">,</tt> <tt class="py-param">curr_values</tt><tt class="py-op">,</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-param">specific_processor</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="process_text-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="process_text-expanded"><a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt id="link-40" 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-40', 'text', 'link-40');">text</a></tt> <tt class="py-op">=</tt> <tt class="py-name">specific_processor</tt><tt class="py-op">(</tt><tt class="py-name">in_string</tt><tt class="py-op">)</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-41" class="py-name"><a title="Bio.PopGen.SimCoal.Template.process_para" class="py-name" href="#" onclick="return doclink('link-41', 'process_para', 'link-23');">process_para</a></tt><tt class="py-op">(</tt><tt id="link-42" 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-42', 'text', 'link-40');">text</a></tt><tt class="py-op">,</tt> <tt class="py-name">out_file_prefix</tt><tt class="py-op">,</tt> <tt class="py-name">para_list</tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
</div><a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"><tt class="py-comment">#def prepare_dir():</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># try:</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># mkdir(sep.join([Config.dataDir, 'SimCoal'])) #Should exist, but...</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># except OSError:</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># pass #Its ok if already exists</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># try:</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># mkdir(sep.join([Config.dataDir, 'SimCoal', 'runs']))</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># except OSError:</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># pass #Its ok if already exists</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"><tt class="py-comment">#sep is because of jython</tt> </tt>
<a name="generate_model"></a><div id="generate_model-def"><a name="L131"></a><tt class="py-lineno">131</tt> <a class="py-toggle" href="#" id="generate_model-toggle" onclick="return toggle('generate_model');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.SimCoal.Template-module.html#generate_model">generate_model</a><tt class="py-op">(</tt><tt class="py-param">par_stream</tt><tt class="py-op">,</tt> <tt class="py-param">out_prefix</tt><tt class="py-op">,</tt> <tt class="py-param">params</tt><tt class="py-op">,</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-param">specific_processor</tt> <tt class="py-op">=</tt> <tt id="link-43" class="py-name" targets="Function Bio.PopGen.SimCoal.Template.no_processor()=Bio.PopGen.SimCoal.Template-module.html#no_processor"><a title="Bio.PopGen.SimCoal.Template.no_processor" class="py-name" href="#" onclick="return doclink('link-43', 'no_processor', 'link-43');">no_processor</a></tt><tt class="py-op">,</tt> <tt class="py-param">out_dir</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="generate_model-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="generate_model-expanded"><a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-comment">#prepare_dir()</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-44" 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-44', 'text', 'link-40');">text</a></tt> <tt class="py-op">=</tt> <tt class="py-name">par_stream</tt><tt class="py-op">.</tt><tt id="link-45" class="py-name" targets="Method Bio.AlignAce.Motif.Motif.read()=Bio.AlignAce.Motif.Motif-class.html#read,Function Bio.AlignIO.read()=Bio.AlignIO-module.html#read,Function Bio.Cluster.read()=Bio.Cluster-module.html#read,Method Bio.EUtils.ReseekFile.ReseekFile.read()=Bio.EUtils.ReseekFile.ReseekFile-class.html#read,Function Bio.Entrez.read()=Bio.Entrez-module.html#read,Method Bio.File.SGMLHandle.read()=Bio.File.SGMLHandle-class.html#read,Method Bio.File.UndoHandle.read()=Bio.File.UndoHandle-class.html#read,Method Bio.FilteredReader.FilteredReader.read()=Bio.FilteredReader.FilteredReader-class.html#read,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.read()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#read,Method Bio.Nexus.Nexus.Nexus.read()=Bio.Nexus.Nexus.Nexus-class.html#read,Function Bio.Prosite.Prodoc.read()=Bio.Prosite.Prodoc-module.html#read,Function Bio.Prosite.read()=Bio.Prosite-module.html#read,Method Bio.SGMLExtractor.SGMLExtractorHandle.read()=Bio.SGMLExtractor.SGMLExtractorHandle-class.html#read,Function Bio.SeqIO.read()=Bio.SeqIO-module.html#read,Function Bio.SwissProt.read()=Bio.SwissProt-module.html#read"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-45', 'read', 'link-45');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt class="py-name">out_file_prefix</tt> <tt class="py-op">=</tt> <tt class="py-name">sep</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">out_dir</tt><tt class="py-op">,</tt> <tt class="py-name">out_prefix</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-46" class="py-name" targets="Function Bio.PopGen.SimCoal.Template.process_text()=Bio.PopGen.SimCoal.Template-module.html#process_text"><a title="Bio.PopGen.SimCoal.Template.process_text" class="py-name" href="#" onclick="return doclink('link-46', 'process_text', 'link-46');">process_text</a></tt><tt class="py-op">(</tt><tt id="link-47" 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-47', 'text', 'link-40');">text</a></tt><tt class="py-op">,</tt> <tt class="py-name">out_file_prefix</tt><tt class="py-op">,</tt> <tt class="py-name">params</tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">specific_processor</tt><tt class="py-op">)</tt> </tt>
