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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.Sequencing-module.html">Package Sequencing</a> ::
Module Ace
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<h1 class="epydoc">Source Code for <a href="Bio.Sequencing.Ace-module.html">Module Bio.Sequencing.Ace</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 2004 by Frank Kauff and Cymon J. Cox. 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-docstring">"""</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">Parser for ACE files output by PHRAP.</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">Written by Frank Kauff (fkauff@duke.edu) and</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">Cymon J. Cox (cymon@duke.edu)</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring">Uses the Biopython Parser interface: ParserSupport.py</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring">Usage:</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">There are two ways of reading an ace file:</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring">1) The function 'read' reads the whole file at once;</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-docstring">2) The function 'parse' reads the file contig after contig.</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-docstring">1) Parse whole ace file at once:</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-docstring"> from Bio.Sequencing import Ace</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-docstring"> acefilerecord=Ace.read(open('my_ace_file.ace'))</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring">This gives you:</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring"> acefilerecord.ncontigs (the number of contigs in the ace file)</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring"> acefilerecord.nreads (the number of reads in the ace file)</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring"> acefilerecord.contigs[] (one instance of the Contig class for each contig)</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">The Contig class holds the info of the CO tag, CT and WA tags, and all the reads used</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring">for this contig in a list of instances of the Read class, e.g.:</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"> contig3=acefilerecord.contigs[2]</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-docstring"> read4=contig3.reads[3]</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-docstring"> RD_of_read4=read4.rd</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-docstring"> DS_of_read4=read4.ds</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-docstring">CT, WA, RT tags from the end of the file can appear anywhere are automatically</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-docstring">sorted into the right place.</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-docstring">see _RecordConsumer for details.</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-docstring">2) Or you can iterate over the contigs of an ace file one by one in the ususal way:</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-docstring"> from Bio.Sequencing import Ace</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-docstring"> contigs=Ace.parse(open('my_ace_file.ace'))</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-docstring"> for contig in contigs:</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-docstring"> print contig.name</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"></tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-docstring">Please note that for memory efficiency, when using the iterator approach, only one</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"><tt class="py-docstring">contig is kept in memory at once. However, there can be a footer to the ACE file</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"><tt class="py-docstring">containing WA, CT, RT or WR tags which contain additional meta-data on the contigs.</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"><tt class="py-docstring">Because the parser doesn't see this data until the final record, it cannot be added to</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"><tt class="py-docstring">the appropriate records. Instead these tags will be returned with the last contig record.</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"><tt class="py-docstring">Thus an ace file does not entirerly suit the concept of iterating. If WA, CT, RT, WR tags</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"><tt class="py-docstring">are needed, the 'read' function rather than the 'parse' function might be more appropriate.</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> </tt>
<a name="rd"></a><div id="rd-def"><a name="L60"></a><tt class="py-lineno"> 60</tt> <a class="py-toggle" href="#" id="rd-toggle" onclick="return toggle('rd');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Sequencing.Ace.rd-class.html">rd</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="rd-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="rd-expanded"><a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-docstring">"""RD (reads), store a read with its name, sequence etc.</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"><tt class="py-docstring"> The location and strand each read is mapped to is held in the AF lines.</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="rd.__init__"></a><div id="rd.__init__-def"><a name="L65"></a><tt class="py-lineno"> 65</tt> <a class="py-toggle" href="#" id="rd.__init__-toggle" onclick="return toggle('rd.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace.rd-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="rd.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="rd.__init__-expanded"><a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-0" 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-0', 'name', 'link-0');">name</a></tt><tt class="py-op">=</tt><tt class="py-string">''</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">padded_bases</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">info_items</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">read_tags</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Method Bio.FSSP.FSSPAlignDict.sequence()=Bio.FSSP.FSSPAlignDict-class.html#sequence,Method Bio.GenBank._FeatureConsumer.sequence()=Bio.GenBank._FeatureConsumer-class.html#sequence,Method Bio.GenBank._RecordConsumer.sequence()=Bio.GenBank._RecordConsumer-class.html#sequence,Method Bio.Phylo.PhyloXMLIO.Writer.sequence()=Bio.Phylo.PhyloXMLIO.Writer-class.html#sequence"><a title="Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.Phylo.PhyloXMLIO.Writer.sequence" class="py-name" href="#" onclick="return doclink('link-1', 'sequence', 'link-1');">sequence</a></tt><tt class="py-op">=</tt><tt class="py-string">''</tt> </tt>
</div></div><a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> </tt>
<a name="qa"></a><div id="qa-def"><a name="L72"></a><tt class="py-lineno"> 72</tt> <a class="py-toggle" href="#" id="qa-toggle" onclick="return toggle('qa');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Sequencing.Ace.qa-class.html">qa</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="qa-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="qa-expanded"><a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-docstring">"""QA (read quality), including which part if any was used as the consensus."""</tt> </tt>
<a name="qa.__init__"></a><div id="qa.__init__-def"><a name="L74"></a><tt class="py-lineno"> 74</tt> <a class="py-toggle" href="#" id="qa.__init__-toggle" onclick="return toggle('qa.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace.qa-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">line</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="qa.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="qa.__init__-expanded"><a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">qual_clipping_start</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">qual_clipping_end</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">align_clipping_start</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">align_clipping_end</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">:</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt id="link-2" class="py-name" targets="Variable Bio.Wise.dnal.Statistics.header=Bio.Wise.dnal.Statistics-class.html#header"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-2', 'header', 'link-2');">header</a></tt><tt class="py-op">=</tt><tt class="py-name">map</tt><tt class="py-op">(</tt><tt class="py-name">eval</tt><tt class="py-op">,</tt><tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-3" 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-3', 'split', 'link-3');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</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>
<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">qual_clipping_start</tt><tt class="py-op">=</tt><tt id="link-4" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-4', 'header', 'link-2');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">qual_clipping_end</tt><tt class="py-op">=</tt><tt id="link-5" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-5', 'header', 'link-2');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">align_clipping_start</tt><tt class="py-op">=</tt><tt id="link-6" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-6', 'header', 'link-2');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">align_clipping_end</tt><tt class="py-op">=</tt><tt id="link-7" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-7', 'header', 'link-2');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt> </tt>
</div></div><a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> </tt>
<a name="ds"></a><div id="ds-def"><a name="L86"></a><tt class="py-lineno"> 86</tt> <a class="py-toggle" href="#" id="ds-toggle" onclick="return toggle('ds');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Sequencing.Ace.ds-class.html">ds</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ds-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="ds-expanded"><a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-docstring">"""DS lines, include file name of a read's chromatogram file."""</tt> </tt>
<a name="ds.__init__"></a><div id="ds.__init__-def"><a name="L88"></a><tt class="py-lineno"> 88</tt> <a class="py-toggle" href="#" id="ds.__init__-toggle" onclick="return toggle('ds.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace.ds-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">line</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="ds.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ds.__init__-expanded"><a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">chromat_file</tt><tt class="py-op">=</tt><tt class="py-string">''</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">phd_file</tt><tt class="py-op">=</tt><tt class="py-string">''</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 class="py-name">time</tt><tt class="py-op">=</tt><tt class="py-string">''</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">chem</tt><tt class="py-op">=</tt><tt class="py-string">''</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dye</tt><tt class="py-op">=</tt><tt class="py-string">''</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">template</tt><tt class="py-op">=</tt><tt class="py-string">''</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">direction</tt><tt class="py-op">=</tt><tt class="py-string">''</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">:</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-name">tags</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-string">'CHROMAT_FILE'</tt><tt class="py-op">,</tt><tt class="py-string">'PHD_FILE'</tt><tt class="py-op">,</tt><tt class="py-string">'TIME'</tt><tt class="py-op">,</tt><tt class="py-string">'CHEM'</tt><tt class="py-op">,</tt><tt class="py-string">'DYE'</tt><tt class="py-op">,</tt><tt class="py-string">'TEMPLATE'</tt><tt class="py-op">,</tt><tt class="py-string">'DIRECTION'</tt><tt class="py-op">]</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-name">poss</tt><tt class="py-op">=</tt><tt class="py-name">map</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-8" class="py-name" targets="Method Bio.NeuralNetwork.Gene.Motif.MotifFinder.find()=Bio.NeuralNetwork.Gene.Motif.MotifFinder-class.html#find,Method Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find()=Bio.NeuralNetwork.Gene.Schema.SchemaFinder-class.html#find,Method Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find()=Bio.NeuralNetwork.Gene.Signature.SignatureFinder-class.html#find,Method Bio.Seq.Seq.find()=Bio.Seq.Seq-class.html#find,Function Bio.triefind.find()=Bio.triefind-module.html#find"><a title="Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.Seq.Seq.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-8', 'find', 'link-8');">find</a></tt><tt class="py-op">,</tt><tt class="py-name">tags</tt><tt class="py-op">)</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-name">tagpos</tt><tt class="py-op">=</tt><tt class="py-name">dict</tt><tt class="py-op">(</tt><tt class="py-name">zip</tt><tt class="py-op">(</tt><tt class="py-name">poss</tt><tt class="py-op">,</tt><tt class="py-name">tags</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt> <tt class="py-keyword">in</tt> <tt class="py-name">tagpos</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">del</tt> <tt class="py-name">tagpos</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-name">ps</tt><tt class="py-op">=</tt><tt class="py-name">tagpos</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Method Bio.Crystal.Crystal.keys()=Bio.Crystal.Crystal-class.html#keys,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#keys,Method Bio.Phylo.PhyloXML.Events.keys()=Bio.Phylo.PhyloXML.Events-class.html#keys,Method Bio.SeqIO._index._IndexedSeqFileDict.keys()=Bio.SeqIO._index._IndexedSeqFileDict-class.html#keys,Method Bio.SeqIO._index._SQLiteManySeqFilesDict.keys()=Bio.SeqIO._index._SQLiteManySeqFilesDict-class.html#keys,Method BioSQL.BioSeqDatabase.BioSeqDatabase.keys()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#keys,Method BioSQL.BioSeqDatabase.DBServer.keys()=BioSQL.BioSeqDatabase.DBServer-class.html#keys"><a title="Bio.Crystal.Crystal.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Phylo.PhyloXML.Events.keys
