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Module FastaIO
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<h1 class="epydoc">Source Code for <a href="Bio.SeqIO.FastaIO-module.html">Module Bio.SeqIO.FastaIO</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 2006-2009 by Peter Cock. All rights reserved.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><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"># 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-comment"># This module is for reading and writing FASTA format files as SeqRecord</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-comment"># objects. The code is partly inspired by earlier Biopython modules,</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-comment"># Bio.Fasta.* and the now deprecated Bio.SeqIO.FASTA</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring">"""Bio.SeqIO support for the "fasta" (aka FastA or Pearson) file format.</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring">You are expected to use this module via the Bio.SeqIO functions."""</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Package Bio.Alphabet=Bio.Alphabet-module.html,Class Bio.Alphabet.Alphabet=Bio.Alphabet.Alphabet-class.html"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-1', 'Alphabet', 'link-1');">Alphabet</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name" targets="Variable Bio.Alphabet.single_letter_alphabet=Bio.Alphabet-module.html#single_letter_alphabet"><a title="Bio.Alphabet.single_letter_alphabet" class="py-name" href="#" onclick="return doclink('link-2', 'single_letter_alphabet', 'link-2');">single_letter_alphabet</a></tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-3" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-3', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Module Bio.Seq=Bio.Seq-module.html,Class Bio.Seq.Seq=Bio.Seq.Seq-class.html"><a title="Bio.Seq
Bio.Seq.Seq" class="py-name" href="#" onclick="return doclink('link-4', 'Seq', 'link-4');">Seq</a></tt> <tt class="py-keyword">import</tt> <tt id="link-5" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq" class="py-name" href="#" onclick="return doclink('link-5', 'Seq', 'link-4');">Seq</a></tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-6" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-6', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-7" class="py-name" targets="Module Bio.SeqRecord=Bio.SeqRecord-module.html,Class Bio.SeqRecord.SeqRecord=Bio.SeqRecord.SeqRecord-class.html"><a title="Bio.SeqRecord
Bio.SeqRecord.SeqRecord" class="py-name" href="#" onclick="return doclink('link-7', 'SeqRecord', 'link-7');">SeqRecord</a></tt> <tt class="py-keyword">import</tt> <tt id="link-8" class="py-name"><a title="Bio.SeqRecord
Bio.SeqRecord.SeqRecord" class="py-name" href="#" onclick="return doclink('link-8', 'SeqRecord', 'link-7');">SeqRecord</a></tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-9" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-9', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-10" class="py-name" targets="Package Bio.SeqIO=Bio.SeqIO-module.html"><a title="Bio.SeqIO" class="py-name" href="#" onclick="return doclink('link-10', 'SeqIO', 'link-10');">SeqIO</a></tt><tt class="py-op">.</tt><tt id="link-11" class="py-name" targets="Module Bio.AlignIO.Interfaces=Bio.AlignIO.Interfaces-module.html,Module Bio.SeqIO.Interfaces=Bio.SeqIO.Interfaces-module.html"><a title="Bio.AlignIO.Interfaces
Bio.SeqIO.Interfaces" class="py-name" href="#" onclick="return doclink('link-11', 'Interfaces', 'link-11');">Interfaces</a></tt> <tt class="py-keyword">import</tt> <tt id="link-12" class="py-name" targets="Class Bio.SeqIO.Interfaces.SequentialSequenceWriter=Bio.SeqIO.Interfaces.SequentialSequenceWriter-class.html"><a title="Bio.SeqIO.Interfaces.SequentialSequenceWriter" class="py-name" href="#" onclick="return doclink('link-12', 'SequentialSequenceWriter', 'link-12');">SequentialSequenceWriter</a></tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-comment">#This is a generator function!</tt> </tt>
<a name="FastaIterator"></a><div id="FastaIterator-def"><a name="L20"></a><tt class="py-lineno"> 20</tt> <a class="py-toggle" href="#" id="FastaIterator-toggle" onclick="return toggle('FastaIterator');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqIO.FastaIO-module.html#FastaIterator">FastaIterator</a><tt class="py-op">(</tt><tt class="py-param">handle</tt><tt class="py-op">,</tt> <tt class="py-param">alphabet</tt> <tt class="py-op">=</tt> <tt id="link-13" class="py-name"><a title="Bio.Alphabet.single_letter_alphabet" class="py-name" href="#" onclick="return doclink('link-13', 'single_letter_alphabet', 'link-2');">single_letter_alphabet</a></tt><tt class="py-op">,</tt> <tt class="py-param">title2ids</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="FastaIterator-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="FastaIterator-expanded"><a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"> <tt class="py-docstring">"""Generator function to iterate over Fasta records (as SeqRecord objects).</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring"> handle - input file</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring"> alphabet - optional alphabet</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring"> title2ids - A function that, when given the title of the FASTA</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring"> file (without the beginning >), will return the id, name and</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring"> description (in that order) for the record as a tuple of strings.</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"> If this is not given, then the entire title line will be used</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring"> as the description, and the first word as the id and name.</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-docstring"> Note that use of title2ids matches that of Bio.Fasta.SequenceParser</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-docstring"> but the defaults are slightly different.</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> <tt class="py-comment">#Skip any text before the first record (e.g. blank lines, comments)</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-name">True</tt><tt class="py-op">:</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt id="link-14" class="py-name" targets="Variable Bio.UniGene.UniGene.handle=Bio.UniGene.UniGene-module.html#handle"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-14', 'handle', 'link-14');">handle</a></tt><tt class="py-op">.</tt><tt id="link-15" class="py-name" targets="Method Bio.File.UndoHandle.readline()=Bio.File.UndoHandle-class.html#readline"><a title="Bio.File.UndoHandle.readline" class="py-name" href="#" onclick="return doclink('link-15', 'readline', 'link-15');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt> <tt class="py-op">==</tt> <tt class="py-string">""</tt> <tt class="py-op">:</tt> <tt class="py-keyword">return</tt> <tt class="py-comment">#Premature end of file, or just empty?</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</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="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-name">True</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">if</tt> <tt class="py-name">line</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="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Records in Fasta files should start with '>' character"</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-name">title2ids</tt><tt class="py-op">:</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt id="link-16" class="py-name" targets="Method Bio.Phylo.PhyloXMLIO.Parser.id()=Bio.Phylo.PhyloXMLIO.Parser-class.html#id,Method Bio.Phylo.PhyloXMLIO.Writer.id()=Bio.Phylo.PhyloXMLIO.Writer-class.html#id"><a title="Bio.Phylo.PhyloXMLIO.Parser.id
Bio.Phylo.PhyloXMLIO.Writer.id" class="py-name" href="#" onclick="return doclink('link-16', 'id', 'link-16');">id</a></tt><tt class="py-op">,</tt> <tt id="link-17" class="py-name" targets="Method Bio.Phylo.PhyloXMLIO.Writer.name()=Bio.Phylo.PhyloXMLIO.Writer-class.html#name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-17', 'name', 'link-17');">name</a></tt><tt class="py-op">,</tt> <tt class="py-name">descr</tt> <tt class="py-op">=</tt> <tt class="py-name">title2ids</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name" targets="Method Bio.Seq.Seq.rstrip()=Bio.Seq.Seq-class.html#rstrip"><a title="Bio.Seq.Seq.rstrip" class="py-name" href="#" onclick="return doclink('link-18', 'rstrip', 'link-18');">rstrip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-name">descr</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name"><a title="Bio.Seq.Seq.rstrip" class="py-name" href="#" onclick="return doclink('link-19', 'rstrip', 'link-18');">rstrip</a></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 id="link-20" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Parser.id
Bio.Phylo.PhyloXMLIO.Writer.id" class="py-name" href="#" onclick="return doclink('link-20', 'id', 'link-16');">id</a></tt> <tt class="py-op">=</tt> <tt class="py-name">descr</tt><tt class="py-op">.</tt><tt id="link-21" class="py-name" targets="Method Bio.Nexus.Trees.Tree.split()=Bio.Nexus.Trees.Tree-class.html#split,Method Bio.Phylo.BaseTree.TreeMixin.split()=Bio.Phylo.BaseTree.TreeMixin-class.html#split,Method Bio.Restriction.Restriction.RestrictionBatch.split()=Bio.Restriction.Restriction.RestrictionBatch-class.html#split,Method Bio.Seq.Seq.split()=Bio.Seq.Seq-class.html#split"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.split" class="py-name" href="#" onclick="return doclink('link-21', 'split', 'link-21');">split</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>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt id="link-22" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-22', 'name', 'link-17');">name</a></tt> <tt class="py-op">=</tt> <tt id="link-23" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Parser.id