</div><a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> </tt>
<a name="get_demography_template"></a><div id="get_demography_template-def"><a name="L139"></a><tt class="py-lineno">139</tt> <a class="py-toggle" href="#" id="get_demography_template-toggle" onclick="return toggle('get_demography_template');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.SimCoal.Template-module.html#get_demography_template">get_demography_template</a><tt class="py-op">(</tt><tt class="py-param">stream</tt><tt class="py-op">,</tt> <tt class="py-param">model</tt><tt class="py-op">,</tt> <tt class="py-param">tp_dir</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="get_demography_template-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="get_demography_template-expanded"><a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"><tt class="py-docstring"> Gets a demograpy template.</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"><tt class="py-docstring"> Most probably this model needs to be sent to GenCases.</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"><tt class="py-docstring"> stream - Writable stream.</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"><tt class="py-docstring"> param - Template file.</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"><tt class="py-docstring"> tp_dir - Directory where to find the template, if None</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"><tt class="py-docstring"> use an internal template</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">tp_dir</tt> <tt class="py-op">==</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-comment">#Internal Template</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt id="link-48" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-48', 'open', 'link-16');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">sep</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt id="link-49" class="py-name"><a title="Bio.PopGen.SimCoal.builtin_tpl_dir" class="py-name" href="#" onclick="return doclink('link-49', 'builtin_tpl_dir', 'link-4');">builtin_tpl_dir</a></tt><tt class="py-op">,</tt> <tt class="py-name">model</tt> <tt class="py-op">+</tt> <tt class="py-string">'.par'</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">'r'</tt><tt class="py-op">)</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-comment">#External template</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt id="link-50" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-50', 'open', 'link-16');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">sep</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">tp_dir</tt><tt class="py-op">,</tt> <tt class="py-name">model</tt> <tt class="py-op">+</tt> <tt class="py-string">'.par'</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">'r'</tt><tt class="py-op">)</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-name">l</tt> <tt class="py-op">=</tt> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-51" class="py-name" targets="Method Bio.EUtils.ReseekFile.ReseekFile.readline()=Bio.EUtils.ReseekFile.ReseekFile-class.html#readline,Method Bio.File.SGMLHandle.readline()=Bio.File.SGMLHandle-class.html#readline,Method Bio.File.UndoHandle.readline()=Bio.File.UndoHandle-class.html#readline,Method Bio.SGMLExtractor.SGMLExtractorHandle.readline()=Bio.SGMLExtractor.SGMLExtractorHandle-class.html#readline"><a title="Bio.EUtils.ReseekFile.ReseekFile.readline
Bio.File.SGMLHandle.readline
Bio.File.UndoHandle.readline
Bio.SGMLExtractor.SGMLExtractorHandle.readline" class="py-name" href="#" onclick="return doclink('link-51', 'readline', 'link-51');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-name">l</tt><tt class="py-op"><></tt><tt class="py-string">''</tt><tt class="py-op">:</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt class="py-name">stream</tt><tt class="py-op">.</tt><tt id="link-52" class="py-name"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-52', 'write', 'link-18');">write</a></tt><tt class="py-op">(</tt><tt class="py-name">l</tt><tt class="py-op">)</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-name">l</tt> <tt class="py-op">=</tt> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-53" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.readline