Bio.SeqIO._index._IndexedSeqFileDict.keys
Bio.SeqIO._index._SQLiteManySeqFilesDict.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys" class="py-name" href="#" onclick="return doclink('link-9', 'keys', 'link-9');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-name">ps</tt><tt class="py-op">.</tt><tt id="link-10" class="py-name" targets="Method Bio.Align.MultipleSeqAlignment.sort()=Bio.Align.MultipleSeqAlignment-class.html#sort,Method Bio.PDB.Residue.DisorderedResidue.sort()=Bio.PDB.Residue.DisorderedResidue-class.html#sort,Method Bio.PDB.Residue.Residue.sort()=Bio.PDB.Residue.Residue-class.html#sort,Method Bio.Sequencing.Ace.ACEFileRecord.sort()=Bio.Sequencing.Ace.ACEFileRecord-class.html#sort"><a title="Bio.Align.MultipleSeqAlignment.sort
Bio.PDB.Residue.DisorderedResidue.sort
Bio.PDB.Residue.Residue.sort
Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-10', 'sort', 'link-10');">sort</a></tt><tt class="py-op">(</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">for</tt> <tt class="py-op">(</tt><tt class="py-name">p1</tt><tt class="py-op">,</tt><tt class="py-name">p2</tt><tt class="py-op">)</tt> <tt class="py-keyword">in</tt> <tt class="py-name">zip</tt><tt class="py-op">(</tt><tt class="py-name">ps</tt><tt class="py-op">,</tt><tt class="py-name">ps</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">+</tt><tt class="py-op">[</tt><tt class="py-name">len</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-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</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">setattr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt><tt class="py-name">tagpos</tt><tt class="py-op">[</tt><tt class="py-name">p1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-11" class="py-name" targets="Method Bio.Seq.Seq.lower()=Bio.Seq.Seq-class.html#lower,Method Bio.Seq.UnknownSeq.lower()=Bio.Seq.UnknownSeq-class.html#lower,Method Bio.SeqRecord.SeqRecord.lower()=Bio.SeqRecord.SeqRecord-class.html#lower"><a title="Bio.Seq.Seq.lower
Bio.Seq.UnknownSeq.lower
Bio.SeqRecord.SeqRecord.lower" class="py-name" href="#" onclick="return doclink('link-11', 'lower', 'link-11');">lower</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-name">p1</tt><tt class="py-op">+</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">tagpos</tt><tt class="py-op">[</tt><tt class="py-name">p1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-name">p2</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-12" 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-12', 'strip', 'link-12');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> </tt>
<a name="af"></a><div id="af-def"><a name="L108"></a><tt class="py-lineno">108</tt> <a class="py-toggle" href="#" id="af-toggle" onclick="return toggle('af');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Sequencing.Ace.af-class.html">af</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="af-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="af-expanded"><a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-docstring">"""AF lines, define the location of the read within the contig.</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"><tt class="py-docstring"> Note attribute coru is short for complemented (C) or uncomplemented (U),</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"><tt class="py-docstring"> since the strand information is stored in an ACE file using either the</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"><tt class="py-docstring"> C or U character.</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="af.__init__"></a><div id="af.__init__-def"><a name="L115"></a><tt class="py-lineno">115</tt> <a class="py-toggle" href="#" id="af.__init__-toggle" onclick="return toggle('af.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace.af-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">line</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="af.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="af.__init__-expanded"><a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-13" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-13', 'name', 'link-0');">name</a></tt><tt class="py-op">=</tt><tt class="py-string">''</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">coru</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">padded_start</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">:</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt id="link-14" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-14', 'header', 'link-2');">header</a></tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-15" 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-15', 'split', 'link-3');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-16" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-16', 'name', 'link-0');">name</a></tt> <tt class="py-op">=</tt> <tt id="link-17" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-17', 'header', 'link-2');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">coru</tt> <tt class="py-op">=</tt> <tt id="link-18" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-18', 'header', 'link-2');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">padded_start</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-19" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-19', 'header', 'link-2');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> </tt>
<a name="bs"></a><div id="bs-def"><a name="L125"></a><tt class="py-lineno">125</tt> <a class="py-toggle" href="#" id="bs-toggle" onclick="return toggle('bs');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Sequencing.Ace.bs-class.html">bs</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="bs-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="bs-expanded"><a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt class="py-docstring">""""BS (base segment), which read was chosen as the consensus at each position."""</tt> </tt>
<a name="bs.__init__"></a><div id="bs.__init__-def"><a name="L127"></a><tt class="py-lineno">127</tt> <a class="py-toggle" href="#" id="bs.__init__-toggle" onclick="return toggle('bs.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace.bs-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">line</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="bs.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="bs.__init__-expanded"><a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-20', 'name', 'link-0');">name</a></tt><tt class="py-op">=</tt><tt class="py-string">''</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">padded_start</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">padded_end</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">:</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt id="link-21" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-21', 'header', 'link-2');">header</a></tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-22" 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-22', 'split', 'link-3');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">padded_start</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-23" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-23', 'header', 'link-2');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">padded_end</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-24" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-24', 'header', 'link-2');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-25" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-25', 'name', 'link-0');">name</a></tt> <tt class="py-op">=</tt> <tt id="link-26" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-26', 'header', 'link-2');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt> </tt>
</div></div><a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> </tt>
<a name="rt"></a><div id="rt-def"><a name="L137"></a><tt class="py-lineno">137</tt> <a class="py-toggle" href="#" id="rt-toggle" onclick="return toggle('rt');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Sequencing.Ace.rt-class.html">rt</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-docstring">"""RT (transient read tags), generated by crossmatch and phrap."""</tt> </tt>
<a name="rt.__init__"></a><div id="rt.__init__-def"><a name="L139"></a><tt class="py-lineno">139</tt> <a class="py-toggle" href="#" id="rt.__init__-toggle" onclick="return toggle('rt.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace.rt-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">line</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="rt.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="rt.__init__-expanded"><a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-27" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-27', 'name', 'link-0');">name</a></tt><tt class="py-op">=</tt><tt class="py-string">''</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tag_type</tt><tt class="py-op">=</tt><tt class="py-string">''</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">program</tt><tt class="py-op">=</tt><tt class="py-string">''</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 class="py-name">padded_start</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">padded_end</tt><tt class="py-op">=</tt><tt class="py-name">None</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-28" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.date()=Bio.GenBank._FeatureConsumer-class.html#date,Method Bio.GenBank._RecordConsumer.date()=Bio.GenBank._RecordConsumer-class.html#date,Method Bio.Phylo.PhyloXMLIO.Parser.date()=Bio.Phylo.PhyloXMLIO.Parser-class.html#date,Method Bio.Phylo.PhyloXMLIO.Writer.date()=Bio.Phylo.PhyloXMLIO.Writer-class.html#date"><a title="Bio.GenBank._FeatureConsumer.date
Bio.GenBank._RecordConsumer.date
Bio.Phylo.PhyloXMLIO.Parser.date
Bio.Phylo.PhyloXMLIO.Writer.date" class="py-name" href="#" onclick="return doclink('link-28', 'date', 'link-28');">date</a></tt><tt class="py-op">=</tt><tt class="py-string">''</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-29" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.comment()=Bio.GenBank._FeatureConsumer-class.html#comment,Method Bio.GenBank._RecordConsumer.comment()=Bio.GenBank._RecordConsumer-class.html#comment"><a title="Bio.GenBank._FeatureConsumer.comment
Bio.GenBank._RecordConsumer.comment" class="py-name" href="#" onclick="return doclink('link-29', 'comment', 'link-29');">comment</a></tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </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">line</tt><tt class="py-op">:</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt id="link-30" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-30', 'header', 'link-2');">header</a></tt><tt class="py-op">=</tt><tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-31" 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-31', 'split', 'link-3');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-32" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-32', 'name', 'link-0');">name</a></tt><tt class="py-op">=</tt><tt id="link-33" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-33', 'header', 'link-2');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tag_type</tt><tt class="py-op">=</tt><tt id="link-34" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-34', 'header', 'link-2');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">program</tt><tt class="py-op">=</tt><tt id="link-35" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-35', 'header', 'link-2');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">padded_start</tt><tt class="py-op">=</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-36" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-36', 'header', 'link-2');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">padded_end</tt><tt class="py-op">=</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-37" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-37', 'header', 'link-2');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">4</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-38" class="py-name"><a title="Bio.GenBank._FeatureConsumer.date
Bio.GenBank._RecordConsumer.date
Bio.Phylo.PhyloXMLIO.Parser.date
Bio.Phylo.PhyloXMLIO.Writer.date" class="py-name" href="#" onclick="return doclink('link-38', 'date', 'link-28');">date</a></tt><tt class="py-op">=</tt><tt id="link-39" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-39', 'header', 'link-2');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">5</tt><tt class="py-op">]</tt> </tt>
</div></div><a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> </tt>