Bio.Phylo.PhyloXMLIO.Writer.id" class="py-name" href="#" onclick="return doclink('link-23', 'id', 'link-16');">id</a></tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> <tt class="py-name">lines</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">line</tt> <tt class="py-op">=</tt> <tt id="link-24" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-24', 'handle', 'link-14');">handle</a></tt><tt class="py-op">.</tt><tt id="link-25" class="py-name"><a title="Bio.File.UndoHandle.readline" class="py-name" href="#" onclick="return doclink('link-25', 'readline', 'link-15');">readline</a></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-keyword">while</tt> <tt class="py-name">True</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">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">line</tt> <tt class="py-op">:</tt> <tt class="py-keyword">break</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</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 class="py-keyword">break</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-comment">#Remove trailing whitespace, and any internal spaces</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt class="py-comment">#(and any embedded \r which are possible in mangled files</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-comment">#when not opened in universal read lines mode)</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-name">lines</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name" targets="Method Bio.Align.MultipleSeqAlignment.append()=Bio.Align.MultipleSeqAlignment-class.html#append,Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-class.html#append,Method Bio.SCOP.Raf.SeqMap.append()=Bio.SCOP.Raf.SeqMap-class.html#append,Method Bio.Seq.MutableSeq.append()=Bio.Seq.MutableSeq-class.html#append,Method Bio.Wise.psw.Alignment.append()=Bio.Wise.psw.Alignment-class.html#append,Method Bio.Wise.psw.AlignmentColumn.append()=Bio.Wise.psw.AlignmentColumn-class.html#append"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-26', 'append', 'link-26');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-27" class="py-name"><a title="Bio.Seq.Seq.rstrip" class="py-name" href="#" onclick="return doclink('link-27', 'rstrip', 'link-18');">rstrip</a></tt><tt class="py-op">(</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">" "</tt><tt class="py-op">,</tt><tt class="py-string">""</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">"\r"</tt><tt class="py-op">,</tt><tt class="py-string">""</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">line</tt> <tt class="py-op">=</tt> <tt id="link-28" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-28', 'handle', 'link-14');">handle</a></tt><tt class="py-op">.</tt><tt id="link-29" class="py-name"><a title="Bio.File.UndoHandle.readline" class="py-name" href="#" onclick="return doclink('link-29', 'readline', 'link-15');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-comment">#Return the record and then continue...</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt id="link-30" class="py-name"><a title="Bio.SeqRecord
Bio.SeqRecord.SeqRecord" class="py-name" href="#" onclick="return doclink('link-30', 'SeqRecord', 'link-7');">SeqRecord</a></tt><tt class="py-op">(</tt><tt id="link-31" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq" class="py-name" href="#" onclick="return doclink('link-31', 'Seq', 'link-4');">Seq</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-name">lines</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">alphabet</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 id="link-32" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Parser.id
Bio.Phylo.PhyloXMLIO.Writer.id" class="py-name" href="#" onclick="return doclink('link-32', 'id', 'link-16');">id</a></tt> <tt class="py-op">=</tt> <tt id="link-33" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Parser.id
Bio.Phylo.PhyloXMLIO.Writer.id" class="py-name" href="#" onclick="return doclink('link-33', 'id', 'link-16');">id</a></tt><tt class="py-op">,</tt> <tt id="link-34" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-34', 'name', 'link-17');">name</a></tt> <tt class="py-op">=</tt> <tt id="link-35" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-35', 'name', 'link-17');">name</a></tt><tt class="py-op">,</tt> <tt id="link-36" class="py-name" targets="Method Bio.Blast.NCBIStandalone._DescriptionConsumer.description()=Bio.Blast.NCBIStandalone._DescriptionConsumer-class.html#description,Method Bio.Phylo.PhyloXMLIO.Writer.description()=Bio.Phylo.PhyloXMLIO.Writer-class.html#description"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description
Bio.Phylo.PhyloXMLIO.Writer.description" class="py-name" href="#" onclick="return doclink('link-36', 'description', 'link-36');">description</a></tt> <tt class="py-op">=</tt> <tt class="py-name">descr</tt><tt class="py-op">)</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">line</tt> <tt class="py-op">:</tt> <tt class="py-keyword">return</tt> <tt class="py-comment">#StopIteration</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">False</tt><tt class="py-op">,</tt> <tt class="py-string">"Should not reach this line"</tt> </tt>
</div><a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> </tt>
<a name="FastaWriter"></a><div id="FastaWriter-def"><a name="L70"></a><tt class="py-lineno"> 70</tt> <a class="py-toggle" href="#" id="FastaWriter-toggle" onclick="return toggle('FastaWriter');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.SeqIO.FastaIO.FastaWriter-class.html">FastaWriter</a><tt class="py-op">(</tt><tt class="py-base-class">SequentialSequenceWriter</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FastaWriter-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="FastaWriter-expanded"><a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-docstring">"""Class to write Fasta format files."""</tt> </tt>
<a name="FastaWriter.__init__"></a><div id="FastaWriter.__init__-def"><a name="L72"></a><tt class="py-lineno"> 72</tt> <a class="py-toggle" href="#" id="FastaWriter.__init__-toggle" onclick="return toggle('FastaWriter.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqIO.FastaIO.FastaWriter-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">handle</tt><tt class="py-op">,</tt> <tt class="py-param">wrap</tt><tt class="py-op">=</tt><tt class="py-number">60</tt><tt class="py-op">,</tt> <tt class="py-param">record2title</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="FastaWriter.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FastaWriter.__init__-expanded"><a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-docstring">"""Create a Fasta writer.</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"><tt class="py-docstring"> handle - Handle to an output file, e.g. as returned</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"><tt class="py-docstring"> by open(filename, "w")</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"><tt class="py-docstring"> wrap - Optional line length used to wrap sequence lines.</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"><tt class="py-docstring"> Defaults to wrapping the sequence at 60 characters</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"><tt class="py-docstring"> Use zero (or None) for no wrapping, giving a single</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"><tt class="py-docstring"> long line for the sequence.</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"><tt class="py-docstring"> record2title - Optional function to return the text to be</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"><tt class="py-docstring"> used for the title line of each record. By default the</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"><tt class="py-docstring"> a combination of the record.id and record.description</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"><tt class="py-docstring"> is used. If the record.description starts with the</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"><tt class="py-docstring"> record.id, then just the record.description is used.</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"><tt class="py-docstring"> You can either use:</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"><tt class="py-docstring"> myWriter = FastaWriter(open(filename,"w"))</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"><tt class="py-docstring"> writer.write_file(myRecords)</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"><tt class="py-docstring"> Or, follow the sequential file writer system, for example:</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"><tt class="py-docstring"> myWriter = FastaWriter(open(filename,"w"))</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"><tt class="py-docstring"> writer.write_header() # does nothing for Fasta files</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"><tt class="py-docstring"> ...</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"><tt class="py-docstring"> Multiple calls to writer.write_record() and/or writer.write_records()</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"><tt class="py-docstring"> ...</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"><tt class="py-docstring"> writer.write_footer() # does nothing for Fasta files</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"><tt class="py-docstring"> writer.close()</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt id="link-37" class="py-name"><a title="Bio.SeqIO.Interfaces.SequentialSequenceWriter" class="py-name" href="#" onclick="return doclink('link-37', 'SequentialSequenceWriter', 'link-12');">SequentialSequenceWriter</a></tt><tt class="py-op">.</tt><tt id="link-38" class="py-name" targets="Method Bio.Affy.CelFile.CelConsumer.__init__()=Bio.Affy.CelFile.CelConsumer-class.html#__init__,Method Bio.Affy.CelFile.CelParser.__init__()=Bio.Affy.CelFile.CelParser-class.html#__init__,Method Bio.Affy.CelFile.CelRecord.__init__()=Bio.Affy.CelFile.CelRecord-class.html#__init__,Method Bio.Affy.CelFile.CelScanner.