Bio.File.SGMLHandle.readline
Bio.File.UndoHandle.readline
Bio.SGMLExtractor.SGMLExtractorHandle.readline" class="py-name" href="#" onclick="return doclink('link-53', 'readline', 'link-51');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-54" class="py-name"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-54', 'close', 'link-19');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> </tt>
<a name="_gen_loci"></a><div id="_gen_loci-def"><a name="L162"></a><tt class="py-lineno">162</tt> <a class="py-toggle" href="#" id="_gen_loci-toggle" onclick="return toggle('_gen_loci');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.SimCoal.Template-module.html#_gen_loci">_gen_loci</a><tt class="py-op">(</tt><tt class="py-param">stream</tt><tt class="py-op">,</tt> <tt class="py-param">loci</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_gen_loci-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_gen_loci-expanded"><a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt class="py-name">stream</tt><tt class="py-op">.</tt><tt id="link-55" class="py-name"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-55', 'write', 'link-18');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">'//Number of contiguous linkage blocks in chromosome\n'</tt><tt class="py-op">)</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-name">stream</tt><tt class="py-op">.</tt><tt id="link-56" class="py-name"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-56', 'write', 'link-18');">write</a></tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">loci</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">'\n'</tt><tt class="py-op">)</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-name">stream</tt><tt class="py-op">.</tt><tt id="link-57" class="py-name"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-57', 'write', 'link-18');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">'//Per Block: Data type, No. of loci, Recombination rate to the right-side locus, plus optional parameters\n'</tt><tt class="py-op">)</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-58" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.locus()=Bio.GenBank._FeatureConsumer-class.html#locus,Method Bio.GenBank._RecordConsumer.locus()=Bio.GenBank._RecordConsumer-class.html#locus,Variable Bio.expressions.genbank.locus=Bio.expressions.genbank-module.html#locus"><a title="Bio.GenBank._FeatureConsumer.locus
Bio.GenBank._RecordConsumer.locus
Bio.expressions.genbank.locus" class="py-name" href="#" onclick="return doclink('link-58', 'locus', 'link-58');">locus</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">loci</tt><tt class="py-op">:</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt class="py-name">stream</tt><tt class="py-op">.</tt><tt id="link-59" class="py-name"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-59', 'write', 'link-18');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">' '</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt id="link-60" class="py-name"><a title="Bio.GenBank._FeatureConsumer.locus
Bio.GenBank._RecordConsumer.locus
Bio.expressions.genbank.locus" class="py-name" href="#" onclick="return doclink('link-60', 'locus', 'link-58');">locus</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> <tt id="link-61" class="py-name" targets="Method Bio.GFF.FeatureAggregate.map()=Bio.GFF.FeatureAggregate-class.html#map"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-61', 'map', 'link-61');">map</a></tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-62" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-62', 'x', 'link-27');">x</a></tt><tt class="py-op">:</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-63" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-63', 'x', 'link-27');">x</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-64" 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-64', 'list', 'link-64');">list</a></tt><tt class="py-op">(</tt><tt id="link-65" class="py-name"><a title="Bio.GenBank._FeatureConsumer.locus
Bio.GenBank._RecordConsumer.locus
Bio.expressions.genbank.locus" class="py-name" href="#" onclick="return doclink('link-65', 'locus', 'link-58');">locus</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">'\n'</tt><tt class="py-op">)</tt> </tt>
</div><a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> </tt>