<a name="ct"></a><div id="ct-def"><a name="L156"></a><tt class="py-lineno">156</tt> <a class="py-toggle" href="#" id="ct-toggle" onclick="return toggle('ct');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Sequencing.Ace.ct-class.html">ct</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ct-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="ct-expanded"><a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-docstring">"""CT (consensus tags)."""</tt> </tt>
<a name="ct.__init__"></a><div id="ct.__init__-def"><a name="L158"></a><tt class="py-lineno">158</tt> <a class="py-toggle" href="#" id="ct.__init__-toggle" onclick="return toggle('ct.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace.ct-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">line</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="ct.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ct.__init__-expanded"><a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-40" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-40', 'name', 'link-0');">name</a></tt><tt class="py-op">=</tt><tt class="py-string">''</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tag_type</tt><tt class="py-op">=</tt><tt class="py-string">''</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">program</tt><tt class="py-op">=</tt><tt class="py-string">''</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">padded_start</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">padded_end</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-41" class="py-name"><a title="Bio.GenBank._FeatureConsumer.date
Bio.GenBank._RecordConsumer.date
Bio.Phylo.PhyloXMLIO.Parser.date
Bio.Phylo.PhyloXMLIO.Writer.date" class="py-name" href="#" onclick="return doclink('link-41', 'date', 'link-28');">date</a></tt><tt class="py-op">=</tt><tt class="py-string">''</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">notrans</tt><tt class="py-op">=</tt><tt class="py-string">''</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">info</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-42" class="py-name"><a title="Bio.GenBank._FeatureConsumer.comment
Bio.GenBank._RecordConsumer.comment" class="py-name" href="#" onclick="return doclink('link-42', 'comment', 'link-29');">comment</a></tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">:</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt id="link-43" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-43', 'header', 'link-2');">header</a></tt><tt class="py-op">=</tt><tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-44" 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-44', 'split', 'link-3');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</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.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-45', 'name', 'link-0');">name</a></tt> <tt class="py-op">=</tt> <tt id="link-46" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-46', 'header', 'link-2');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tag_type</tt> <tt class="py-op">=</tt> <tt id="link-47" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-47', 'header', 'link-2');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">program</tt> <tt class="py-op">=</tt> <tt id="link-48" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-48', 'header', 'link-2');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">padded_start</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-49" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-49', 'header', 'link-2');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">padded_end</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-50" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-50', 'header', 'link-2');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">4</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-51" class="py-name"><a title="Bio.GenBank._FeatureConsumer.date
Bio.GenBank._RecordConsumer.date
Bio.Phylo.PhyloXMLIO.Parser.date
Bio.Phylo.PhyloXMLIO.Writer.date" class="py-name" href="#" onclick="return doclink('link-51', 'date', 'link-28');">date</a></tt> <tt class="py-op">=</tt> <tt id="link-52" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-52', 'header', 'link-2');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">5</tt><tt class="py-op">]</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-53" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-53', 'header', 'link-2');">header</a></tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt class="py-number">7</tt><tt class="py-op">:</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">notrans</tt> <tt class="py-op">=</tt> <tt id="link-54" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-54', 'header', 'link-2');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">6</tt><tt class="py-op">]</tt> </tt>
</div></div><a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> </tt>
<a name="wa"></a><div id="wa-def"><a name="L179"></a><tt class="py-lineno">179</tt> <a class="py-toggle" href="#" id="wa-toggle" onclick="return toggle('wa');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Sequencing.Ace.wa-class.html">wa</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="wa-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="wa-expanded"><a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-docstring">"""WA (whole assembly tag), holds the assembly program name, version, etc."""</tt> </tt>
<a name="wa.__init__"></a><div id="wa.__init__-def"><a name="L181"></a><tt class="py-lineno">181</tt> <a class="py-toggle" href="#" id="wa.__init__-toggle" onclick="return toggle('wa.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace.wa-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">line</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="wa.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="wa.__init__-expanded"><a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tag_type</tt><tt class="py-op">=</tt><tt class="py-string">''</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">program</tt><tt class="py-op">=</tt><tt class="py-string">''</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-55" class="py-name"><a title="Bio.GenBank._FeatureConsumer.date
Bio.GenBank._RecordConsumer.date
Bio.Phylo.PhyloXMLIO.Parser.date
Bio.Phylo.PhyloXMLIO.Writer.date" class="py-name" href="#" onclick="return doclink('link-55', 'date', 'link-28');">date</a></tt><tt class="py-op">=</tt><tt class="py-string">''</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">info</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">:</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt id="link-56" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-56', 'header', 'link-2');">header</a></tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-57" 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-57', 'split', 'link-3');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tag_type</tt> <tt class="py-op">=</tt> <tt id="link-58" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-58', 'header', 'link-2');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">program</tt> <tt class="py-op">=</tt> <tt id="link-59" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-59', 'header', 'link-2');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-60" class="py-name"><a title="Bio.GenBank._FeatureConsumer.date
Bio.GenBank._RecordConsumer.date
Bio.Phylo.PhyloXMLIO.Parser.date
Bio.Phylo.PhyloXMLIO.Writer.date" class="py-name" href="#" onclick="return doclink('link-60', 'date', 'link-28');">date</a></tt> <tt class="py-op">=</tt> <tt id="link-61" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-61', 'header', 'link-2');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> </tt>
</div></div><a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> </tt>
<a name="wr"></a><div id="wr-def"><a name="L192"></a><tt class="py-lineno">192</tt> <a class="py-toggle" href="#" id="wr-toggle" onclick="return toggle('wr');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Sequencing.Ace.wr-class.html">wr</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="wr-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="wr-expanded"><a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-docstring">"""WR lines."""</tt> </tt>
<a name="wr.__init__"></a><div id="wr.__init__-def"><a name="L194"></a><tt class="py-lineno">194</tt> <a class="py-toggle" href="#" id="wr.__init__-toggle" onclick="return toggle('wr.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace.wr-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">line</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="wr.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="wr.__init__-expanded"><a name="L195"></a><tt class="py-lineno">195</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.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-62', 'name', 'link-0');">name</a></tt><tt class="py-op">=</tt><tt class="py-string">''</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">aligned</tt><tt class="py-op">=</tt><tt class="py-string">''</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">program</tt><tt class="py-op">=</tt><tt class="py-string">''</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-63" class="py-name"><a title="Bio.GenBank._FeatureConsumer.date
Bio.GenBank._RecordConsumer.date
Bio.Phylo.PhyloXMLIO.Parser.date
Bio.Phylo.PhyloXMLIO.Writer.date" class="py-name" href="#" onclick="return doclink('link-63', 'date', 'link-28');">date</a></tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">:</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt id="link-64" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-64', 'header', 'link-2');">header</a></tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-65" 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-65', 'split', 'link-3');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-66" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-66', 'name', 'link-0');">name</a></tt> <tt class="py-op">=</tt> <tt id="link-67" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-67', 'header', 'link-2');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">aligned</tt> <tt class="py-op">=</tt> <tt id="link-68" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-68', 'header', 'link-2');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">program</tt> <tt class="py-op">=</tt> <tt id="link-69" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-69', 'header', 'link-2');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-70" class="py-name"><a title="Bio.GenBank._FeatureConsumer.date
Bio.GenBank._RecordConsumer.date
Bio.Phylo.PhyloXMLIO.Parser.date
Bio.Phylo.PhyloXMLIO.Writer.date" class="py-name" href="#" onclick="return doclink('link-70', 'date', 'link-28');">date</a></tt> <tt class="py-op">=</tt> <tt id="link-71" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-71', 'header', 'link-2');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt> </tt>
</div></div><a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> </tt>
<a name="Reads"></a><div id="Reads-def"><a name="L206"></a><tt class="py-lineno">206</tt> <a class="py-toggle" href="#" id="Reads-toggle" onclick="return toggle('Reads');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Sequencing.Ace.Reads-class.html">Reads</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Reads-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Reads-expanded"><a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> <tt class="py-docstring">"""Holds information about a read supporting an ACE contig."""</tt> </tt>
<a name="Reads.__init__"></a><div id="Reads.__init__-def"><a name="L208"></a><tt class="py-lineno">208</tt> <a class="py-toggle" href="#" id="Reads.__init__-toggle" onclick="return toggle('Reads.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace.Reads-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">line</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="Reads.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Reads.__init__-expanded"><a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-72" class="py-name" targets="Class Bio.Sequencing.Ace.rd=Bio.Sequencing.Ace.rd-class.html"><a title="Bio.Sequencing.Ace.rd" class="py-name" href="#" onclick="return doclink('link-72', 'rd', 'link-72');">rd</a></tt><tt class="py-op">=</tt><tt class="py-name">None</tt> <tt class="py-comment"># one per read</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-73" class="py-name" targets="Class Bio.Sequencing.Ace.qa=Bio.Sequencing.Ace.qa-class.html"><a title="Bio.Sequencing.Ace.qa" class="py-name" href="#" onclick="return doclink('link-73', 'qa', 'link-73');">qa</a></tt><tt class="py-op">=</tt><tt class="py-name">None</tt> <tt class="py-comment"># one per read</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-74" class="py-name" targets="Class Bio.Sequencing.Ace.ds=Bio.Sequencing.Ace.ds-class.html"><a title="Bio.Sequencing.Ace.ds" class="py-name" href="#" onclick="return doclink('link-74', 'ds', 'link-74');">ds</a></tt><tt class="py-op">=</tt><tt class="py-name">None</tt> <tt class="py-comment"># none or one per read</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-75" class="py-name" targets="Class Bio.Sequencing.Ace.rt=Bio.Sequencing.Ace.rt-class.html"><a title="Bio.Sequencing.Ace.rt" class="py-name" href="#" onclick="return doclink('link-75', 'rt', 'link-75');">rt</a></tt><tt class="py-op">=</tt><tt class="py-name">None</tt> <tt class="py-comment"># none or many per read</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-76" class="py-name" targets="Class Bio.Sequencing.Ace.wr=Bio.Sequencing.Ace.wr-class.html"><a title="Bio.Sequencing.Ace.wr" class="py-name" href="#" onclick="return doclink('link-76', 'wr', 'link-76');">wr</a></tt><tt class="py-op">=</tt><tt class="py-name">None</tt> <tt class="py-comment"># none or many per read</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">:</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</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.Sequencing.Ace.rd" class="py-name" href="#" onclick="return doclink('link-77', 'rd', 'link-72');">rd</a></tt> <tt class="py-op">=</tt> <tt id="link-78" class="py-name"><a title="Bio.Sequencing.Ace.rd" class="py-name" href="#" onclick="return doclink('link-78', 'rd', 'link-72');">rd</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt id="link-79" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-79', 'header', 'link-2');">header</a></tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-80" 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-80', 'split', 'link-3');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-81" class="py-name"><a title="Bio.Sequencing.Ace.rd" class="py-name" href="#" onclick="return doclink('link-81', 'rd', 'link-72');">rd</a></tt><tt class="py-op">.