__init__()=Bio.Affy.CelFile.CelScanner-class.html#__init__,Method Bio.Affy.CelFile.Record.__init__()=Bio.Affy.CelFile.Record-class.html#__init__,Method Bio.Align.AlignInfo.PSSM.__init__()=Bio.Align.AlignInfo.PSSM-class.html#__init__,Method Bio.Align.AlignInfo.SummaryInfo.__init__()=Bio.Align.AlignInfo.SummaryInfo-class.html#__init__,Method Bio.Align.Applications._Clustalw.ClustalwCommandline.__init__()=Bio.Align.Applications._Clustalw.ClustalwCommandline-class.html#__init__,Method Bio.Align.Applications._Dialign.DialignCommandline.__init__()=Bio.Align.Applications._Dialign.DialignCommandline-class.html#__init__,Method Bio.Align.Applications._Mafft.MafftCommandline.__init__()=Bio.Align.Applications._Mafft.MafftCommandline-class.html#__init__,Method Bio.Align.Applications._Muscle.MuscleCommandline.__init__()=Bio.Align.Applications._Muscle.MuscleCommandline-class.html#__init__,Method Bio.Align.Applications._Prank.PrankCommandline.__init__()=Bio.Align.Applications._Prank.PrankCommandline-class.html#__init__,Method Bio.Align.Applications._Probcons.ProbconsCommandline.__init__()=Bio.Align.Applications._Probcons.ProbconsCommandline-class.html#__init__,Method Bio.Align.Applications._TCoffee.TCoffeeCommandline.__init__()=Bio.Align.Applications._TCoffee.TCoffeeCommandline-class.html#__init__,Method Bio.Align.Generic.Alignment.__init__()=Bio.Align.Generic.Alignment-class.html#__init__,Method Bio.Align.MultipleSeqAlignment.__init__()=Bio.Align.MultipleSeqAlignment-class.html#__init__,Method Bio.AlignIO.Interfaces.AlignmentIterator.__init__()=Bio.AlignIO.Interfaces.AlignmentIterator-class.html#__init__,Method Bio.AlignIO.Interfaces.AlignmentWriter.__init__()=Bio.AlignIO.Interfaces.AlignmentWriter-class.html#__init__,Method Bio.AlignIO.Interfaces.SequentialAlignmentWriter.__init__()=Bio.AlignIO.Interfaces.SequentialAlignmentWriter-class.html#__init__,Method Bio.Alphabet.AlphabetEncoder.__init__()=Bio.Alphabet.AlphabetEncoder-class.html#__init__,Method Bio.Alphabet.Gapped.__init__()=Bio.Alphabet.Gapped-class.html#__init__,Method Bio.Alphabet.HasStopCodon.__init__()=Bio.Alphabet.HasStopCodon-class.html#__init__,Method Bio.Application.AbstractCommandline.__init__()=Bio.Application.AbstractCommandline-class.html#__init__,Method Bio.Application.ApplicationError.__init__()=Bio.Application.ApplicationError-class.html#__init__,Method Bio.Application._AbstractParameter.__init__()=Bio.Application._AbstractParameter-class.html#__init__,Method Bio.Application._Argument.__init__()=Bio.Application._Argument-class.html#__init__,Method Bio.Application._Option.__init__()=Bio.Application._Option-class.html#__init__,Method Bio.Application._Switch.__init__()=Bio.Application._Switch-class.html#__init__,Method Bio.Blast.Applications.BlastallCommandline.__init__()=Bio.Blast.Applications.BlastallCommandline-class.html#__init__,Method Bio.Blast.Applications.BlastpgpCommandline.__init__()=Bio.Blast.Applications.BlastpgpCommandline-class.html#__init__,Method Bio.Blast.Applications.FastacmdCommandline.__init__()=Bio.Blast.Applications.FastacmdCommandline-class.html#__init__,Method Bio.Blast.Applications.NcbiblastformatterCommandline.__init__()=Bio.Blast.Applications.NcbiblastformatterCommandline-class.html#__init__,Method Bio.Blast.Applications.NcbiblastnCommandline.__init__()=Bio.Blast.Applications.NcbiblastnCommandline-class.html#__init__,Method Bio.Blast.Applications.NcbiblastpCommandline.__init__()=Bio.Blast.Applications.NcbiblastpCommandline-class.html#__init__,Method Bio.Blast.Applications.NcbiblastxCommandline.__init__()=Bio.Blast.Applications.NcbiblastxCommandline-class.html#__init__,Method Bio.Blast.Applications.NcbipsiblastCommandline.__init__()=Bio.Blast.Applications.NcbipsiblastCommandline-class.html#__init__,Method Bio.Blast.Applications.NcbirpsblastCommandline.__init__()=Bio.Blast.Applications.NcbirpsblastCommandline-class.html#__init__,Method Bio.Blast.Applications.NcbirpstblastnCommandline.__init__()=Bio.Blast.Applications.NcbirpstblastnCommandline-class.html#__init__,Method Bio.Blast.Applications.NcbitblastnCommandline.__init__()=Bio.Blast.Applications.NcbitblastnCommandline-class.html#__init__,Method Bio.Blast.Applications.NcbitblastxCommandline.__init__()=Bio.Blast.Applications.NcbitblastxCommandline-class.html#__init__,Method Bio.Blast.Applications.RpsBlastCommandline.__init__()=Bio.Blast.Applications.RpsBlastCommandline-class.html#__init__,Method Bio.Blast.Applications._BlastAllOrPgpCommandLine.__init__()=Bio.Blast.Applications._BlastAllOrPgpCommandLine-class.html#__init__,Method Bio.Blast.Applications._BlastCommandLine.__init__()=Bio.Blast.Applications._BlastCommandLine-class.html#__init__,Method Bio.Blast.Applications._NcbibaseblastCommandline.__init__()=Bio.Blast.Applications._NcbibaseblastCommandline-class.html#__init__,Method Bio.Blast.Applications._Ncbiblast2SeqCommandline.__init__()=Bio.Blast.Applications._Ncbiblast2SeqCommandline-class.html#__init__,Method Bio.Blast.Applications._NcbiblastCommandline.__init__()=Bio.Blast.Applications._NcbiblastCommandline-class.html#__init__,Method Bio.Blast.Applications._NcbiblastMain2SeqCommandline.__init__()=Bio.Blast.Applications._NcbiblastMain2SeqCommandline-class.html#__init__,Method Bio.Blast.NCBIStandalone.BlastErrorParser.__init__()=Bio.Blast.NCBIStandalone.BlastErrorParser-class.html#__init__,Method Bio.Blast.NCBIStandalone.BlastParser.__init__()=Bio.Blast.NCBIStandalone.BlastParser-class.html#__init__,Method Bio.Blast.NCBIStandalone.Iterator.__init__()=Bio.Blast.NCBIStandalone.Iterator-class.html#__init__,Method Bio.Blast.NCBIStandalone.PSIBlastParser.__init__()=Bio.Blast.NCBIStandalone.PSIBlastParser-class.html#__init__,Method Bio.Blast.NCBIStandalone._BlastConsumer.__init__()=Bio.Blast.NCBIStandalone._BlastConsumer-class.html#__init__,Method Bio.Blast.NCBIStandalone._BlastErrorConsumer.__init__()=Bio.Blast.NCBIStandalone._BlastErrorConsumer-class.html#__init__,Method Bio.Blast.NCBIStandalone._PSIBlastConsumer.__init__()=Bio.Blast.NCBIStandalone._PSIBlastConsumer-class.html#__init__,Method Bio.Blast.NCBIXML.BlastParser.__init__()=Bio.Blast.NCBIXML.BlastParser-class.html#__init__,Method Bio.Blast.NCBIXML._XMLparser.__init__()=Bio.Blast.NCBIXML._XMLparser-class.html#__init__,Method Bio.Blast.ParseBlastTable.BlastTableEntry.__init__()=Bio.Blast.ParseBlastTable.BlastTableEntry-class.html#__init__,Method Bio.Blast.ParseBlastTable.BlastTableReader.__init__()=Bio.Blast.ParseBlastTable.BlastTableReader-class.html#__init__,Method Bio.Blast.ParseBlastTable.BlastTableRec.__init__()=Bio.Blast.ParseBlastTable.BlastTableRec-class.html#__init__,Method Bio.Blast.Record.Alignment.__init__()=Bio.Blast.Record.Alignment-class.html#__init__,Method Bio.Blast.Record.Blast.__init__()=Bio.Blast.Record.Blast-class.html#__init__,Method Bio.Blast.Record.DatabaseReport.__init__()=Bio.Blast.Record.DatabaseReport-class.html#__init__,Method Bio.Blast.Record.Description.__init__()=Bio.Blast.Record.Description-class.html#__init__,Method Bio.Blast.Record.HSP.__init__()=Bio.Blast.Record.HSP-class.html#__init__,Method Bio.Blast.Record.Header.__init__()=Bio.Blast.Record.Header-class.html#__init__,Method Bio.Blast.Record.MultipleAlignment.__init__()=Bio.Blast.Record.MultipleAlignment-class.html#__init__,Method Bio.Blast.Record.PSIBlast.__init__()=Bio.Blast.Record.PSIBlast-class.html#__init__,Method Bio.Blast.Record.Parameters.__init__()=Bio.Blast.Record.Parameters-class.html#__init__,Method Bio.Blast.Record.Round.__init__()=Bio.Blast.Record.Round-class.html#__init__,Method Bio.CAPS.CAPSMap.__init__()=Bio.CAPS.CAPSMap-class.html#__init__,Method Bio.CAPS.DifferentialCutsite.__init__()=Bio.CAPS.DifferentialCutsite-class.html#__init__,Method Bio.Cluster.Record.__init__()=Bio.Cluster.Record-class.html#__init__,Method Bio.Compass.Iterator.__init__()=Bio.Compass.Iterator-class.html#__init__,Method Bio.Compass.Record.__init__()=Bio.Compass.Record-class.html#__init__,Method Bio.Compass.RecordParser.__init__()=Bio.Compass.RecordParser-class.html#__init__,Method Bio.Compass._Consumer.__init__()=Bio.Compass._Consumer-class.html#__init__,Method Bio.Compass._Scanner.__init__()=Bio.Compass._Scanner-class.html#__init__,Method Bio.Crystal.Chain.__init__()=Bio.Crystal.Chain-class.html#__init__,Method Bio.Crystal.Crystal.__init__()=Bio.Crystal.Crystal-class.html#__init__,Method Bio.Crystal.Hetero.__init__()=Bio.Crystal.Hetero-class.html#__init__,Method Bio.Data.CodonTable.AmbiguousCodonTable.__init__()=Bio.Data.CodonTable.AmbiguousCodonTable-class.html#__init__,Method Bio.Data.CodonTable.AmbiguousForwardTable.__init__()=Bio.Data.CodonTable.AmbiguousForwardTable-class.html#__init__,Method Bio.Data.CodonTable.CodonTable.__init__()=Bio.Data.CodonTable.CodonTable-class.html#__init__,Method Bio.Data.CodonTable.NCBICodonTable.__init__()=Bio.Data.CodonTable.NCBICodonTable-class.html#__init__,Method Bio.DocSQL.Create.__init__()=Bio.DocSQL.Create-class.html#__init__,Method Bio.DocSQL.Insert.__init__()=Bio.DocSQL.Insert-class.html#__init__,Method Bio.DocSQL.IterationCursor.__init__()=Bio.DocSQL.IterationCursor-class.html#__init__,Method Bio.DocSQL.Query.__init__()=Bio.DocSQL.Query-class.html#__init__,Method Bio.DocSQL.QueryAll.__init__()=Bio.DocSQL.QueryAll-class.html#__init__,Method Bio.DocSQL.QueryGeneric.__init__()=Bio.DocSQL.QueryGeneric-class.html#__init__,Method Bio.DocSQL.QueryRow.__init__()=Bio.DocSQL.QueryRow-class.html#__init__,Method Bio.DocSQL.QuerySingle.__init__()=Bio.DocSQL.QuerySingle-class.html#__init__,Method Bio.Emboss.Applications.DiffseqCommandline.__init__()=Bio.Emboss.Applications.DiffseqCommandline-class.html#__init__,Method Bio.Emboss.Applications.EInvertedCommandline.__init__()=Bio.Emboss.Applications.EInvertedCommandline-class.html#__init__,Method Bio.Emboss.Applications.ETandemCommandline.__init__()=Bio.Emboss.Applications.ETandemCommandline-class.html#__init__,Method Bio.Emboss.Applications.Est2GenomeCommandline.__init__()=Bio.Emboss.Applications.Est2GenomeCommandline-class.html#__init__,Method Bio.Emboss.Applications.FConsenseCommandline.__init__()=Bio.Emboss.Applications.FConsenseCommandline-class.html#__init__,Method Bio.Emboss.Applications.FDNADistCommandline.