<a name="get_chr_template"></a><div id="get_chr_template-def"><a name="L171"></a><tt class="py-lineno">171</tt> <a class="py-toggle" href="#" id="get_chr_template-toggle" onclick="return toggle('get_chr_template');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.SimCoal.Template-module.html#get_chr_template">get_chr_template</a><tt class="py-op">(</tt><tt class="py-param">stream</tt><tt class="py-op">,</tt> <tt class="py-param">chrs</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="get_chr_template-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="get_chr_template-expanded"><a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"><tt class="py-docstring"> Writes a Simcoal2 loci template part.</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"><tt class="py-docstring"> stream - Writable stream.</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"><tt class="py-docstring"> chr - Chromosome list.</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"><tt class="py-docstring"> Current loci list:</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"><tt class="py-docstring"> [(chr_repeats,[(marker, (params))])]</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"><tt class="py-docstring"> chr_repeats --> Number of chromosome repeats</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"><tt class="py-docstring"> marker --> 'SNP', 'DNA', 'RFLP', 'MICROSAT'</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"><tt class="py-docstring"> params --> Simcoal2 parameters for markers (list of floats</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"><tt class="py-docstring"> or ints - if to be processed by generate_model)</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-name">num_chrs</tt> <tt class="py-op">=</tt> <tt class="py-name">reduce</tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-66" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-66', 'x', 'link-27');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">y</tt><tt class="py-op">:</tt> <tt id="link-67" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-67', 'x', 'link-27');">x</a></tt> <tt class="py-op">+</tt> <tt class="py-name">y</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">chrs</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> <tt class="py-name">stream</tt><tt class="py-op">.</tt><tt id="link-68" class="py-name"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-68', 'write', 'link-18');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">'//Number of independent (unlinked) chromosomes, and "chromosome structure" flag: 0 for identical structure across chromosomes, and 1 for different structures on different chromosomes.\n'</tt><tt class="py-op">)</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</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">chrs</tt><tt class="py-op">)</tt> <tt class="py-op">></tt> <tt class="py-number">1</tt> <tt class="py-keyword">or</tt> <tt class="py-name">num_chrs</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> <tt class="py-name">stream</tt><tt class="py-op">.</tt><tt id="link-69" class="py-name"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-69', 'write', 'link-18');">write</a></tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">num_chrs</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">' 1\n'</tt><tt class="py-op">)</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt class="py-name">stream</tt><tt class="py-op">.</tt><tt id="link-70" class="py-name"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-70', 'write', 'link-18');">write</a></tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">num_chrs</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">' 0\n'</tt><tt class="py-op">)</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">chr</tt> <tt class="py-keyword">in</tt> <tt class="py-name">chrs</tt><tt class="py-op">:</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-name">repeats</tt> <tt class="py-op">=</tt> <tt class="py-name">chr</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-name">loci</tt> <tt class="py-op">=</tt> <tt class="py-name">chr</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</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">chrs</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="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt id="link-71" class="py-name" targets="Function Bio.PopGen.SimCoal.Template._gen_loci()=Bio.PopGen.SimCoal.Template-module.html#_gen_loci"><a title="Bio.PopGen.SimCoal.Template._gen_loci" class="py-name" href="#" onclick="return doclink('link-71', '_gen_loci', 'link-71');">_gen_loci</a></tt><tt class="py-op">(</tt><tt class="py-name">stream</tt><tt class="py-op">,</tt> <tt class="py-name">loci</tt><tt class="py-op">)</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-72" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-72', 'i', 'link-25');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">repeats</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt id="link-73" class="py-name"><a title="Bio.PopGen.SimCoal.Template._gen_loci" class="py-name" href="#" onclick="return doclink('link-73', '_gen_loci', 'link-71');">_gen_loci</a></tt><tt class="py-op">(</tt><tt class="py-name">stream</tt><tt class="py-op">,</tt> <tt class="py-name">loci</tt><tt class="py-op">)</tt> </tt>
</div><a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> </tt>