</tt><tt id="link-82" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-82', 'name', 'link-0');">name</a></tt> <tt class="py-op">=</tt> <tt id="link-83" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-83', 'header', 'link-2');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-84" class="py-name"><a title="Bio.Sequencing.Ace.rd" class="py-name" href="#" onclick="return doclink('link-84', 'rd', 'link-72');">rd</a></tt><tt class="py-op">.</tt><tt class="py-name">padded_bases</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-85" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-85', 'header', 'link-2');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-86" class="py-name"><a title="Bio.Sequencing.Ace.rd" class="py-name" href="#" onclick="return doclink('link-86', 'rd', 'link-72');">rd</a></tt><tt class="py-op">.</tt><tt class="py-name">info_items</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-87" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-87', 'header', 'link-2');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-88" class="py-name"><a title="Bio.Sequencing.Ace.rd" class="py-name" href="#" onclick="return doclink('link-88', 'rd', 'link-72');">rd</a></tt><tt class="py-op">.</tt><tt class="py-name">read_tags</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-89" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-89', 'header', 'link-2');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">4</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> </tt>
<a name="Contig"></a><div id="Contig-def"><a name="L222"></a><tt class="py-lineno">222</tt> <a class="py-toggle" href="#" id="Contig-toggle" onclick="return toggle('Contig');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Sequencing.Ace.Contig-class.html">Contig</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Contig-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Contig-expanded"><a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt class="py-docstring">"""Holds information about a contig from an ACE record."""</tt> </tt>
<a name="Contig.__init__"></a><div id="Contig.__init__-def"><a name="L224"></a><tt class="py-lineno">224</tt> <a class="py-toggle" href="#" id="Contig.__init__-toggle" onclick="return toggle('Contig.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace.Contig-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">line</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="Contig.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Contig.__init__-expanded"><a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-90" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-90', 'name', 'link-0');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nbases</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nreads</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nsegments</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">uorc</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-91" class="py-name"><a title="Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.Phylo.PhyloXMLIO.Writer.sequence" class="py-name" href="#" onclick="return doclink('link-91', 'sequence', 'link-1');">sequence</a></tt><tt class="py-op">=</tt><tt class="py-string">""</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">quality</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-92" class="py-name" targets="Class Bio.Sequencing.Ace.af=Bio.Sequencing.Ace.af-class.html"><a title="Bio.Sequencing.Ace.af" class="py-name" href="#" onclick="return doclink('link-92', 'af', 'link-92');">af</a></tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-93" class="py-name" targets="Class Bio.Sequencing.Ace.bs=Bio.Sequencing.Ace.bs-class.html"><a title="Bio.Sequencing.Ace.bs" class="py-name" href="#" onclick="return doclink('link-93', 'bs', 'link-93');">bs</a></tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">reads</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-94" class="py-name" targets="Class Bio.Sequencing.Ace.ct=Bio.Sequencing.Ace.ct-class.html"><a title="Bio.Sequencing.Ace.ct" class="py-name" href="#" onclick="return doclink('link-94', 'ct', 'link-94');">ct</a></tt><tt class="py-op">=</tt><tt class="py-name">None</tt> <tt class="py-comment"># none or many</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-95" class="py-name" targets="Class Bio.Sequencing.Ace.wa=Bio.Sequencing.Ace.wa-class.html"><a title="Bio.Sequencing.Ace.wa" class="py-name" href="#" onclick="return doclink('link-95', 'wa', 'link-95');">wa</a></tt><tt class="py-op">=</tt><tt class="py-name">None</tt> <tt class="py-comment"># none or many</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">:</tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> <tt id="link-96" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-96', 'header', 'link-2');">header</a></tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-97" 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-97', 'split', 'link-3');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-98" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-98', 'name', 'link-0');">name</a></tt> <tt class="py-op">=</tt> <tt id="link-99" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-99', 'header', 'link-2');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nbases</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-100" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-100', 'header', 'link-2');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nreads</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-101" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-101', 'header', 'link-2');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nsegments</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-102" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-102', 'header', 'link-2');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">4</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">uorc</tt> <tt class="py-op">=</tt> <tt id="link-103" class="py-name"><a title="Bio.Wise.dnal.Statistics.header" class="py-name" href="#" onclick="return doclink('link-103', 'header', 'link-2');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">5</tt><tt class="py-op">]</tt> </tt>
</div></div><a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> </tt>
<a name="parse"></a><div id="parse-def"><a name="L245"></a><tt class="py-lineno">245</tt> <a class="py-toggle" href="#" id="parse-toggle" onclick="return toggle('parse');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace-module.html#parse">parse</a><tt class="py-op">(</tt><tt class="py-param">handle</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="parse-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="parse-expanded"><a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> <tt class="py-docstring">"""parse(handle)</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"><tt class="py-docstring"> where handle is a file-like object.</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"><tt class="py-docstring"> This function returns an iterator that allows you to iterate</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"><tt class="py-docstring"> over the ACE file record by record:</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"><tt class="py-docstring"> records = parse(handle)</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"><tt class="py-docstring"> for record in records:</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"><tt class="py-docstring"> # do something with the record</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"><tt class="py-docstring"> where each record is a Contig object.</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"> <tt id="link-104" 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-104', 'handle', 'link-104');">handle</a></tt> <tt class="py-op">=</tt> <tt class="py-name">iter</tt><tt class="py-op">(</tt><tt id="link-105" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-105', 'handle', 'link-104');">handle</a></tt><tt class="py-op">)</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</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="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> <tt class="py-comment"># at beginning, skip the AS and look for first CO command</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</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="L267"></a><tt class="py-lineno">267</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-106" class="py-name" targets="Method Bio.Seq.Seq.startswith()=Bio.Seq.Seq-class.html#startswith"><a title="Bio.Seq.Seq.startswith" class="py-name" href="#" onclick="return doclink('link-106', 'startswith', 'link-106');">startswith</a></tt><tt class="py-op">(</tt><tt class="py-string">'CO'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt id="link-107" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-107', 'handle', 'link-104');">handle</a></tt><tt class="py-op">.</tt><tt id="link-108" class="py-name" targets="Method Bio.AlignIO.ClustalIO.ClustalIterator.next()=Bio.AlignIO.ClustalIO.ClustalIterator-class.html#next,Method Bio.AlignIO.EmbossIO.EmbossIterator.next()=Bio.AlignIO.EmbossIO.EmbossIterator-class.html#next,Method Bio.AlignIO.Interfaces.AlignmentIterator.next()=Bio.AlignIO.Interfaces.AlignmentIterator-class.html#next,Method Bio.AlignIO.PhylipIO.PhylipIterator.next()=Bio.AlignIO.PhylipIO.PhylipIterator-class.html#next,Method Bio.AlignIO.StockholmIO.StockholmIterator.next()=Bio.AlignIO.StockholmIO.StockholmIterator-class.html#next,Method Bio.Blast.NCBIStandalone.Iterator.next()=Bio.Blast.NCBIStandalone.Iterator-class.html#next,Method Bio.Blast.ParseBlastTable.BlastTableReader.next()=Bio.Blast.ParseBlastTable.BlastTableReader-class.html#next,Method Bio.Compass.Iterator.next()=Bio.Compass.Iterator-class.html#next,Method Bio.DocSQL.IterationCursor.next()=Bio.DocSQL.IterationCursor-class.html#next,Method Bio.File.UndoHandle.next()=Bio.File.UndoHandle-class.html#next,Method Bio.GenBank.Iterator.next()=Bio.GenBank.Iterator-class.html#next,Method Bio.Nexus.Nexus.CharBuffer.next()=Bio.Nexus.Nexus.CharBuffer-class.html#next,Method Bio.PopGen.GenePop.Controller._FileIterator.next()=Bio.PopGen.GenePop.Controller._FileIterator-class.html#next,Method Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next()=Bio.SeqIO.Interfaces.InterlacedSequenceIterator-class.html#next,Method Bio.SeqIO.Interfaces.SequenceIterator.next()=Bio.SeqIO.Interfaces.SequenceIterator-class.html#next,Method Bio.UniGene.Iterator.next()=Bio.UniGene.Iterator-class.html#next"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.File.UndoHandle.next
Bio.GenBank.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.PopGen.GenePop.Controller._FileIterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.UniGene.Iterator.next" class="py-name" href="#" onclick="return doclink('link-108', 'next', 'link-108');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">StopIteration</tt><tt class="py-op">:</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> <tt class="py-name">record</tt> <tt class="py-op">=</tt> <tt id="link-109" class="py-name" targets="Class Bio.Sequencing.Ace.Contig=Bio.Sequencing.Ace.Contig-class.html"><a title="Bio.Sequencing.Ace.Contig" class="py-name" href="#" onclick="return doclink('link-109', 'Contig', 'link-109');">Contig</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> </tt>
<a name="L275"></a><tt class="py-lineno">275</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-110" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-110', 'handle', 'link-104');">handle</a></tt><tt class="py-op">:</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-111" class="py-name"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-111', 'strip', 'link-12');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</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>
<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-112" class="py-name"><a title="Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.Phylo.PhyloXMLIO.Writer.sequence" class="py-name" href="#" onclick="return doclink('link-112', 'sequence', 'link-1');">sequence</a></tt><tt class="py-op">+=</tt><tt class="py-name">line</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> </tt>