__init__()=Bio.Emboss.Applications.FDNADistCommandline-class.html#__init__,Method Bio.Emboss.Applications.FDNAParsCommandline.__init__()=Bio.Emboss.Applications.FDNAParsCommandline-class.html#__init__,Method Bio.Emboss.Applications.FNeighborCommandline.__init__()=Bio.Emboss.Applications.FNeighborCommandline-class.html#__init__,Method Bio.Emboss.Applications.FProtDistCommandline.__init__()=Bio.Emboss.Applications.FProtDistCommandline-class.html#__init__,Method Bio.Emboss.Applications.FProtParsCommandline.__init__()=Bio.Emboss.Applications.FProtParsCommandline-class.html#__init__,Method Bio.Emboss.Applications.FSeqBootCommandline.__init__()=Bio.Emboss.Applications.FSeqBootCommandline-class.html#__init__,Method Bio.Emboss.Applications.FTreeDistCommandline.__init__()=Bio.Emboss.Applications.FTreeDistCommandline-class.html#__init__,Method Bio.Emboss.Applications.FuzznucCommandline.__init__()=Bio.Emboss.Applications.FuzznucCommandline-class.html#__init__,Method Bio.Emboss.Applications.IepCommandline.__init__()=Bio.Emboss.Applications.IepCommandline-class.html#__init__,Method Bio.Emboss.Applications.NeedleCommandline.__init__()=Bio.Emboss.Applications.NeedleCommandline-class.html#__init__,Method Bio.Emboss.Applications.PalindromeCommandline.__init__()=Bio.Emboss.Applications.PalindromeCommandline-class.html#__init__,Method Bio.Emboss.Applications.Primer3Commandline.__init__()=Bio.Emboss.Applications.Primer3Commandline-class.html#__init__,Method 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Bio.Emboss.Applications.DiffseqCommandline.__init__
Bio.Emboss.Applications.EInvertedCommandline.__init__
Bio.Emboss.Applications.ETandemCommandline.__init__
Bio.Emboss.Applications.Est2GenomeCommandline.__init__
Bio.Emboss.Applications.FConsenseCommandline.__init__
Bio.Emboss.Applications.FDNADistCommandline.__init__
Bio.Emboss.Applications.FDNAParsCommandline.__init__
Bio.Emboss.Applications.FNeighborCommandline.__init__
Bio.Emboss.Applications.FProtDistCommandline.__init__
Bio.Emboss.Applications.FProtParsCommandline.__init__
Bio.Emboss.Applications.FSeqBootCommandline.__init__
Bio.Emboss.Applications.FTreeDistCommandline.__init__
Bio.Emboss.Applications.FuzznucCommandline.__init__
Bio.Emboss.Applications.IepCommandline.__init__
Bio.Emboss.Applications.NeedleCommandline.__init__
Bio.Emboss.Applications.PalindromeCommandline.__init__
Bio.Emboss.Applications.Primer3Commandline.__init__
Bio.Emboss.Applications.PrimerSearchCommandline.__init__
Bio.Emboss.Applications.SeqmatchallCommandline.__init__
Bio.Emboss.Applications.SeqretCommandline.__init__
Bio.Emboss.Applications.TranalignCommandline.__init__
Bio.Emboss.Applications.WaterCommandline.__init__
Bio.Emboss.Applications._EmbossCommandLine.__init__
Bio.Emboss.Applications._EmbossMinimalCommandLine.__init__
Bio.Emboss.Primer3.Primers.__init__
Bio.Emboss.Primer3.Record.__init__
Bio.Emboss.PrimerSearch.Amplifier.__init__
Bio.Emboss.PrimerSearch.InputRecord.__init__
Bio.Emboss.PrimerSearch.OutputRecord.__init__
Bio.Entrez.Parser.CorruptedXMLError.__init__
Bio.Entrez.Parser.DataHandler.__init__
Bio.Entrez.Parser.NotXMLError.__init__
Bio.Entrez.Parser.StructureElement.__init__
Bio.Entrez.Parser.ValidationError.__init__
Bio.ExPASy.Enzyme.Record.__init__
Bio.ExPASy.Prodoc.Record.__init__
Bio.ExPASy.Prodoc.Reference.__init__
Bio.ExPASy.Prosite.Record.__init__
Bio.ExPASy.ScanProsite.ContentHandler.__init__
Bio.ExPASy.ScanProsite.Parser.__init__
Bio.ExPASy.ScanProsite.Record.__init__
Bio.FSSP.FSSPAlignDict.__init__
Bio.FSSP.FSSPAlignRec.__init__
Bio.FSSP.FSSPHeader.__init__
Bio.FSSP.FSSPSumRec.__init__
Bio.FSSP.FSSPTools.FSSPMultAlign.__init__
Bio.FSSP.PosAlign.__init__
Bio.FSSP.fssp_rec.fff_rec.__init__
Bio.File.SGMLStripper.MyParser.__init__
Bio.File.SGMLStripper.__init__
Bio.File.UndoHandle.__init__
Bio.GA.Crossover.General.SafeFitnessCrossover.__init__
Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover.__init__
Bio.GA.Crossover.GeneralPoint.InterleaveCrossover.__init__
Bio.GA.Crossover.Point.SinglePointCrossover.__init__
Bio.GA.Crossover.TwoPoint.TwoPointCrossover.__init__
Bio.GA.Crossover.Uniform.UniformCrossover.__init__
Bio.GA.Evolver.GenerationEvolver.__init__
Bio.GA.Evolver.SteadyStateEvolver.__init__
Bio.GA.Mutation.General.SafeFitnessMutation.__init__
Bio.GA.Mutation.Simple.ConversionMutation.__init__
Bio.GA.Mutation.Simple.SinglePositionMutation.__init__
Bio.GA.Organism.Organism.__init__
Bio.GA.Repair.Stabilizing.AmbiguousRepair.__init__
Bio.GA.Selection.Abstract.AbstractSelection.__init__
Bio.GA.Selection.Diversity.DiversitySelection.__init__
Bio.GA.Selection.RouletteWheel.RouletteWheelSelection.__init__
Bio.GA.Selection.Tournament.TournamentSelection.__init__
Bio.GenBank.FeatureParser.__init__
Bio.GenBank.Iterator.__init__
Bio.GenBank.LocationParser.AbsoluteLocation.__init__
Bio.GenBank.LocationParser.Between.__init__
Bio.GenBank.LocationParser.FeatureName.__init__
Bio.GenBank.LocationParser.Function.__init__
Bio.GenBank.LocationParser.HighBound.__init__
Bio.GenBank.LocationParser.Integer.__init__
Bio.GenBank.LocationParser.LocationParser.__init__
Bio.GenBank.LocationParser.LocationScanner.__init__
Bio.GenBank.LocationParser.LowBound.__init__
Bio.GenBank.LocationParser.Path.__init__
Bio.GenBank.LocationParser.Range.__init__
Bio.GenBank.LocationParser.Symbol.__init__
Bio.GenBank.LocationParser.Token.__init__
Bio.GenBank.LocationParser.TwoBound.__init__
Bio.GenBank.Record.Feature.__init__
Bio.GenBank.Record.Qualifier.__init__
Bio.GenBank.Record.Record.__init__
Bio.GenBank.Record.Reference.__init__
Bio.GenBank.RecordParser.__init__
Bio.GenBank.Scanner.InsdcScanner.__init__
Bio.GenBank._BaseGenBankConsumer.__init__
Bio.GenBank._FeatureConsumer.__init__
Bio.GenBank._RecordConsumer.__init__
Bio.GenBank.utils.FeatureValueCleaner.__init__
Bio.Geo.Record.Record.__init__
Bio.Graphics.BasicChromosome.Chromosome.__init__
Bio.Graphics.BasicChromosome.ChromosomeSegment.__init__
Bio.Graphics.BasicChromosome.Organism.__init__
Bio.Graphics.BasicChromosome.TelomereSegment.__init__
Bio.Graphics.BasicChromosome._ChromosomeComponent.__init__
Bio.Graphics.Comparative.ComparativeScatterPlot.__init__
Bio.Graphics.DisplayRepresentation.ChromosomeCounts.__init__
Bio.Graphics.Distribution.BarChartDistribution.__init__
Bio.Graphics.Distribution.DistributionPage.__init__
Bio.Graphics.Distribution.LineDistribution.__init__
Bio.Graphics.GenomeDiagram._AbstractDrawer.AbstractDrawer.__init__
Bio.Graphics.GenomeDiagram._CircularDrawer.CircularDrawer.__init__
Bio.Graphics.GenomeDiagram._Colors.ColorTranslator.__init__
Bio.Graphics.GenomeDiagram._Diagram.Diagram.__init__
Bio.Graphics.GenomeDiagram._Feature.Feature.__init__
Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.__init__
Bio.Graphics.GenomeDiagram._Graph.GraphData.__init__
Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.__init__
Bio.Graphics.GenomeDiagram._LinearDrawer.LinearDrawer.__init__
Bio.Graphics.GenomeDiagram._Track.Track.__init__
Bio.HMM.DynamicProgramming.AbstractDPAlgorithms.__init__
Bio.HMM.DynamicProgramming.LogDPAlgorithms.__init__
Bio.HMM.DynamicProgramming.ScaledDPAlgorithms.__init__
Bio.HMM.MarkovModel.HiddenMarkovModel.__init__
Bio.HMM.MarkovModel.MarkovModelBuilder.__init__
Bio.HMM.Trainer.AbstractTrainer.__init__
Bio.HMM.Trainer.BaumWelchTrainer.__init__
Bio.HMM.Trainer.KnownStateTrainer.__init__
Bio.HMM.Trainer.TrainingSequence.__init__
Bio.HotRand.HotCache.__init__
Bio.HotRand.HotRandom.__init__
Bio.Index._InMemoryIndex.__init__
Bio.Index._ShelveIndex.__init__
Bio.KDTree.KDTree.KDTree.__init__
Bio.KEGG.Compound.Record.__init__
Bio.KEGG.Enzyme.Record.__init__
Bio.LogisticRegression.LogisticRegression.__init__
Bio.MarkovModel.MarkovModel.__init__
Bio.MaxEntropy.MaxEntropy.__init__
Bio.Motif.Applications._AlignAce.AlignAceCommandline.__init__
Bio.Motif.Applications._AlignAce.CompareAceCommandline.__init__
Bio.Motif.Parsers.AlignAce.Record.__init__
Bio.Motif.Parsers.MAST.Record.__init__
Bio.Motif.Parsers.MEME.MEMEInstance.__init__
Bio.Motif.Parsers.MEME.MEMEMotif.__init__
Bio.Motif.Parsers.MEME.MEMERecord.__init__
Bio.Motif.Thresholds.ScoreDistribution.__init__
Bio.Motif._Motif.Motif.__init__
Bio.NMR.xpktools.Peaklist.__init__
Bio.NMR.xpktools.XpkEntry.__init__
Bio.NaiveBayes.NaiveBayes.__init__
Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.__init__
Bio.NeuralNetwork.BackPropagation.Network.BasicNetwork.__init__
Bio.NeuralNetwork.Gene.Motif.MotifCoder.__init__
Bio.NeuralNetwork.Gene.Motif.MotifFinder.__init__
Bio.NeuralNetwork.Gene.Pattern.PatternIO.__init__
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.__init__
Bio.NeuralNetwork.Gene.Schema.DifferentialSchemaFitness.__init__
Bio.NeuralNetwork.Gene.Schema.GeneticAlgorithmFinder.__init__
Bio.NeuralNetwork.Gene.Schema.MostCountSchemaFitness.__init__
Bio.NeuralNetwork.Gene.Schema.RandomMotifGenerator.__init__
Bio.NeuralNetwork.Gene.Schema.Schema.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaCoder.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaFactory.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.__init__
Bio.NeuralNetwork.Gene.Schema.SimpleFinisher.__init__
Bio.NeuralNetwork.Gene.Signature.SignatureCoder.__init__
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.__init__
Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop.__init__
Bio.NeuralNetwork.Training.ExampleManager.__init__
Bio.NeuralNetwork.Training.TrainingExample.__init__
Bio.Nexus.Nexus.Block.__init__
Bio.Nexus.Nexus.CharBuffer.__init__
Bio.Nexus.Nexus.Commandline.__init__
Bio.Nexus.Nexus.Nexus.__init__
Bio.Nexus.Nexus.StepMatrix.__init__
Bio.Nexus.Nodes.Chain.__init__
Bio.Nexus.Nodes.Node.__init__
Bio.Nexus.Trees.NodeData.__init__
Bio.Nexus.Trees.Tree.__init__
Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap.__init__
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__init__
Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap.__init__
Bio.PDB.Atom.Atom.__init__
Bio.PDB.Atom.DisorderedAtom.__init__
Bio.PDB.Chain.Chain.__init__
Bio.PDB.DSSP'.DSSP.__init__
Bio.PDB.Dice.ChainSelector.__init__
