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Module TabIO
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<h1 class="epydoc">Source Code for <a href="Bio.SeqIO.TabIO-module.html">Module Bio.SeqIO.TabIO</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 2008-2010 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>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">"""Bio.SeqIO support for the "tab" (simple tab separated) file format.</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">You are expected to use this module via the Bio.SeqIO functions.</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring">The "tab" format is an ad-hoc plain text file format where each sequence is</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring">on one (long) line. Each line contains the identifier/description, followed</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring">by a tab, followed by the sequence. For example, consider the following</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring">short FASTA format file:</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring">>ID123456 possible binding site?</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring">CATCNAGATGACACTACGACTACGACTCAGACTAC</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-docstring">>ID123457 random sequence</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring">ACACTACGACTACGACTCAGACTACAAN</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring">Apart from the descriptions, this can be represented in the simple two column</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-docstring">tab separated format as follows:</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">ID123456(tab)CATCNAGATGACACTACGACTACGACTCAGACTAC</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring">ID123457(tab)ACACTACGACTACGACTCAGACTACAAN</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring">When reading this file, "ID123456" or "ID123457" will be taken as the record's</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring">.id and .name property. There is no other information to record.</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">Similarly, when writing to this format, Biopython will ONLY record the record's</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring">.id and .seq (and not the description or any other information) as in the</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-docstring">example above.</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</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="L35"></a><tt class="py-lineno"> 35</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="L36"></a><tt class="py-lineno"> 36</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="L37"></a><tt class="py-lineno"> 37</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="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-comment">#This is a generator function!</tt> </tt>
<a name="TabIterator"></a><div id="TabIterator-def"><a name="L40"></a><tt class="py-lineno"> 40</tt> <a class="py-toggle" href="#" id="TabIterator-toggle" onclick="return toggle('TabIterator');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqIO.TabIO-module.html#TabIterator">TabIterator</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-op">:</tt> </tt>
</div><div id="TabIterator-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="TabIterator-expanded"><a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-docstring">"""Iterates over tab separated lines (as SeqRecord objects).</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt class="py-docstring"> Each line of the file should contain one tab only, dividing the line</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-docstring"> into an identifier and the full sequence.</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-docstring"> handle - input file</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-docstring"> alphabet - optional alphabet</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-docstring"> The first field is taken as the record's .id and .name (regardless of</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-docstring"> any spaces within the text) and the second field is the sequence.</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"><tt class="py-docstring"> Any blank lines are ignored.</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt id="link-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>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt id="link-15" 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-15', 'title', 'link-15');">title</a></tt><tt class="py-op">,</tt> <tt id="link-16" 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-16', 'seq', 'link-16');">seq</a></tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-17" 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-17', 'split', 'link-17');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">"\t"</tt><tt class="py-op">)</tt> <tt class="py-comment">#will fail if more than one tab!</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name" targets="Method Bio.File.SGMLStripper.strip()=Bio.File.SGMLStripper-class.html#strip,Method Bio.Seq.Seq.strip()=Bio.Seq.Seq-class.html#strip"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-18', 'strip', 'link-18');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-string">""</tt><tt class="py-op">:</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-comment">#It's a blank line, ignore it</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</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">"Each line should have one tab separating the"</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-string">" title and sequence, this line has %i tabs: %s"</tt> \ </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-19" 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-19', 'count', 'link-19');">count</a></tt><tt class="py-op">(</tt><tt class="py-string">"\t"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt id="link-20" 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-20', 'title', 'link-15');">title</a></tt> <tt class="py-op">=</tt> <tt id="link-21" 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-21', 'title', 'link-15');">title</a></tt><tt class="py-op">.</tt><tt id="link-22" class="py-name"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-22', 'strip', 'link-18');">strip</a></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-23" class="py-name"><a title="Bio.SeqRecord.SeqRecord.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-23', 'seq', 'link-16');">seq</a></tt> <tt class="py-op">=</tt> <tt id="link-24" class="py-name"><a title="Bio.SeqRecord.SeqRecord.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-24', 'seq', 'link-16');">seq</a></tt><tt class="py-op">.</tt><tt id="link-25" class="py-name"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-25', 'strip', 'link-18');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-comment">#removes the trailing new line</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt id="link-26" class="py-name"><a title="Bio.SeqRecord
Bio.SeqRecord.SeqRecord" class="py-name" href="#" onclick="return doclink('link-26', 'SeqRecord', 'link-7');">SeqRecord</a></tt><tt class="py-op">(</tt><tt id="link-27" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq" class="py-name" href="#" onclick="return doclink('link-27', 'Seq', 'link-4');">Seq</a></tt><tt class="py-op">(</tt><tt id="link-28" class="py-name"><a title="Bio.SeqRecord.SeqRecord.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-28', 'seq', 'link-16');">seq</a></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="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt id="link-29" 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-29', 'id', 'link-29');">id</a></tt><tt class="py-op">=</tt><tt id="link-30" 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-30', 'title', 'link-15');">title</a></tt><tt class="py-op">,</tt> <tt id="link-31" 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-31', 'name', 'link-31');">name</a></tt><tt class="py-op">=</tt><tt id="link-32" 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-32', 'title', 'link-15');">title</a></tt><tt class="py-op">,</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt id="link-33" 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-33', 'description', 'link-33');">description</a></tt><tt class="py-op">=</tt><tt class="py-string">""</tt><tt class="py-op">)</tt> </tt>