<a name="L281"></a><tt class="py-lineno">281</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-113" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-113', 'handle', 'link-104');">handle</a></tt><tt class="py-op">:</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</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-114" class="py-name"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-114', 'strip', 'link-12');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</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 id="link-115" class="py-name"><a title="Bio.Seq.Seq.startswith" class="py-name" href="#" onclick="return doclink('link-115', 'startswith', 'link-106');">startswith</a></tt><tt class="py-op">(</tt><tt class="py-string">"BQ"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</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">"Failed to find BQ line"</tt><tt class="py-op">)</tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"> </tt>
<a name="L287"></a><tt class="py-lineno">287</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-116" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-116', 'handle', 'link-104');">handle</a></tt><tt class="py-op">:</tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</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 id="link-117" class="py-name"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-117', 'strip', 'link-12');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt class="py-name">quality</tt><tt class="py-op">.</tt><tt id="link-118" class="py-name" targets="Method Bio.Align.MultipleSeqAlignment.extend()=Bio.Align.MultipleSeqAlignment-class.html#extend,Method Bio.SCOP.Raf.SeqMap.extend()=Bio.SCOP.Raf.SeqMap-class.html#extend,Method Bio.Seq.MutableSeq.extend()=Bio.Seq.MutableSeq-class.html#extend"><a title="Bio.Align.MultipleSeqAlignment.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-118', 'extend', 'link-118');">extend</a></tt><tt class="py-op">(</tt><tt class="py-name">map</tt><tt class="py-op">(</tt><tt class="py-name">int</tt><tt class="py-op">,</tt><tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-119" 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-119', 'split', 'link-3');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"> </tt>
<a name="L292"></a><tt class="py-lineno">292</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-120" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-120', 'handle', 'link-104');">handle</a></tt><tt class="py-op">:</tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</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-121" class="py-name"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-121', 'strip', 'link-12');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"> </tt>
<a name="L296"></a><tt class="py-lineno">296</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="L297"></a><tt class="py-lineno">297</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 id="link-122" class="py-name"><a title="Bio.Seq.Seq.startswith" class="py-name" href="#" onclick="return doclink('link-122', 'startswith', 'link-106');">startswith</a></tt><tt class="py-op">(</tt><tt class="py-string">"AF "</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-123" class="py-name"><a title="Bio.Sequencing.Ace.af" class="py-name" href="#" onclick="return doclink('link-123', 'af', 'link-92');">af</a></tt><tt class="py-op">.</tt><tt id="link-124" 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-124', 'append', 'link-124');">append</a></tt><tt class="py-op">(</tt><tt id="link-125" class="py-name"><a title="Bio.Sequencing.Ace.af" class="py-name" href="#" onclick="return doclink('link-125', 'af', 'link-92');">af</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt id="link-126" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-126', 'handle', 'link-104');">handle</a></tt><tt class="py-op">.</tt><tt id="link-127" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.File.UndoHandle.next
Bio.GenBank.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.PopGen.GenePop.Controller._FileIterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.UniGene.Iterator.next" class="py-name" href="#" onclick="return doclink('link-127', 'next', 'link-108');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">StopIteration</tt><tt class="py-op">:</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</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">"Unexpected end of AF block"</tt><tt class="py-op">)</tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"> </tt>
<a name="L305"></a><tt class="py-lineno">305</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="L306"></a><tt class="py-lineno">306</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-128" class="py-name"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-128', 'strip', 'link-12');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt id="link-129" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-129', 'handle', 'link-104');">handle</a></tt><tt class="py-op">.</tt><tt id="link-130" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.File.UndoHandle.next
Bio.GenBank.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.PopGen.GenePop.Controller._FileIterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.UniGene.Iterator.next" class="py-name" href="#" onclick="return doclink('link-130', 'next', 'link-108');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">StopIteration</tt><tt class="py-op">:</tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</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">"Unexpected end of file"</tt><tt class="py-op">)</tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"> </tt>
<a name="L313"></a><tt class="py-lineno">313</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="L314"></a><tt class="py-lineno">314</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 id="link-131" class="py-name"><a title="Bio.Seq.Seq.startswith" class="py-name" href="#" onclick="return doclink('link-131', 'startswith', 'link-106');">startswith</a></tt><tt class="py-op">(</tt><tt class="py-string">"BS "</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-132" class="py-name"><a title="Bio.Sequencing.Ace.bs" class="py-name" href="#" onclick="return doclink('link-132', 'bs', 'link-93');">bs</a></tt><tt class="py-op">.</tt><tt id="link-133" class="py-name"><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-133', 'append', 'link-124');">append</a></tt><tt class="py-op">(</tt><tt id="link-134" class="py-name"><a title="Bio.Sequencing.Ace.bs" class="py-name" href="#" onclick="return doclink('link-134', 'bs', 'link-93');">bs</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt id="link-135" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-135', 'handle', 'link-104');">handle</a></tt><tt class="py-op">.</tt><tt id="link-136" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.File.UndoHandle.next
Bio.GenBank.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.PopGen.GenePop.Controller._FileIterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.UniGene.Iterator.next" class="py-name" href="#" onclick="return doclink('link-136', 'next', 'link-108');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">StopIteration</tt><tt class="py-op">:</tt> </tt>
<a name="L320"></a><tt class="py-lineno">320</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">"Failed to find end of BS block"</tt><tt class="py-op">)</tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"> </tt>
<a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"> <tt class="py-comment"># now read all the read data</tt> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt> <tt class="py-line"> <tt class="py-comment"># it starts with a 'RD', and then a mandatory QA</tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"> <tt class="py-comment"># then follows an optional DS</tt> </tt>
<a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"> <tt class="py-comment"># CT,RT,WA,WR may or may not be there in unlimited quantity. They might refer to the actual read or contig,</tt> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"> <tt class="py-comment"># or, if encountered at the end of file, to any previous read or contig. the sort() method deals</tt> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"> <tt class="py-comment"># with that later.</tt> </tt>
<a name="L328"></a><tt class="py-lineno">328</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="L329"></a><tt class="py-lineno">329</tt> <tt class="py-line"> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"> <tt class="py-comment"># each read must have a rd and qa</tt> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</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="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"> <tt class="py-comment"># If I've met the condition, then stop reading the line.</tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</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-137" class="py-name"><a title="Bio.Seq.Seq.startswith" class="py-name" href="#" onclick="return doclink('link-137', 'startswith', 'link-106');">startswith</a></tt><tt class="py-op">(</tt><tt class="py-string">"RD "</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt id="link-138" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-138', 'handle', 'link-104');">handle</a></tt><tt class="py-op">.</tt><tt id="link-139" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.File.UndoHandle.next
Bio.GenBank.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.PopGen.GenePop.Controller._FileIterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.UniGene.Iterator.next" class="py-name" href="#" onclick="return doclink('link-139', 'next', 'link-108');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">StopIteration</tt><tt class="py-op">:</tt> </tt>
<a name="L338"></a><tt class="py-lineno">338</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">"Failed to find RD line"</tt><tt class="py-op">)</tt> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt> <tt class="py-line"> </tt>
<a name="L340"></a><tt class="py-lineno">340</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt class="py-name">reads</tt><tt class="py-op">.</tt><tt id="link-140" class="py-name"><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-140', 'append', 'link-124');">append</a></tt><tt class="py-op">(</tt><tt id="link-141" class="py-name" targets="Class Bio.Sequencing.Ace.Reads=Bio.Sequencing.Ace.Reads-class.html"><a title="Bio.Sequencing.Ace.Reads" class="py-name" href="#" onclick="return doclink('link-141', 'Reads', 'link-141');">Reads</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt> <tt class="py-line"> </tt>
<a name="L342"></a><tt class="py-lineno">342</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-142" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-142', 'handle', 'link-104');">handle</a></tt><tt class="py-op">:</tt> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-143" class="py-name"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-143', 'strip', 'link-12');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</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>
<a name="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt class="py-name">reads</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-144" class="py-name"><a title="Bio.Sequencing.Ace.rd" class="py-name" href="#" onclick="return doclink('link-144', 'rd', 'link-72');">rd</a></tt><tt class="py-op">.</tt><tt id="link-145" class="py-name"><a title="Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.Phylo.PhyloXMLIO.Writer.sequence" class="py-name" href="#" onclick="return doclink('link-145', 'sequence', 'link-1');">sequence</a></tt><tt class="py-op">+=</tt><tt class="py-name">line</tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt> <tt class="py-line"> </tt>
<a name="L348"></a><tt class="py-lineno">348</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-146" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-146', 'handle', 'link-104');">handle</a></tt><tt class="py-op">:</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</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-147" class="py-name"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-147', 'strip', 'link-12');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</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 id="link-148" class="py-name"><a title="Bio.Seq.Seq.startswith" class="py-name" href="#" onclick="return doclink('link-148', 'startswith', 'link-106');">startswith</a></tt><tt class="py-op">(</tt><tt class="py-string">"QA "</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</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">"Failed to find QA line"</tt><tt class="py-op">)</tt> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt class="py-name">reads</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-149" class="py-name"><a title="Bio.Sequencing.Ace.qa" class="py-name" href="#" onclick="return doclink('link-149', 'qa', 'link-73');">qa</a></tt> <tt class="py-op">=</tt> <tt id="link-150" class="py-name"><a title="Bio.Sequencing.Ace.qa" class="py-name" href="#" onclick="return doclink('link-150', 'qa', 'link-73');">qa</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt> <tt class="py-line"> </tt>
<a name="L355"></a><tt class="py-lineno">355</tt> <tt class="py-line"> <tt class="py-comment"># now one ds can follow</tt> </tt>
<a name="L356"></a><tt class="py-lineno">356</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-151" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-151', 'handle', 'link-104');">handle</a></tt><tt class="py-op">:</tt> </tt>
<a name="L357"></a><tt class="py-lineno">357</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-152" class="py-name"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-152', 'strip', 'link-12');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt> <tt class="py-line"> </tt>