Bio.PDB.Entity.DisorderedEntityWrapper.__init__
Bio.PDB.Entity.Entity.__init__
Bio.PDB.FragmentMapper'.Fragment.__init__
Bio.PDB.FragmentMapper'.FragmentMapper.__init__
Bio.PDB.HSExposure.ExposureCN.__init__
Bio.PDB.HSExposure.HSExposureCA.__init__
Bio.PDB.HSExposure.HSExposureCB.__init__
Bio.PDB.HSExposure._AbstractHSExposure.__init__
Bio.PDB.MMCIF2Dict.MMCIF2Dict.__init__
Bio.PDB.Model.Model.__init__
Bio.PDB.NACCESS.NACCESS.__init__
Bio.PDB.NACCESS.NACCESS_atomic.__init__
Bio.PDB.NeighborSearch.NeighborSearch.__init__
Bio.PDB.PDBIO'.PDBIO.__init__
Bio.PDB.PDBList'.PDBList.__init__
Bio.PDB.PDBParser'.PDBParser.__init__
Bio.PDB.PSEA.PSEA.__init__
Bio.PDB.Polypeptide.CaPPBuilder.__init__
Bio.PDB.Polypeptide.PPBuilder.__init__
Bio.PDB.Polypeptide._PPBuilder.__init__
Bio.PDB.Residue.DisorderedResidue.__init__
Bio.PDB.Residue.Residue.__init__
Bio.PDB.ResidueDepth'.ResidueDepth.__init__
Bio.PDB.Structure.Structure.__init__
Bio.PDB.StructureAlignment'.StructureAlignment.__init__
Bio.PDB.StructureBuilder.StructureBuilder.__init__
Bio.PDB.Superimposer'.Superimposer.__init__
Bio.PDB.Vector'.Vector.__init__
Bio.ParserSupport.EventGenerator.__init__
Bio.ParserSupport.SGMLStrippingConsumer.__init__
Bio.ParserSupport.TaggingConsumer.__init__
Bio.Parsers.spark.GenericASTBuilder.__init__
Bio.Parsers.spark.GenericASTMatcher.__init__
Bio.Parsers.spark.GenericASTTraversal.__init__
Bio.Parsers.spark.GenericParser.__init__
Bio.Parsers.spark.GenericScanner.__init__
Bio.Pathway.Network.__init__
Bio.Pathway.Reaction.__init__
Bio.Pathway.Rep.Graph.Graph.__init__
Bio.Pathway.Rep.HashSet.HashSet.__init__
Bio.Pathway.Rep.MultiGraph.MultiGraph.__init__
Bio.Pathway.System.__init__
Bio.Phylo.Applications._Phyml.PhymlCommandline.__init__
Bio.Phylo.BaseTree.Clade.__init__
Bio.Phylo.BaseTree.Tree.__init__
Bio.Phylo.Newick.Clade.__init__
Bio.Phylo.Newick.Tree.__init__
Bio.Phylo.NewickIO.Parser.__init__
Bio.Phylo.NewickIO.Writer.__init__
Bio.Phylo.PAML._paml.Paml.__init__
Bio.Phylo.PAML.baseml.Baseml.__init__
Bio.Phylo.PAML.codeml.Codeml.__init__
Bio.Phylo.PAML.yn00.Yn00.__init__
Bio.Phylo.PhyloXML.Accession.__init__
Bio.Phylo.PhyloXML.Annotation.__init__
Bio.Phylo.PhyloXML.BinaryCharacters.__init__
Bio.Phylo.PhyloXML.BranchColor.__init__
Bio.Phylo.PhyloXML.Clade.__init__
Bio.Phylo.PhyloXML.CladeRelation.__init__
Bio.Phylo.PhyloXML.Confidence.__init__
Bio.Phylo.PhyloXML.Date.__init__
Bio.Phylo.PhyloXML.Distribution.__init__
Bio.Phylo.PhyloXML.DomainArchitecture.__init__
Bio.Phylo.PhyloXML.Events.__init__
Bio.Phylo.PhyloXML.Id.__init__
Bio.Phylo.PhyloXML.MolSeq.__init__
Bio.Phylo.PhyloXML.Other.__init__
Bio.Phylo.PhyloXML.Phylogeny.__init__
Bio.Phylo.PhyloXML.Phyloxml.__init__
Bio.Phylo.PhyloXML.Point.__init__
Bio.Phylo.PhyloXML.Polygon.__init__
Bio.Phylo.PhyloXML.Property.__init__
Bio.Phylo.PhyloXML.ProteinDomain.__init__
Bio.Phylo.PhyloXML.Reference.__init__
Bio.Phylo.PhyloXML.Sequence.__init__
Bio.Phylo.PhyloXML.SequenceRelation.__init__
Bio.Phylo.PhyloXML.Taxonomy.__init__
Bio.Phylo.PhyloXML.Uri.__init__
Bio.Phylo.PhyloXMLIO.Parser.__init__
Bio.Phylo.PhyloXMLIO.Writer.__init__
Bio.PopGen.Async.Async.__init__
Bio.PopGen.Async.DirectoryRetriever.__init__
Bio.PopGen.Async.FileRetriever.__init__
Bio.PopGen.Async.Local.Local.__init__
Bio.PopGen.FDist.Async.FDistAsync.__init__
Bio.PopGen.FDist.Async.SplitFDist.__init__
Bio.PopGen.FDist.Controller.FDistController.__init__
Bio.PopGen.FDist.Record.__init__
Bio.PopGen.GenePop.Controller.GenePopController.__init__
Bio.PopGen.GenePop.Controller._FileIterator.__init__
Bio.PopGen.GenePop.Controller._GenePopCommandline.__init__
Bio.PopGen.GenePop.EasyController.EasyController.__init__
Bio.PopGen.GenePop.FileParser.FileRecord.__init__
Bio.PopGen.GenePop.LargeFileParser.Record.__init__
Bio.PopGen.GenePop.Record.__init__
Bio.PopGen.SimCoal.Async.SimCoalCache.__init__
Bio.PopGen.SimCoal.Cache.SimCoalCache.__init__
Bio.PopGen.SimCoal.Controller.SimCoalController.__init__
Bio.Restriction.PrintFormat.PrintFormat.__init__
Bio.Restriction.Restriction.Analysis.__init__
Bio.Restriction.Restriction.FormattedSeq.__init__
Bio.Restriction.Restriction.RestrictionBatch.__init__
Bio.Restriction.Restriction.RestrictionType.__init__
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.__init__
Bio.Restriction._Update.RestrictionCompiler.TypeCompiler.__init__
Bio.Restriction._Update.RestrictionCompiler.newenzyme.__init__
Bio.Restriction._Update.Update.ConnectionError.__init__
Bio.Restriction._Update.Update.FtpNameError.__init__
Bio.Restriction._Update.Update.FtpPasswordError.__init__
Bio.Restriction._Update.Update.RebaseUpdate.__init__
Bio.SCOP.Astral.__init__
Bio.SCOP.Cla.Index.__init__
Bio.SCOP.Cla.Record.__init__
Bio.SCOP.Des.Record.__init__
Bio.SCOP.Dom.Record.__init__
Bio.SCOP.Domain.__init__
Bio.SCOP.Hie.Record.__init__
Bio.SCOP.Node.__init__
Bio.SCOP.Raf.Res.__init__
Bio.SCOP.Raf.SeqMap.__init__
Bio.SCOP.Raf.SeqMapIndex.__init__
Bio.SCOP.Residues'.Residues.__init__
Bio.SCOP.Scop.__init__
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__
Bio.Search.Algorithm.__init__
Bio.Search.Database.__init__
Bio.Search.HSP.__init__
Bio.Search.HSPSeq.__init__
Bio.Search.Hit.__init__
Bio.Search.HomologySeq.__init__
Bio.Search.Query.__init__
Bio.Search.Search.__init__
Bio.Search.TableInfo.__init__
Bio.Search._SeqLength.__init__
Bio.Seq.MutableSeq.__init__
Bio.Seq.Seq.__init__
Bio.Seq.UnknownSeq.__init__
Bio.SeqFeature.AbstractPosition.__init__
Bio.SeqFeature.AfterPosition.__init__
Bio.SeqFeature.BeforePosition.__init__
Bio.SeqFeature.BetweenPosition.__init__
Bio.SeqFeature.ExactPosition.__init__
Bio.SeqFeature.FeatureLocation.__init__
Bio.SeqFeature.OneOfPosition.__init__
Bio.SeqFeature.PositionGap.__init__
Bio.SeqFeature.Reference.__init__
Bio.SeqFeature.SeqFeature.__init__
Bio.SeqFeature.UnknownPosition.__init__
Bio.SeqFeature.WithinPosition.__init__
Bio.SeqIO.FastaIO.FastaWriter.__init__
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceWriter.__init__
Bio.SeqIO.Interfaces.SequentialSequenceWriter.__init__
Bio.SeqIO.PhdIO.PhdWriter.__init__
Bio.SeqIO.QualityIO.QualPhredWriter.__init__
Bio.SeqIO.SeqXmlIO.SeqXmlIterator.__init__
Bio.SeqIO.SeqXmlIO.SeqXmlWriter.__init__
Bio.SeqIO.SeqXmlIO.XMLRecordIterator.__init__
Bio.SeqIO.SffIO.SffWriter.__init__
Bio.SeqIO.SffIO._AddTellHandle.__init__
Bio.SeqIO.UniprotIO.Parser.__init__
Bio.SeqIO._index.IntelliGeneticsRandomAccess.__init__
Bio.SeqIO._index.SeqFileRandomAccess.__init__
Bio.SeqIO._index.SequentialSeqFileRandomAccess.__init__
Bio.SeqIO._index.SffRandomAccess.__init__
Bio.SeqIO._index._IndexedSeqFileDict.__init__
Bio.SeqIO._index._SQLiteManySeqFilesDict.__init__
Bio.SeqRecord.SeqRecord.__init__
Bio.SeqRecord._RestrictedDict.__init__
Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.__init__
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__
Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__
Bio.Sequencing.Ace.ACEFileRecord.__init__
Bio.Sequencing.Ace.Contig.__init__
Bio.Sequencing.Ace.Reads.__init__
Bio.Sequencing.Ace.af.__init__
Bio.Sequencing.Ace.bs.__init__
Bio.Sequencing.Ace.ct.__init__
Bio.Sequencing.Ace.ds.__init__
Bio.Sequencing.Ace.qa.__init__
Bio.Sequencing.Ace.rd.__init__
Bio.Sequencing.Ace.rt.__init__
Bio.Sequencing.Ace.wa.__init__
Bio.Sequencing.Ace.wr.__init__
Bio.Sequencing.Applications._Novoalign.NovoalignCommandline.__init__
Bio.Sequencing.Phd.Record.__init__
Bio.SubsMat.FreqTable.FreqTable.__init__
Bio.SubsMat.SeqMat.__init__
Bio.SwissProt.KeyWList.Record.__init__
Bio.SwissProt.Record.__init__
Bio.SwissProt.Reference.__init__
Bio.UniGene.Iterator.__init__
Bio.UniGene.ProtsimLine.__init__
Bio.UniGene.Record.__init__
Bio.UniGene.RecordParser.__init__
Bio.UniGene.STSLine.__init__
Bio.UniGene.SequenceLine.__init__
Bio.UniGene.UnigeneProtsimRecord.__init__
Bio.UniGene.UnigeneRecord.__init__
Bio.UniGene.UnigeneSTSRecord.__init__
Bio.UniGene.UnigeneSequenceRecord.__init__
Bio.UniGene._RecordConsumer.__init__
Bio.UniGene._Scanner.__init__
Bio.Wise.dnal.Statistics.__init__
Bio.Wise.psw.AlignmentColumn.__init__
Bio.Wise.psw.ColumnUnit.__init__
Bio.kNN.kNN.__init__
Bio.pairwise2.affine_penalty.__init__
Bio.pairwise2.dictionary_match.__init__
Bio.pairwise2.identity_match.__init__
BioSQL.BioSeq.DBSeq.__init__
BioSQL.BioSeq.DBSeqRecord.__init__
BioSQL.BioSeqDatabase.Adaptor.__init__
BioSQL.BioSeqDatabase.BioSeqDatabase.__init__
BioSQL.BioSeqDatabase.DBServer.__init__
BioSQL.DBUtils.Generic_dbutils.__init__
BioSQL.Loader.DatabaseLoader.__init__
BioSQL.Loader.DatabaseRemover.__init__" class="py-name" href="#" onclick="return doclink('link-38', '__init__', 'link-38');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt id="link-39" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-39', 'handle', 'link-14');">handle</a></tt><tt class="py-op">)</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-comment">#self.handle = handle</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">wrap</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">wrap</tt><tt class="py-op">:</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">wrap</tt> <tt class="py-op"><</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">wrap</tt> <tt class="py-op">=</tt> <tt class="py-name">wrap</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">record2title</tt> <tt class="py-op">=</tt> <tt class="py-name">record2title</tt> </tt>
</div><a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> </tt>