</div><a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> </tt>
<a name="TabWriter"></a><div id="TabWriter-def"><a name="L70"></a><tt class="py-lineno"> 70</tt> <a class="py-toggle" href="#" id="TabWriter-toggle" onclick="return toggle('TabWriter');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.SeqIO.TabIO.TabWriter-class.html">TabWriter</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="TabWriter-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="TabWriter-expanded"><a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-docstring">"""Class to write simple tab separated format files.</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"><tt class="py-docstring"> Each line consists of "id(tab)sequence" only.</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"> Any description, name or other annotation is not recorded.</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="TabWriter.write_record"></a><div id="TabWriter.write_record-def"><a name="L77"></a><tt class="py-lineno"> 77</tt> <a class="py-toggle" href="#" id="TabWriter.write_record-toggle" onclick="return toggle('TabWriter.write_record');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqIO.TabIO.TabWriter-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="TabWriter.write_record-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="TabWriter.write_record-expanded"><a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-docstring">"""Write a single tab line to the file."""</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</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="L80"></a><tt class="py-lineno"> 80</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="L81"></a><tt class="py-lineno"> 81</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="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt id="link-34" 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-34', 'title', 'link-15');">title</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-35" 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-35', 'clean', 'link-35');">clean</a></tt><tt class="py-op">(</tt><tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-36" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Parser.id
Bio.Phylo.PhyloXMLIO.Writer.id" class="py-name" href="#" onclick="return doclink('link-36', 'id', 'link-29');">id</a></tt><tt class="py-op">)</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt id="link-37" class="py-name"><a title="Bio.SeqRecord.SeqRecord.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-37', 'seq', 'link-16');">seq</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-38" 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-38', '_get_seq_string', 'link-38');">_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="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-string">"\t"</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt id="link-39" 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-39', 'title', 'link-15');">title</a></tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</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-40" 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-40', 'title', 'link-15');">title</a></tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</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-41" 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-41', 'title', 'link-15');">title</a></tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-string">"\t"</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt id="link-42" class="py-name"><a title="Bio.SeqRecord.SeqRecord.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-42', 'seq', 'link-16');">seq</a></tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</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-43" class="py-name"><a title="Bio.SeqRecord.SeqRecord.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-43', 'seq', 'link-16');">seq</a></tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</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-44" class="py-name"><a title="Bio.SeqRecord.SeqRecord.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-44', 'seq', 'link-16');">seq</a></tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-45" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-45', 'handle', 'link-14');">handle</a></tt><tt class="py-op">.</tt><tt id="link-46" 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-46', 'write', 'link-46');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"%s\t%s\n"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-47" 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-47', 'title', 'link-15');">title</a></tt><tt class="py-op">,</tt> <tt id="link-48" class="py-name"><a title="Bio.SeqRecord.SeqRecord.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-48', 'seq', 'link-16');">seq</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</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="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"Running quick self test"</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt class="py-name">StringIO</tt> <tt class="py-keyword">import</tt> <tt class="py-name">StringIO</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-comment">#This example has a trailing blank line which should be ignored</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt id="link-49" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-49', 'handle', 'link-14');">handle</a></tt> <tt class="py-op">=</tt> <tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-string">"Alpha\tAAAAAAA\nBeta\tCCCCCCC\n\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-name">records</tt> <tt class="py-op">=</tt> <tt id="link-50" class="py-name" targets="Method Bio.Pathway.Rep.HashSet.HashSet.list()=Bio.Pathway.Rep.HashSet.HashSet-class.html#list"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-50', 'list', 'link-50');">list</a></tt><tt class="py-op">(</tt><tt id="link-51" class="py-name" targets="Function Bio.SeqIO.TabIO.TabIterator()=Bio.SeqIO.TabIO-module.html#TabIterator"><a title="Bio.SeqIO.TabIO.TabIterator" class="py-name" href="#" onclick="return doclink('link-51', 'TabIterator', 'link-51');">TabIterator</a></tt><tt class="py-op">(</tt><tt id="link-52" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-52', 'handle', 'link-14');">handle</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">records</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">2</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt id="link-53" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-53', 'handle', 'link-14');">handle</a></tt> <tt class="py-op">=</tt> <tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-string">"Alpha\tAAAAAAA\tExtra\nBeta\tCCCCCCC\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-name">records</tt> <tt class="py-op">=</tt> <tt id="link-54" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-54', 'list', 'link-50');">list</a></tt><tt class="py-op">(</tt><tt id="link-55" class="py-name"><a title="Bio.SeqIO.TabIO.TabIterator" class="py-name" href="#" onclick="return doclink('link-55', 'TabIterator', 'link-51');">TabIterator</a></tt><tt class="py-op">(</tt><tt id="link-56" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-56', 'handle', 'link-14');">handle</a></tt><tt class="py-op">)</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">assert</tt> <tt class="py-name">False</tt><tt class="py-op">,</tt> <tt class="py-string">"Should have reject this invalid example!"</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">ValueError</tt><tt class="py-op">:</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-comment">#Good!</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"Done"</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> </tt><script type="text/javascript">
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