<a name="L362"></a><tt class="py-lineno">362</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-153" class="py-name"><a title="Bio.Seq.Seq.startswith" class="py-name" href="#" onclick="return doclink('link-153', 'startswith', 'link-106');">startswith</a></tt><tt class="py-op">(</tt><tt class="py-string">"DS "</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt class="py-name">reads</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-154" class="py-name"><a title="Bio.Sequencing.Ace.ds" class="py-name" href="#" onclick="return doclink('link-154', 'ds', 'link-74');">ds</a></tt> <tt class="py-op">=</tt> <tt id="link-155" class="py-name"><a title="Bio.Sequencing.Ace.ds" class="py-name" href="#" onclick="return doclink('link-155', 'ds', 'link-74');">ds</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt> <tt class="py-line"> <tt class="py-comment"># the file could just end, or there's some more stuff. In ace files, anything can happen.</tt> </tt>
<a name="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"> <tt class="py-comment"># the following tags are interspersed between reads and can appear multiple times. </tt> </tt>
<a name="L367"></a><tt class="py-lineno">367</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="L368"></a><tt class="py-lineno">368</tt> <tt class="py-line"> <tt class="py-comment"># something left </tt> </tt>
<a name="L369"></a><tt class="py-lineno">369</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L370"></a><tt class="py-lineno">370</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="L371"></a><tt class="py-lineno">371</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-156" class="py-name"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-156', 'strip', 'link-12');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L372"></a><tt class="py-lineno">372</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L373"></a><tt class="py-lineno">373</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt id="link-157" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-157', 'handle', 'link-104');">handle</a></tt><tt class="py-op">.</tt><tt id="link-158" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.File.UndoHandle.next
Bio.GenBank.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.PopGen.GenePop.Controller._FileIterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.UniGene.Iterator.next" class="py-name" href="#" onclick="return doclink('link-158', 'next', 'link-108');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L374"></a><tt class="py-lineno">374</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">StopIteration</tt><tt class="py-op">:</tt> </tt>
<a name="L375"></a><tt class="py-lineno">375</tt> <tt class="py-line"> <tt class="py-comment"># file ends here</tt> </tt>
<a name="L376"></a><tt class="py-lineno">376</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L377"></a><tt class="py-lineno">377</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-159" class="py-name"><a title="Bio.Seq.Seq.startswith" class="py-name" href="#" onclick="return doclink('link-159', 'startswith', 'link-106');">startswith</a></tt><tt class="py-op">(</tt><tt class="py-string">"RT{"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L378"></a><tt class="py-lineno">378</tt> <tt class="py-line"> <tt class="py-comment"># now if we're at the end of the file, this rt could</tt> </tt>
<a name="L379"></a><tt class="py-lineno">379</tt> <tt class="py-line"> <tt class="py-comment"># belong to a previous read, not the actual one.</tt> </tt>
<a name="L380"></a><tt class="py-lineno">380</tt> <tt class="py-line"> <tt class="py-comment"># we store it here were it appears, the user can sort later.</tt> </tt>
<a name="L381"></a><tt class="py-lineno">381</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt class="py-name">reads</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-160" class="py-name"><a title="Bio.Sequencing.Ace.rt" class="py-name" href="#" onclick="return doclink('link-160', 'rt', 'link-75');">rt</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L382"></a><tt class="py-lineno">382</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt class="py-name">reads</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-161" class="py-name"><a title="Bio.Sequencing.Ace.rt" class="py-name" href="#" onclick="return doclink('link-161', 'rt', 'link-75');">rt</a></tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L383"></a><tt class="py-lineno">383</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-162" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-162', 'handle', 'link-104');">handle</a></tt><tt class="py-op">:</tt> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt> <tt class="py-line"> <tt class="py-name">line</tt><tt class="py-op">=</tt><tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-163" class="py-name"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-163', 'strip', 'link-12');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L385"></a><tt class="py-lineno">385</tt> <tt class="py-line"> <tt class="py-comment">#if line=="COMMENT{":</tt> </tt>
<a name="L386"></a><tt class="py-lineno">386</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-164" class="py-name"><a title="Bio.Seq.Seq.startswith" class="py-name" href="#" onclick="return doclink('link-164', 'startswith', 'link-106');">startswith</a></tt><tt class="py-op">(</tt><tt class="py-string">"COMMENT{"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L387"></a><tt class="py-lineno">387</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">8</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-165" class="py-name"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-165', 'strip', 'link-12');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L388"></a><tt class="py-lineno">388</tt> <tt class="py-line"> <tt class="py-comment">#MIRA 3.0.5 would miss the new line out :(</tt> </tt>
<a name="L389"></a><tt class="py-lineno">389</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt class="py-name">reads</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-166" class="py-name"><a title="Bio.Sequencing.Ace.rt" class="py-name" href="#" onclick="return doclink('link-166', 'rt', 'link-75');">rt</a></tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-167" class="py-name"><a title="Bio.GenBank._FeatureConsumer.comment
Bio.GenBank._RecordConsumer.comment" class="py-name" href="#" onclick="return doclink('link-167', 'comment', 'link-29');">comment</a></tt><tt class="py-op">.</tt><tt id="link-168" class="py-name"><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-168', 'append', 'link-124');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">8</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L390"></a><tt class="py-lineno">390</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-169" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-169', 'handle', 'link-104');">handle</a></tt><tt class="py-op">:</tt> </tt>
<a name="L391"></a><tt class="py-lineno">391</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-170" class="py-name"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-170', 'strip', 'link-12');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L392"></a><tt class="py-lineno">392</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-171" class="py-name" targets="Method Bio.Seq.Seq.endswith()=Bio.Seq.Seq-class.html#endswith"><a title="Bio.Seq.Seq.endswith" class="py-name" href="#" onclick="return doclink('link-171', 'endswith', 'link-171');">endswith</a></tt><tt class="py-op">(</tt><tt class="py-string">"C}"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L393"></a><tt class="py-lineno">393</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L394"></a><tt class="py-lineno">394</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt class="py-name">reads</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-172" class="py-name"><a title="Bio.Sequencing.Ace.rt" class="py-name" href="#" onclick="return doclink('link-172', 'rt', 'link-75');">rt</a></tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-173" class="py-name"><a title="Bio.GenBank._FeatureConsumer.comment
Bio.GenBank._RecordConsumer.comment" class="py-name" href="#" onclick="return doclink('link-173', 'comment', 'link-29');">comment</a></tt><tt class="py-op">.</tt><tt id="link-174" class="py-name"><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-174', 'append', 'link-124');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L395"></a><tt class="py-lineno">395</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">line</tt><tt class="py-op">==</tt><tt class="py-string">'}'</tt><tt class="py-op">:</tt> </tt>
<a name="L396"></a><tt class="py-lineno">396</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L397"></a><tt class="py-lineno">397</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L398"></a><tt class="py-lineno">398</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt class="py-name">reads</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-175" class="py-name"><a title="Bio.Sequencing.Ace.rt" class="py-name" href="#" onclick="return doclink('link-175', 'rt', 'link-75');">rt</a></tt><tt class="py-op">.</tt><tt id="link-176" class="py-name"><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-176', 'append', 'link-124');">append</a></tt><tt class="py-op">(</tt><tt id="link-177" class="py-name"><a title="Bio.Sequencing.Ace.rt" class="py-name" href="#" onclick="return doclink('link-177', 'rt', 'link-75');">rt</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L399"></a><tt class="py-lineno">399</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L400"></a><tt class="py-lineno">400</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-178" class="py-name"><a title="Bio.Seq.Seq.startswith" class="py-name" href="#" onclick="return doclink('link-178', 'startswith', 'link-106');">startswith</a></tt><tt class="py-op">(</tt><tt class="py-string">"WR{"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L401"></a><tt class="py-lineno">401</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt class="py-name">reads</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-179" class="py-name"><a title="Bio.Sequencing.Ace.wr" class="py-name" href="#" onclick="return doclink('link-179', 'wr', 'link-76');">wr</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L402"></a><tt class="py-lineno">402</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt class="py-name">reads</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-180" class="py-name"><a title="Bio.Sequencing.Ace.wr" class="py-name" href="#" onclick="return doclink('link-180', 'wr', 'link-76');">wr</a></tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L403"></a><tt class="py-lineno">403</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-181" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-181', 'handle', 'link-104');">handle</a></tt><tt class="py-op">:</tt> </tt>
<a name="L404"></a><tt class="py-lineno">404</tt> <tt class="py-line"> <tt class="py-name">line</tt><tt class="py-op">=</tt><tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-182" class="py-name"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-182', 'strip', 'link-12');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L405"></a><tt class="py-lineno">405</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">break</tt> </tt>
<a name="L406"></a><tt class="py-lineno">406</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt class="py-name">reads</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-183" class="py-name"><a title="Bio.Sequencing.Ace.wr" class="py-name" href="#" onclick="return doclink('link-183', 'wr', 'link-76');">wr</a></tt><tt class="py-op">.</tt><tt id="link-184" class="py-name"><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-184', 'append', 'link-124');">append</a></tt><tt class="py-op">(</tt><tt id="link-185" class="py-name"><a title="Bio.Sequencing.Ace.wr" class="py-name" href="#" onclick="return doclink('link-185', 'wr', 'link-76');">wr</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L407"></a><tt class="py-lineno">407</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L408"></a><tt class="py-lineno">408</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-186" class="py-name"><a title="Bio.Seq.Seq.startswith" class="py-name" href="#" onclick="return doclink('link-186', 'startswith', 'link-106');">startswith</a></tt><tt class="py-op">(</tt><tt class="py-string">"WA{"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L409"></a><tt class="py-lineno">409</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-187" class="py-name"><a title="Bio.Sequencing.Ace.wa" class="py-name" href="#" onclick="return doclink('link-187', 'wa', 'link-95');">wa</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L410"></a><tt class="py-lineno">410</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-188" class="py-name"><a title="Bio.Sequencing.Ace.wa" class="py-name" href="#" onclick="return doclink('link-188', 'wa', 'link-95');">wa</a></tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L411"></a><tt class="py-lineno">411</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L412"></a><tt class="py-lineno">412</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt id="link-189" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-189', 'handle', 'link-104');">handle</a></tt><tt class="py-op">.</tt><tt id="link-190" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.File.UndoHandle.next