<a name="FastaWriter.write_record"></a><div id="FastaWriter.write_record-def"><a name="L111"></a><tt class="py-lineno">111</tt> <a class="py-toggle" href="#" id="FastaWriter.write_record-toggle" onclick="return toggle('FastaWriter.write_record');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqIO.FastaIO.FastaWriter-class.html#write_record">write_record</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">record</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FastaWriter.write_record-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FastaWriter.write_record-expanded"><a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-docstring">"""Write a single Fasta record to the file."""</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_header_written</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_footer_written</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_record_written</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">record2title</tt><tt class="py-op">:</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt id="link-40" class="py-name" targets="Method Bio.Blast.NCBIStandalone._AlignmentConsumer.title()=Bio.Blast.NCBIStandalone._AlignmentConsumer-class.html#title,Method Bio.GenBank._FeatureConsumer.title()=Bio.GenBank._FeatureConsumer-class.html#title,Method Bio.GenBank._RecordConsumer.title()=Bio.GenBank._RecordConsumer-class.html#title"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title" class="py-name" href="#" onclick="return doclink('link-40', 'title', 'link-40');">title</a></tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-41" class="py-name" targets="Method Bio.AlignIO.Interfaces.AlignmentWriter.clean()=Bio.AlignIO.Interfaces.AlignmentWriter-class.html#clean,Method Bio.SeqIO.Interfaces.SequenceWriter.clean()=Bio.SeqIO.Interfaces.SequenceWriter-class.html#clean"><a title="Bio.AlignIO.Interfaces.AlignmentWriter.clean
Bio.SeqIO.Interfaces.SequenceWriter.clean" class="py-name" href="#" onclick="return doclink('link-41', 'clean', 'link-41');">clean</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">record2title</tt><tt class="py-op">(</tt><tt class="py-name">record</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt id="link-42" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Parser.id
Bio.Phylo.PhyloXMLIO.Writer.id" class="py-name" href="#" onclick="return doclink('link-42', 'id', 'link-16');">id</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-43" class="py-name"><a title="Bio.AlignIO.Interfaces.AlignmentWriter.clean
Bio.SeqIO.Interfaces.SequenceWriter.clean" class="py-name" href="#" onclick="return doclink('link-43', 'clean', 'link-41');">clean</a></tt><tt class="py-op">(</tt><tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-44" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Parser.id
Bio.Phylo.PhyloXMLIO.Writer.id" class="py-name" href="#" onclick="return doclink('link-44', 'id', 'link-16');">id</a></tt><tt class="py-op">)</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt id="link-45" class="py-name"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description
Bio.Phylo.PhyloXMLIO.Writer.description" class="py-name" href="#" onclick="return doclink('link-45', 'description', 'link-36');">description</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-46" class="py-name"><a title="Bio.AlignIO.Interfaces.AlignmentWriter.clean
Bio.SeqIO.Interfaces.SequenceWriter.clean" class="py-name" href="#" onclick="return doclink('link-46', 'clean', 'link-41');">clean</a></tt><tt class="py-op">(</tt><tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-47" class="py-name"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description
Bio.Phylo.PhyloXMLIO.Writer.description" class="py-name" href="#" onclick="return doclink('link-47', 'description', 'link-36');">description</a></tt><tt class="py-op">)</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-comment">#if description[:len(id)]==id:</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-48" class="py-name"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description
Bio.Phylo.PhyloXMLIO.Writer.description" class="py-name" href="#" onclick="return doclink('link-48', 'description', 'link-36');">description</a></tt> <tt class="py-keyword">and</tt> <tt id="link-49" class="py-name"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description
Bio.Phylo.PhyloXMLIO.Writer.description" class="py-name" href="#" onclick="return doclink('link-49', 'description', 'link-36');">description</a></tt><tt class="py-op">.</tt><tt id="link-50" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.split" class="py-name" href="#" onclick="return doclink('link-50', 'split', 'link-21');">split</a></tt><tt class="py-op">(</tt><tt class="py-name">None</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-number">0</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt id="link-51" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Parser.id
Bio.Phylo.PhyloXMLIO.Writer.id" class="py-name" href="#" onclick="return doclink('link-51', 'id', 'link-16');">id</a></tt><tt class="py-op">:</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-comment">#The description includes the id at the start</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt id="link-52" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title" class="py-name" href="#" onclick="return doclink('link-52', 'title', 'link-40');">title</a></tt> <tt class="py-op">=</tt> <tt id="link-53" class="py-name"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description
Bio.Phylo.PhyloXMLIO.Writer.description" class="py-name" href="#" onclick="return doclink('link-53', 'description', 'link-36');">description</a></tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-54" class="py-name"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description
Bio.Phylo.PhyloXMLIO.Writer.description" class="py-name" href="#" onclick="return doclink('link-54', 'description', 'link-36');">description</a></tt><tt class="py-op">:</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt id="link-55" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title" class="py-name" href="#" onclick="return doclink('link-55', 'title', 'link-40');">title</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"%s %s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-56" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Parser.id
Bio.Phylo.PhyloXMLIO.Writer.id" class="py-name" href="#" onclick="return doclink('link-56', 'id', 'link-16');">id</a></tt><tt class="py-op">,</tt> <tt id="link-57" class="py-name"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description
Bio.Phylo.PhyloXMLIO.Writer.description" class="py-name" href="#" onclick="return doclink('link-57', 'description', 'link-36');">description</a></tt><tt class="py-op">)</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt id="link-58" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title" class="py-name" href="#" onclick="return doclink('link-58', 'title', 'link-40');">title</a></tt> <tt class="py-op">=</tt> <tt id="link-59" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Parser.id
Bio.Phylo.PhyloXMLIO.Writer.id" class="py-name" href="#" onclick="return doclink('link-59', 'id', 'link-16');">id</a></tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-string">"\n"</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt id="link-60" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title" class="py-name" href="#" onclick="return doclink('link-60', 'title', 'link-40');">title</a></tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-string">"\r"</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt id="link-61" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title" class="py-name" href="#" onclick="return doclink('link-61', 'title', 'link-40');">title</a></tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-62" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-62', 'handle', 'link-14');">handle</a></tt><tt class="py-op">.</tt><tt id="link-63" class="py-name" targets="Function Bio.AlignIO.write()=Bio.AlignIO-module.html#write,Method Bio.Graphics.GenomeDiagram._Diagram.Diagram.write()=Bio.Graphics.GenomeDiagram._Diagram.Diagram-class.html#write,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.write()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#write,Method Bio.Phylo.NewickIO.Writer.write()=Bio.Phylo.NewickIO.Writer-class.html#write,Function Bio.Phylo.NewickIO.write()=Bio.Phylo.NewickIO-module.html#write,Function Bio.Phylo.NexusIO.write()=Bio.Phylo.NexusIO-module.html#write,Method Bio.Phylo.PhyloXMLIO.Writer.write()=Bio.Phylo.PhyloXMLIO.Writer-class.html#write,Function Bio.Phylo.PhyloXMLIO.write()=Bio.Phylo.PhyloXMLIO-module.html#write,Function Bio.Phylo._io.write()=Bio.Phylo._io-module.html#write,Function Bio.SeqIO.write()=Bio.SeqIO-module.html#write"><a title="Bio.AlignIO.write
Bio.Graphics.GenomeDiagram._Diagram.Diagram.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.Phylo.NewickIO.Writer.write
Bio.Phylo.NewickIO.write
Bio.Phylo.NexusIO.write
Bio.Phylo.PhyloXMLIO.Writer.write
Bio.Phylo.PhyloXMLIO.write
Bio.Phylo._io.write
Bio.SeqIO.write" class="py-name" href="#" onclick="return doclink('link-63', 'write', 'link-63');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">">%s\n"</tt> <tt class="py-op">%</tt> <tt id="link-64" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title" class="py-name" href="#" onclick="return doclink('link-64', 'title', 'link-40');">title</a></tt><tt class="py-op">)</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt id="link-65" class="py-name" targets="Variable Bio.Seq.Seq.data=Bio.Seq.Seq-class.html#data,Variable BioSQL.BioSeq.DBSeq.data=BioSQL.BioSeq.DBSeq-class.html#data"><a title="Bio.Seq.Seq.data
BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-65', 'data', 'link-65');">data</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-66" class="py-name" targets="Method Bio.SeqIO.Interfaces.SequenceWriter._get_seq_string()=Bio.SeqIO.Interfaces.SequenceWriter-class.html#_get_seq_string"><a title="Bio.SeqIO.Interfaces.SequenceWriter._get_seq_string" class="py-name" href="#" onclick="return doclink('link-66', '_get_seq_string', 'link-66');">_get_seq_string</a></tt><tt class="py-op">(</tt><tt class="py-name">record</tt><tt class="py-op">)</tt> <tt class="py-comment">#Catches sequence being None</tt> </tt>
<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 class="py-keyword">assert</tt> <tt class="py-string">"\n"</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt id="link-67" class="py-name"><a title="Bio.Seq.Seq.data
BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-67', 'data', 'link-65');">data</a></tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-string">"\r"</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt id="link-68" class="py-name"><a title="Bio.Seq.Seq.data
BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-68', 'data', 'link-65');">data</a></tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">wrap</tt><tt class="py-op">:</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-69" 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-69', 'i', 'link-69');">i</a></tt> <tt class="py-keyword">in</tt> <tt id="link-70" class="py-name" targets="Method Bio.Graphics.GenomeDiagram._Diagram.Diagram.range()=Bio.Graphics.GenomeDiagram._Diagram.Diagram-class.html#range,Method Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range()=Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet-class.html#range,Method Bio.Graphics.GenomeDiagram._Graph.GraphData.range()=Bio.Graphics.GenomeDiagram._Graph.GraphData-class.html#range,Method Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range()=Bio.Graphics.GenomeDiagram._GraphSet.GraphSet-class.html#range,Method Bio.Graphics.GenomeDiagram._Track.Track.range()=Bio.Graphics.GenomeDiagram._Track.Track-class.html#range"><a title="Bio.Graphics.GenomeDiagram._Diagram.Diagram.range
Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range
Bio.Graphics.GenomeDiagram._Graph.GraphData.range
Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range
Bio.Graphics.GenomeDiagram._Track.Track.range" class="py-name" href="#" onclick="return doclink('link-70', 'range', 'link-70');">range</a></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-71" class="py-name"><a title="Bio.Seq.Seq.data
BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-71', 'data', 'link-65');">data</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">wrap</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-72" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-72', 'handle', 'link-14');">handle</a></tt><tt class="py-op">.</tt><tt id="link-73" class="py-name"><a title="Bio.AlignIO.write
Bio.Graphics.GenomeDiagram._Diagram.Diagram.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.Phylo.NewickIO.Writer.write
Bio.Phylo.NewickIO.write
Bio.Phylo.NexusIO.write
Bio.Phylo.PhyloXMLIO.Writer.write
Bio.Phylo.PhyloXMLIO.write
Bio.Phylo._io.write
Bio.SeqIO.write" class="py-name" href="#" onclick="return doclink('link-73', 'write', 'link-63');">write</a></tt><tt class="py-op">(</tt><tt id="link-74" class="py-name"><a title="Bio.Seq.Seq.data
BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-74', 'data', 'link-65');">data</a></tt><tt class="py-op">[</tt><tt id="link-75" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-75', 'i', 'link-69');">i</a></tt><tt class="py-op">:</tt><tt id="link-76" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-76', 'i', 'link-69');">i</a></tt><tt class="py-op">+</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">wrap</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="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-77" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-77', 'handle', 'link-14');">handle</a></tt><tt class="py-op">.</tt><tt id="link-78" class="py-name"><a title="Bio.AlignIO.write
Bio.Graphics.GenomeDiagram._Diagram.Diagram.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.Phylo.NewickIO.Writer.write
Bio.Phylo.NewickIO.write
Bio.Phylo.NexusIO.write
Bio.Phylo.PhyloXMLIO.Writer.write
Bio.Phylo.PhyloXMLIO.write
Bio.Phylo._io.write
Bio.SeqIO.write" class="py-name" href="#" onclick="return doclink('link-78', 'write', 'link-63');">write</a></tt><tt class="py-op">(</tt><tt id="link-79" class="py-name"><a title="Bio.Seq.Seq.data
BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-79', 'data', 'link-65');">data</a></tt> <tt class="py-op">+</tt> <tt class="py-string">"\n"</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"><tt class="py-keyword">if</tt> <tt class="py-name">__name__</tt> <tt class="py-op">==</tt> <tt class="py-string">"__main__"</tt><tt class="py-op">:</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"Running quick self test"</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">os</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt id="link-80" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-80', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-81" class="py-name"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-81', 'Alphabet', 'link-1');">Alphabet</a></tt> <tt class="py-keyword">import</tt> <tt id="link-82" class="py-name" targets="Variable Bio.Alphabet.generic_protein=Bio.Alphabet-module.html#generic_protein"><a title="Bio.Alphabet.generic_protein" class="py-name" href="#" onclick="return doclink('link-82', 'generic_protein', 'link-82');">generic_protein</a></tt><tt class="py-op">,</tt> <tt id="link-83" class="py-name" targets="Variable Bio.Alphabet.generic_nucleotide=Bio.Alphabet-module.html#generic_nucleotide"><a title="Bio.Alphabet.generic_nucleotide" class="py-name" href="#" onclick="return doclink('link-83', 'generic_nucleotide', 'link-83');">generic_nucleotide</a></tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-comment">#Download the files from here:</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-comment">#ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Nanoarchaeum_equitans</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt class="py-name">fna_filename</tt> <tt class="py-op">=</tt> <tt class="py-string">"NC_005213.fna"</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-name">faa_filename</tt> <tt class="py-op">=</tt> <tt class="py-string">"NC_005213.faa"</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> </tt>
<a name="genbank_name_function"></a><div id="genbank_name_function-def"><a name="L158"></a><tt class="py-lineno">158</tt> <a class="py-toggle" href="#" id="genbank_name_function-toggle" onclick="return toggle('genbank_name_function');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqIO.FastaIO-module.html#genbank_name_function">genbank_name_function</a><tt class="py-op">(</tt><tt class="py-param">text</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="genbank_name_function-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="genbank_name_function-expanded"><a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-name">text</tt><tt class="py-op">,</tt> <tt class="py-name">descr</tt> <tt class="py-op">=</tt> <tt class="py-name">text</tt><tt class="py-op">.</tt><tt id="link-84" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.split" class="py-name" href="#" onclick="return doclink('link-84', 'split', 'link-21');">split</a></tt><tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt id="link-85" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Parser.id
Bio.Phylo.PhyloXMLIO.Writer.id" class="py-name" href="#" onclick="return doclink('link-85', 'id', 'link-16');">id</a></tt> <tt class="py-op">=</tt> <tt class="py-name">text</tt><tt class="py-op">.</tt><tt id="link-86" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.split" class="py-name" href="#" onclick="return doclink('link-86', 'split', 'link-21');">split</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-number">3</tt><tt class="py-op">]</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt id="link-87" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-87', 'name', 'link-17');">name</a></tt> <tt class="py-op">=</tt> <tt id="link-88" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Parser.id
Bio.Phylo.PhyloXMLIO.Writer.id" class="py-name" href="#" onclick="return doclink('link-88', 'id', 'link-16');">id</a></tt><tt class="py-op">.</tt><tt id="link-89" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.split" class="py-name" href="#" onclick="return doclink('link-89', 'split', 'link-21');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">"."</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-90" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Parser.id
Bio.Phylo.PhyloXMLIO.Writer.id" class="py-name" href="#" onclick="return doclink('link-90', 'id', 'link-16');">id</a></tt><tt class="py-op">,</tt> <tt id="link-91" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-91', 'name', 'link-17');">name</a></tt><tt class="py-op">,</tt> <tt class="py-name">descr</tt> </tt>
</div><a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> </tt>
<a name="print_record"></a><div id="print_record-def"><a name="L164"></a><tt class="py-lineno">164</tt> <a class="py-toggle" href="#" id="print_record-toggle" onclick="return toggle('print_record');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqIO.FastaIO-module.html#print_record">print_record</a><tt class="py-op">(</tt><tt class="py-param">record</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="print_record-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="print_record-expanded"><a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-comment">#See also bug 2057</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt class="py-comment">#http://bugzilla.open-bio.org/show_bug.cgi?id=2057</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"ID:"</tt> <tt class="py-op">+</tt> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-92" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Parser.id
Bio.Phylo.PhyloXMLIO.Writer.id" class="py-name" href="#" onclick="return doclink('link-92', 'id', 'link-16');">id</a></tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"Name:"</tt> <tt class="py-op">+</tt> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-93" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-93', 'name', 'link-17');">name</a></tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"Descr:"</tt> <tt class="py-op">+</tt> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-94" class="py-name"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description