<a name="generate_simcoal_from_template"></a><div id="generate_simcoal_from_template-def"><a name="L200"></a><tt class="py-lineno">200</tt> <a class="py-toggle" href="#" id="generate_simcoal_from_template-toggle" onclick="return toggle('generate_simcoal_from_template');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.SimCoal.Template-module.html#generate_simcoal_from_template">generate_simcoal_from_template</a><tt class="py-op">(</tt><tt class="py-param">model</tt><tt class="py-op">,</tt> <tt class="py-param">chrs</tt><tt class="py-op">,</tt> <tt class="py-param">params</tt><tt class="py-op">,</tt> <tt class="py-param">out_dir</tt> <tt class="py-op">=</tt> <tt class="py-string">'.'</tt><tt class="py-op">,</tt> <tt class="py-param">tp_dir</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="generate_simcoal_from_template-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="generate_simcoal_from_template-expanded"><a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"><tt class="py-docstring"> Writes a complete SimCoal2 template file.</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"><tt class="py-docstring"> This joins together get_demography_template and get_chr_template,</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"><tt class="py-docstring"> which are feed into generate_model</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"><tt class="py-docstring"> Please check the three functions for parameters (model from</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"><tt class="py-docstring"> get_demography_template, chrs from get_chr_template and</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"><tt class="py-docstring"> params from generate_model).</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> <tt class="py-name">stream</tt> <tt class="py-op">=</tt> <tt id="link-74" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-74', 'open', 'link-16');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">out_dir</tt> <tt class="py-op">+</tt> <tt class="py-name">sep</tt> <tt class="py-op">+</tt> <tt class="py-string">'tmp.par'</tt><tt class="py-op">,</tt> <tt class="py-string">'w'</tt><tt class="py-op">)</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt id="link-75" class="py-name" targets="Function Bio.PopGen.SimCoal.Template.get_demography_template()=Bio.PopGen.SimCoal.Template-module.html#get_demography_template"><a title="Bio.PopGen.SimCoal.Template.get_demography_template" class="py-name" href="#" onclick="return doclink('link-75', 'get_demography_template', 'link-75');">get_demography_template</a></tt><tt class="py-op">(</tt><tt class="py-name">stream</tt><tt class="py-op">,</tt> <tt class="py-name">model</tt><tt class="py-op">,</tt> <tt class="py-name">tp_dir</tt><tt class="py-op">)</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> <tt id="link-76" class="py-name" targets="Function Bio.PopGen.SimCoal.Template.get_chr_template()=Bio.PopGen.SimCoal.Template-module.html#get_chr_template"><a title="Bio.PopGen.SimCoal.Template.get_chr_template" class="py-name" href="#" onclick="return doclink('link-76', 'get_chr_template', 'link-76');">get_chr_template</a></tt><tt class="py-op">(</tt><tt class="py-name">stream</tt><tt class="py-op">,</tt> <tt class="py-name">chrs</tt><tt class="py-op">)</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-name">stream</tt><tt class="py-op">.</tt><tt id="link-77" class="py-name"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-77', 'close', 'link-19');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt class="py-comment">#par_stream = open(out_dir + sep + 'tmp.par', 'r')</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#print par_stream.read()</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#par_stream.close()</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">par_stream</tt> <tt class="py-op">=</tt> <tt id="link-78" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-78', 'open', 'link-16');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">out_dir</tt> <tt class="py-op">+</tt> <tt class="py-name">sep</tt> <tt class="py-op">+</tt> <tt class="py-string">'tmp.par'</tt><tt class="py-op">,</tt> <tt class="py-string">'r'</tt><tt class="py-op">)</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt id="link-79" class="py-name" targets="Function Bio.PopGen.SimCoal.Template.generate_model()=Bio.PopGen.SimCoal.Template-module.html#generate_model"><a title="Bio.PopGen.SimCoal.Template.generate_model" class="py-name" href="#" onclick="return doclink('link-79', 'generate_model', 'link-79');">generate_model</a></tt><tt class="py-op">(</tt><tt class="py-name">par_stream</tt><tt class="py-op">,</tt> <tt class="py-name">model</tt><tt class="py-op">,</tt> <tt class="py-name">params</tt><tt class="py-op">,</tt> <tt class="py-name">out_dir</tt> <tt class="py-op">=</tt> <tt class="py-name">out_dir</tt><tt class="py-op">)</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> <tt class="py-name">par_stream</tt><tt class="py-op">.</tt><tt id="link-80" class="py-name"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-80', 'close', 'link-19');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> </tt><script type="text/javascript">
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