Bio.GenBank.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.PopGen.GenePop.Controller._FileIterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.UniGene.Iterator.next" class="py-name" href="#" onclick="return doclink('link-190', 'next', 'link-108');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L413"></a><tt class="py-lineno">413</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">StopIteration</tt><tt class="py-op">:</tt> </tt>
<a name="L414"></a><tt class="py-lineno">414</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">"Failed to read WA block"</tt><tt class="py-op">)</tt> </tt>
<a name="L415"></a><tt class="py-lineno">415</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-191" class="py-name"><a title="Bio.Sequencing.Ace.wa" class="py-name" href="#" onclick="return doclink('link-191', 'wa', 'link-95');">wa</a></tt><tt class="py-op">.</tt><tt id="link-192" class="py-name"><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-192', 'append', 'link-124');">append</a></tt><tt class="py-op">(</tt><tt id="link-193" class="py-name"><a title="Bio.Sequencing.Ace.wa" class="py-name" href="#" onclick="return doclink('link-193', 'wa', 'link-95');">wa</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L416"></a><tt class="py-lineno">416</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-194" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-194', 'handle', 'link-104');">handle</a></tt><tt class="py-op">:</tt> </tt>
<a name="L417"></a><tt class="py-lineno">417</tt> <tt class="py-line"> <tt class="py-name">line</tt><tt class="py-op">=</tt><tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-195" class="py-name"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-195', 'strip', 'link-12');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L418"></a><tt class="py-lineno">418</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">break</tt> </tt>
<a name="L419"></a><tt class="py-lineno">419</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-196" class="py-name"><a title="Bio.Sequencing.Ace.wa" class="py-name" href="#" onclick="return doclink('link-196', 'wa', 'link-95');">wa</a></tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">info</tt><tt class="py-op">.</tt><tt id="link-197" class="py-name"><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-197', 'append', 'link-124');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L420"></a><tt class="py-lineno">420</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L421"></a><tt class="py-lineno">421</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-198" class="py-name"><a title="Bio.Seq.Seq.startswith" class="py-name" href="#" onclick="return doclink('link-198', 'startswith', 'link-106');">startswith</a></tt><tt class="py-op">(</tt><tt class="py-string">"CT{"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L422"></a><tt class="py-lineno">422</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-199" class="py-name"><a title="Bio.Sequencing.Ace.ct" class="py-name" href="#" onclick="return doclink('link-199', 'ct', 'link-94');">ct</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L423"></a><tt class="py-lineno">423</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-200" class="py-name"><a title="Bio.Sequencing.Ace.ct" class="py-name" href="#" onclick="return doclink('link-200', 'ct', 'link-94');">ct</a></tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L424"></a><tt class="py-lineno">424</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L425"></a><tt class="py-lineno">425</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt id="link-201" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-201', 'handle', 'link-104');">handle</a></tt><tt class="py-op">.</tt><tt id="link-202" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.File.UndoHandle.next
Bio.GenBank.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.PopGen.GenePop.Controller._FileIterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.UniGene.Iterator.next" class="py-name" href="#" onclick="return doclink('link-202', 'next', 'link-108');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L426"></a><tt class="py-lineno">426</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">StopIteration</tt><tt class="py-op">:</tt> </tt>
<a name="L427"></a><tt class="py-lineno">427</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">"Failed to read CT block"</tt><tt class="py-op">)</tt> </tt>
<a name="L428"></a><tt class="py-lineno">428</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-203" class="py-name"><a title="Bio.Sequencing.Ace.ct" class="py-name" href="#" onclick="return doclink('link-203', 'ct', 'link-94');">ct</a></tt><tt class="py-op">.</tt><tt id="link-204" class="py-name"><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-204', 'append', 'link-124');">append</a></tt><tt class="py-op">(</tt><tt id="link-205" class="py-name"><a title="Bio.Sequencing.Ace.ct" class="py-name" href="#" onclick="return doclink('link-205', 'ct', 'link-94');">ct</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L429"></a><tt class="py-lineno">429</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-206" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-206', 'handle', 'link-104');">handle</a></tt><tt class="py-op">:</tt> </tt>
<a name="L430"></a><tt class="py-lineno">430</tt> <tt class="py-line"> <tt class="py-name">line</tt><tt class="py-op">=</tt><tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-207" class="py-name"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-207', 'strip', 'link-12');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L431"></a><tt class="py-lineno">431</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">"COMMENT{"</tt><tt class="py-op">:</tt> </tt>
<a name="L432"></a><tt class="py-lineno">432</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-208" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-208', 'handle', 'link-104');">handle</a></tt><tt class="py-op">:</tt> </tt>
<a name="L433"></a><tt class="py-lineno">433</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-209" class="py-name"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-209', 'strip', 'link-12');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L434"></a><tt class="py-lineno">434</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-210" class="py-name"><a title="Bio.Seq.Seq.endswith" class="py-name" href="#" onclick="return doclink('link-210', 'endswith', 'link-171');">endswith</a></tt><tt class="py-op">(</tt><tt class="py-string">"C}"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L435"></a><tt class="py-lineno">435</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L436"></a><tt class="py-lineno">436</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-211" class="py-name"><a title="Bio.Sequencing.Ace.ct" class="py-name" href="#" onclick="return doclink('link-211', 'ct', 'link-94');">ct</a></tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-212" class="py-name"><a title="Bio.GenBank._FeatureConsumer.comment
Bio.GenBank._RecordConsumer.comment" class="py-name" href="#" onclick="return doclink('link-212', 'comment', 'link-29');">comment</a></tt><tt class="py-op">.</tt><tt id="link-213" class="py-name"><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-213', 'append', 'link-124');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L437"></a><tt class="py-lineno">437</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">line</tt><tt class="py-op">==</tt><tt class="py-string">'}'</tt><tt class="py-op">:</tt> </tt>
<a name="L438"></a><tt class="py-lineno">438</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L439"></a><tt class="py-lineno">439</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L440"></a><tt class="py-lineno">440</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-214" class="py-name"><a title="Bio.Sequencing.Ace.ct" class="py-name" href="#" onclick="return doclink('link-214', 'ct', 'link-94');">ct</a></tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">info</tt><tt class="py-op">.</tt><tt id="link-215" class="py-name"><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-215', 'append', 'link-124');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L441"></a><tt class="py-lineno">441</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L442"></a><tt class="py-lineno">442</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L443"></a><tt class="py-lineno">443</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L444"></a><tt class="py-lineno">444</tt> <tt class="py-line"> </tt>
<a name="L445"></a><tt class="py-lineno">445</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 id="link-216" class="py-name"><a title="Bio.Seq.Seq.startswith" class="py-name" href="#" onclick="return doclink('link-216', 'startswith', 'link-106');">startswith</a></tt><tt class="py-op">(</tt><tt class="py-string">'RD'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-comment"># another read?</tt> </tt>
<a name="L446"></a><tt class="py-lineno">446</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L447"></a><tt class="py-lineno">447</tt> <tt class="py-line"> </tt>
<a name="L448"></a><tt class="py-lineno">448</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-name">record</tt> </tt>
</div><a name="L449"></a><tt class="py-lineno">449</tt> <tt class="py-line"> </tt>
<a name="ACEFileRecord"></a><div id="ACEFileRecord-def"><a name="L450"></a><tt class="py-lineno">450</tt> <a class="py-toggle" href="#" id="ACEFileRecord-toggle" onclick="return toggle('ACEFileRecord');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Sequencing.Ace.ACEFileRecord-class.html">ACEFileRecord</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ACEFileRecord-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="ACEFileRecord-expanded"><a name="L451"></a><tt class="py-lineno">451</tt> <tt class="py-line"> <tt class="py-docstring">"""Holds data of an ACE file.</tt> </tt>
<a name="L452"></a><tt class="py-lineno">452</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="ACEFileRecord.__init__"></a><div id="ACEFileRecord.__init__-def"><a name="L453"></a><tt class="py-lineno">453</tt> <a class="py-toggle" href="#" id="ACEFileRecord.__init__-toggle" onclick="return toggle('ACEFileRecord.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace.ACEFileRecord-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ACEFileRecord.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ACEFileRecord.__init__-expanded"><a name="L454"></a><tt class="py-lineno">454</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ncontigs</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L455"></a><tt class="py-lineno">455</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nreads</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L456"></a><tt class="py-lineno">456</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">contigs</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L457"></a><tt class="py-lineno">457</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-217" class="py-name"><a title="Bio.Sequencing.Ace.wa" class="py-name" href="#" onclick="return doclink('link-217', 'wa', 'link-95');">wa</a></tt><tt class="py-op">=</tt><tt class="py-name">None</tt> <tt class="py-comment"># none or many</tt> </tt>
</div><a name="L458"></a><tt class="py-lineno">458</tt> <tt class="py-line"> </tt>
<a name="ACEFileRecord.sort"></a><div id="ACEFileRecord.sort-def"><a name="L459"></a><tt class="py-lineno">459</tt> <a class="py-toggle" href="#" id="ACEFileRecord.sort-toggle" onclick="return toggle('ACEFileRecord.sort');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace.ACEFileRecord-class.html#sort">sort</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ACEFileRecord.sort-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ACEFileRecord.sort-expanded"><a name="L460"></a><tt class="py-lineno">460</tt> <tt class="py-line"> <tt class="py-docstring">"""Sorts wr, rt and ct tags into the appropriate contig / read instance, if possible. """</tt> </tt>
<a name="L461"></a><tt class="py-lineno">461</tt> <tt class="py-line"> </tt>
<a name="L462"></a><tt class="py-lineno">462</tt> <tt class="py-line"> <tt id="link-218" class="py-name"><a title="Bio.Sequencing.Ace.ct" class="py-name" href="#" onclick="return doclink('link-218', 'ct', 'link-94');">ct</a></tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L463"></a><tt class="py-lineno">463</tt> <tt class="py-line"> <tt id="link-219" class="py-name"><a title="Bio.Sequencing.Ace.rt" class="py-name" href="#" onclick="return doclink('link-219', 'rt', 'link-75');">rt</a></tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L464"></a><tt class="py-lineno">464</tt> <tt class="py-line"> <tt id="link-220" class="py-name"><a title="Bio.Sequencing.Ace.wr" class="py-name" href="#" onclick="return doclink('link-220', 'wr', 'link-76');">wr</a></tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L465"></a><tt class="py-lineno">465</tt> <tt class="py-line"> <tt class="py-comment"># search for tags that aren't in the right position</tt> </tt>
<a name="L466"></a><tt class="py-lineno">466</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-221" 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-221', 'i', 'link-221');">i</a></tt> <tt class="py-keyword">in</tt> <tt id="link-222" 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-222', 'range', 'link-222');">range</a></tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">contigs</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L467"></a><tt class="py-lineno">467</tt> <tt class="py-line"> <tt class="py-name">c</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">contigs</tt><tt class="py-op">[</tt><tt id="link-223" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-223', 'i', 'link-221');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L468"></a><tt class="py-lineno">468</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt id="link-224" class="py-name"><a title="Bio.Sequencing.Ace.wa" class="py-name" href="#" onclick="return doclink('link-224', 'wa', 'link-95');">wa</a></tt><tt class="py-op">:</tt> </tt>