Bio.Phylo.PhyloXMLIO.Writer.description" class="py-name" href="#" onclick="return doclink('link-94', 'description', 'link-36');">description</a></tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-95" class="py-name" targets="Variable Bio.SeqRecord.SeqRecord.seq=Bio.SeqRecord.SeqRecord-class.html#seq,Variable BioSQL.BioSeq.DBSeqRecord.seq=BioSQL.BioSeq.DBSeqRecord-class.html#seq"><a title="Bio.SeqRecord.SeqRecord.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-95', 'seq', 'link-95');">seq</a></tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">feature</tt> <tt class="py-keyword">in</tt> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-96" class="py-name" targets="Variable BioSQL.BioSeq.DBSeqRecord.annotations=BioSQL.BioSeq.DBSeqRecord-class.html#annotations"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-96', 'annotations', 'link-96');">annotations</a></tt><tt class="py-op">:</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'/%s=%s'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">feature</tt><tt class="py-op">,</tt> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-97" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-97', 'annotations', 'link-96');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-name">feature</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-98" class="py-name" targets="Variable BioSQL.BioSeq.DBSeqRecord.dbxrefs=BioSQL.BioSeq.DBSeqRecord-class.html#dbxrefs"><a title="BioSQL.BioSeq.DBSeqRecord.dbxrefs" class="py-name" href="#" onclick="return doclink('link-98', 'dbxrefs', 'link-98');">dbxrefs</a></tt><tt class="py-op">:</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"Database cross references:"</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-99" class="py-name" targets="Variable Bio.Statistics.lowess.x=Bio.Statistics.lowess-module.html#x"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-99', 'x', 'link-99');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-100" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.dbxrefs" class="py-name" href="#" onclick="return doclink('link-100', 'dbxrefs', 'link-98');">dbxrefs</a></tt> <tt class="py-op">:</tt> <tt class="py-keyword">print</tt> <tt class="py-string">" - %s"</tt> <tt class="py-op">%</tt> <tt id="link-101" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-101', 'x', 'link-99');">x</a></tt> </tt>
</div><a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">isfile</tt><tt class="py-op">(</tt><tt class="py-name">fna_filename</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"--------"</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"FastaIterator (single sequence)"</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-name">iterator</tt> <tt class="py-op">=</tt> <tt id="link-102" class="py-name" targets="Function Bio.SeqIO.FastaIO.FastaIterator()=Bio.SeqIO.FastaIO-module.html#FastaIterator"><a title="Bio.SeqIO.FastaIO.FastaIterator" class="py-name" href="#" onclick="return doclink('link-102', 'FastaIterator', 'link-102');">FastaIterator</a></tt><tt class="py-op">(</tt><tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">fna_filename</tt><tt class="py-op">,</tt> <tt class="py-string">"r"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">alphabet</tt><tt class="py-op">=</tt><tt id="link-103" class="py-name"><a title="Bio.Alphabet.generic_nucleotide" class="py-name" href="#" onclick="return doclink('link-103', 'generic_nucleotide', 'link-83');">generic_nucleotide</a></tt><tt class="py-op">,</tt> <tt class="py-name">title2ids</tt><tt class="py-op">=</tt><tt class="py-name">genbank_name_function</tt><tt class="py-op">)</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt id="link-104" class="py-name" targets="Method Bio.Crystal.Chain.count()=Bio.Crystal.Chain-class.html#count,Method Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count()=Bio.NeuralNetwork.Gene.Pattern.PatternRepository-class.html#count,Method Bio.Seq.MutableSeq.count()=Bio.Seq.MutableSeq-class.html#count,Method Bio.Seq.Seq.count()=Bio.Seq.Seq-class.html#count,Method Bio.Seq.UnknownSeq.count()=Bio.Seq.UnknownSeq-class.html#count"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.Seq.UnknownSeq.count" class="py-name" href="#" onclick="return doclink('link-104', 'count', 'link-104');">count</a></tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">record</tt> <tt class="py-keyword">in</tt> <tt class="py-name">iterator</tt><tt class="py-op">:</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> <tt id="link-105" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.Seq.UnknownSeq.count" class="py-name" href="#" onclick="return doclink('link-105', 'count', 'link-104');">count</a></tt><tt class="py-op">=</tt><tt id="link-106" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.Seq.UnknownSeq.count" class="py-name" href="#" onclick="return doclink('link-106', 'count', 'link-104');">count</a></tt><tt class="py-op">+</tt><tt class="py-number">1</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-name">print_record</tt><tt class="py-op">(</tt><tt class="py-name">record</tt><tt class="py-op">)</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-107" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.Seq.UnknownSeq.count" class="py-name" href="#" onclick="return doclink('link-107', 'count', 'link-104');">count</a></tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">record</tt><tt class="py-op">.</tt><tt class="py-name">__class__</tt><tt class="py-op">)</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">isfile</tt><tt class="py-op">(</tt><tt class="py-name">faa_filename</tt><tt class="py-op">)</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">print</tt> <tt class="py-string">"--------"</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"FastaIterator (multiple sequences)"</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> <tt class="py-name">iterator</tt> <tt class="py-op">=</tt> <tt id="link-108" class="py-name"><a title="Bio.SeqIO.FastaIO.FastaIterator" class="py-name" href="#" onclick="return doclink('link-108', 'FastaIterator', 'link-102');">FastaIterator</a></tt><tt class="py-op">(</tt><tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">faa_filename</tt><tt class="py-op">,</tt> <tt class="py-string">"r"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">alphabet</tt><tt class="py-op">=</tt><tt id="link-109" class="py-name"><a title="Bio.Alphabet.generic_protein" class="py-name" href="#" onclick="return doclink('link-109', 'generic_protein', 'link-82');">generic_protein</a></tt><tt class="py-op">,</tt> <tt class="py-name">title2ids</tt><tt class="py-op">=</tt><tt class="py-name">genbank_name_function</tt><tt class="py-op">)</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt id="link-110" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.Seq.UnknownSeq.count" class="py-name" href="#" onclick="return doclink('link-110', 'count', 'link-104');">count</a></tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">record</tt> <tt class="py-keyword">in</tt> <tt class="py-name">iterator</tt><tt class="py-op">:</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt id="link-111" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.Seq.UnknownSeq.count" class="py-name" href="#" onclick="return doclink('link-111', 'count', 'link-104');">count</a></tt><tt class="py-op">=</tt><tt id="link-112" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.Seq.UnknownSeq.count" class="py-name" href="#" onclick="return doclink('link-112', 'count', 'link-104');">count</a></tt><tt class="py-op">+</tt><tt class="py-number">1</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt class="py-name">print_record</tt><tt class="py-op">(</tt><tt class="py-name">record</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">break</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-113" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.Seq.UnknownSeq.count" class="py-name" href="#" onclick="return doclink('link-113', 'count', 'link-104');">count</a></tt><tt class="py-op">></tt><tt class="py-number">0</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">record</tt><tt class="py-op">.</tt><tt class="py-name">__class__</tt><tt class="py-op">)</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt class="py-name">cStringIO</tt> <tt class="py-keyword">import</tt> <tt class="py-name">StringIO</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"--------"</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"FastaIterator (empty input file)"</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-comment">#Just to make sure no errors happen</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-name">iterator</tt> <tt class="py-op">=</tt> <tt id="link-114" class="py-name"><a title="Bio.SeqIO.FastaIO.FastaIterator" class="py-name" href="#" onclick="return doclink('link-114', 'FastaIterator', 'link-102');">FastaIterator</a></tt><tt class="py-op">(</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-string">""</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt id="link-115" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.Seq.UnknownSeq.count" class="py-name" href="#" onclick="return doclink('link-115', 'count', 'link-104');">count</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">record</tt> <tt class="py-keyword">in</tt> <tt class="py-name">iterator</tt><tt class="py-op">:</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> <tt id="link-116" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.Seq.UnknownSeq.count" class="py-name" href="#" onclick="return doclink('link-116', 'count', 'link-104');">count</a></tt> <tt class="py-op">=</tt> <tt id="link-117" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.Seq.UnknownSeq.count" class="py-name" href="#" onclick="return doclink('link-117', 'count', 'link-104');">count</a></tt><tt class="py-op">+</tt><tt class="py-number">1</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-118" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.Seq.UnknownSeq.count" class="py-name" href="#" onclick="return doclink('link-118', 'count', 'link-104');">count</a></tt><tt class="py-op">==</tt><tt class="py-number">0</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"Done"</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> </tt><script type="text/javascript">
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