<a name="L469"></a><tt class="py-lineno">469</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-225" class="py-name"><a title="Bio.Sequencing.Ace.wa" class="py-name" href="#" onclick="return doclink('link-225', 'wa', 'link-95');">wa</a></tt><tt class="py-op">:</tt> </tt>
<a name="L470"></a><tt class="py-lineno">470</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-226" class="py-name"><a title="Bio.Sequencing.Ace.wa" class="py-name" href="#" onclick="return doclink('link-226', 'wa', 'link-95');">wa</a></tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L471"></a><tt class="py-lineno">471</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-227" class="py-name"><a title="Bio.Sequencing.Ace.wa" class="py-name" href="#" onclick="return doclink('link-227', 'wa', 'link-95');">wa</a></tt><tt class="py-op">.</tt><tt id="link-228" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-228', 'extend', 'link-118');">extend</a></tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt id="link-229" class="py-name"><a title="Bio.Sequencing.Ace.wa" class="py-name" href="#" onclick="return doclink('link-229', 'wa', 'link-95');">wa</a></tt><tt class="py-op">)</tt> </tt>
<a name="L472"></a><tt class="py-lineno">472</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt id="link-230" class="py-name"><a title="Bio.Sequencing.Ace.ct" class="py-name" href="#" onclick="return doclink('link-230', 'ct', 'link-94');">ct</a></tt><tt class="py-op">:</tt> </tt>
<a name="L473"></a><tt class="py-lineno">473</tt> <tt class="py-line"> <tt class="py-name">newcts</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-name">ct_tag</tt> <tt class="py-keyword">for</tt> <tt class="py-name">ct_tag</tt> <tt class="py-keyword">in</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt id="link-231" class="py-name"><a title="Bio.Sequencing.Ace.ct" class="py-name" href="#" onclick="return doclink('link-231', 'ct', 'link-94');">ct</a></tt> <tt class="py-keyword">if</tt> <tt class="py-name">ct_tag</tt><tt class="py-op">.</tt><tt id="link-232" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-232', 'name', 'link-0');">name</a></tt><tt class="py-op">!=</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt id="link-233" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-233', 'name', 'link-0');">name</a></tt><tt class="py-op">]</tt> </tt>
<a name="L474"></a><tt class="py-lineno">474</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-234" 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-234', 'x', 'link-234');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">newcts</tt><tt class="py-op">:</tt> </tt>
<a name="L475"></a><tt class="py-lineno">475</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">contigs</tt><tt class="py-op">[</tt><tt id="link-235" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-235', 'i', 'link-221');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-236" class="py-name"><a title="Bio.Sequencing.Ace.ct" class="py-name" href="#" onclick="return doclink('link-236', 'ct', 'link-94');">ct</a></tt><tt class="py-op">.</tt><tt id="link-237" class="py-name" targets="Method Bio.Crystal.Chain.remove()=Bio.Crystal.Chain-class.html#remove,Method Bio.Graphics.BasicChromosome._ChromosomeComponent.remove()=Bio.Graphics.BasicChromosome._ChromosomeComponent-class.html#remove,Method Bio.Pathway.Rep.HashSet.HashSet.remove()=Bio.Pathway.Rep.HashSet.HashSet-class.html#remove,Method Bio.Restriction.Restriction.RestrictionBatch.remove()=Bio.Restriction.Restriction.RestrictionBatch-class.html#remove,Method Bio.Seq.MutableSeq.remove()=Bio.Seq.MutableSeq-class.html#remove,Method BioSQL.Loader.DatabaseRemover.remove()=BioSQL.Loader.DatabaseRemover-class.html#remove"><a title="Bio.Crystal.Chain.remove
Bio.Graphics.BasicChromosome._ChromosomeComponent.remove
Bio.Pathway.Rep.HashSet.HashSet.remove
Bio.Restriction.Restriction.RestrictionBatch.remove
Bio.Seq.MutableSeq.remove
BioSQL.Loader.DatabaseRemover.remove" class="py-name" href="#" onclick="return doclink('link-237', 'remove', 'link-237');">remove</a></tt><tt class="py-op">(</tt><tt id="link-238" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-238', 'x', 'link-234');">x</a></tt><tt class="py-op">)</tt> </tt>
<a name="L476"></a><tt class="py-lineno">476</tt> <tt class="py-line"> <tt id="link-239" class="py-name"><a title="Bio.Sequencing.Ace.ct" class="py-name" href="#" onclick="return doclink('link-239', 'ct', 'link-94');">ct</a></tt><tt class="py-op">.</tt><tt id="link-240" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-240', 'extend', 'link-118');">extend</a></tt><tt class="py-op">(</tt><tt class="py-name">newcts</tt><tt class="py-op">)</tt> </tt>
<a name="L477"></a><tt class="py-lineno">477</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">j</tt> <tt class="py-keyword">in</tt> <tt id="link-241" class="py-name"><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-241', 'range', 'link-222');">range</a></tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">reads</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L478"></a><tt class="py-lineno">478</tt> <tt class="py-line"> <tt class="py-name">r</tt> <tt class="py-op">=</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">reads</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt> </tt>
<a name="L479"></a><tt class="py-lineno">479</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">r</tt><tt class="py-op">.</tt><tt id="link-242" class="py-name"><a title="Bio.Sequencing.Ace.rt" class="py-name" href="#" onclick="return doclink('link-242', 'rt', 'link-75');">rt</a></tt><tt class="py-op">:</tt> </tt>
<a name="L480"></a><tt class="py-lineno">480</tt> <tt class="py-line"> <tt class="py-name">newrts</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-name">rt_tag</tt> <tt class="py-keyword">for</tt> <tt class="py-name">rt_tag</tt> <tt class="py-keyword">in</tt> <tt class="py-name">r</tt><tt class="py-op">.</tt><tt id="link-243" class="py-name"><a title="Bio.Sequencing.Ace.rt" class="py-name" href="#" onclick="return doclink('link-243', 'rt', 'link-75');">rt</a></tt> <tt class="py-keyword">if</tt> <tt class="py-name">rt_tag</tt><tt class="py-op">.</tt><tt id="link-244" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-244', 'name', 'link-0');">name</a></tt><tt class="py-op">!=</tt><tt class="py-name">r</tt><tt class="py-op">.</tt><tt id="link-245" class="py-name"><a title="Bio.Sequencing.Ace.rd" class="py-name" href="#" onclick="return doclink('link-245', 'rd', 'link-72');">rd</a></tt><tt class="py-op">.</tt><tt id="link-246" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-246', 'name', 'link-0');">name</a></tt><tt class="py-op">]</tt> </tt>
<a name="L481"></a><tt class="py-lineno">481</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-247" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-247', 'x', 'link-234');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">newrts</tt><tt class="py-op">:</tt> </tt>
<a name="L482"></a><tt class="py-lineno">482</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">contigs</tt><tt class="py-op">[</tt><tt id="link-248" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-248', 'i', 'link-221');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">reads</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-249" class="py-name"><a title="Bio.Sequencing.Ace.rt" class="py-name" href="#" onclick="return doclink('link-249', 'rt', 'link-75');">rt</a></tt><tt class="py-op">.</tt><tt id="link-250" class="py-name"><a title="Bio.Crystal.Chain.remove
Bio.Graphics.BasicChromosome._ChromosomeComponent.remove
Bio.Pathway.Rep.HashSet.HashSet.remove
Bio.Restriction.Restriction.RestrictionBatch.remove
Bio.Seq.MutableSeq.remove
BioSQL.Loader.DatabaseRemover.remove" class="py-name" href="#" onclick="return doclink('link-250', 'remove', 'link-237');">remove</a></tt><tt class="py-op">(</tt><tt id="link-251" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-251', 'x', 'link-234');">x</a></tt><tt class="py-op">)</tt> </tt>
<a name="L483"></a><tt class="py-lineno">483</tt> <tt class="py-line"> <tt id="link-252" class="py-name"><a title="Bio.Sequencing.Ace.rt" class="py-name" href="#" onclick="return doclink('link-252', 'rt', 'link-75');">rt</a></tt><tt class="py-op">.</tt><tt id="link-253" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-253', 'extend', 'link-118');">extend</a></tt><tt class="py-op">(</tt><tt class="py-name">newrts</tt><tt class="py-op">)</tt> </tt>
<a name="L484"></a><tt class="py-lineno">484</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">r</tt><tt class="py-op">.</tt><tt id="link-254" class="py-name"><a title="Bio.Sequencing.Ace.wr" class="py-name" href="#" onclick="return doclink('link-254', 'wr', 'link-76');">wr</a></tt><tt class="py-op">:</tt> </tt>
<a name="L485"></a><tt class="py-lineno">485</tt> <tt class="py-line"> <tt class="py-name">newwrs</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-name">wr_tag</tt> <tt class="py-keyword">for</tt> <tt class="py-name">wr_tag</tt> <tt class="py-keyword">in</tt> <tt class="py-name">r</tt><tt class="py-op">.</tt><tt id="link-255" class="py-name"><a title="Bio.Sequencing.Ace.wr" class="py-name" href="#" onclick="return doclink('link-255', 'wr', 'link-76');">wr</a></tt> <tt class="py-keyword">if</tt> <tt class="py-name">wr_tag</tt><tt class="py-op">.</tt><tt id="link-256" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-256', 'name', 'link-0');">name</a></tt><tt class="py-op">!=</tt><tt class="py-name">r</tt><tt class="py-op">.</tt><tt id="link-257" class="py-name"><a title="Bio.Sequencing.Ace.rd" class="py-name" href="#" onclick="return doclink('link-257', 'rd', 'link-72');">rd</a></tt><tt class="py-op">.</tt><tt id="link-258" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-258', 'name', 'link-0');">name</a></tt><tt class="py-op">]</tt> </tt>
<a name="L486"></a><tt class="py-lineno">486</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-259" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-259', 'x', 'link-234');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">newwrs</tt><tt class="py-op">:</tt> </tt>
<a name="L487"></a><tt class="py-lineno">487</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">contigs</tt><tt class="py-op">[</tt><tt id="link-260" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-260', 'i', 'link-221');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">reads</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-261" class="py-name"><a title="Bio.Sequencing.Ace.wr" class="py-name" href="#" onclick="return doclink('link-261', 'wr', 'link-76');">wr</a></tt><tt class="py-op">.</tt><tt id="link-262" class="py-name"><a title="Bio.Crystal.Chain.remove
Bio.Graphics.BasicChromosome._ChromosomeComponent.remove
Bio.Pathway.Rep.HashSet.HashSet.remove
Bio.Restriction.Restriction.RestrictionBatch.remove
Bio.Seq.MutableSeq.remove
BioSQL.Loader.DatabaseRemover.remove" class="py-name" href="#" onclick="return doclink('link-262', 'remove', 'link-237');">remove</a></tt><tt class="py-op">(</tt><tt id="link-263" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-263', 'x', 'link-234');">x</a></tt><tt class="py-op">)</tt> </tt>
<a name="L488"></a><tt class="py-lineno">488</tt> <tt class="py-line"> <tt id="link-264" class="py-name"><a title="Bio.Sequencing.Ace.wr" class="py-name" href="#" onclick="return doclink('link-264', 'wr', 'link-76');">wr</a></tt><tt class="py-op">.</tt><tt id="link-265" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-265', 'extend', 'link-118');">extend</a></tt><tt class="py-op">(</tt><tt class="py-name">newwrs</tt><tt class="py-op">)</tt> </tt>
<a name="L489"></a><tt class="py-lineno">489</tt> <tt class="py-line"> <tt class="py-comment"># now sort them into their proper place</tt> </tt>
<a name="L490"></a><tt class="py-lineno">490</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-266" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-266', 'i', 'link-221');">i</a></tt> <tt class="py-keyword">in</tt> <tt id="link-267" class="py-name"><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-267', 'range', 'link-222');">range</a></tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">contigs</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L491"></a><tt class="py-lineno">491</tt> <tt class="py-line"> <tt class="py-name">c</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">contigs</tt><tt class="py-op">[</tt><tt id="link-268" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-268', 'i', 'link-221');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L492"></a><tt class="py-lineno">492</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">ct_tag</tt> <tt class="py-keyword">in</tt> <tt id="link-269" class="py-name"><a title="Bio.Sequencing.Ace.ct" class="py-name" href="#" onclick="return doclink('link-269', 'ct', 'link-94');">ct</a></tt><tt class="py-op">:</tt> </tt>
<a name="L493"></a><tt class="py-lineno">493</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">ct_tag</tt><tt class="py-op">.</tt><tt id="link-270" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-270', 'name', 'link-0');">name</a></tt><tt class="py-op">==</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt id="link-271" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-271', 'name', 'link-0');">name</a></tt><tt class="py-op">:</tt> </tt>
<a name="L494"></a><tt class="py-lineno">494</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">contigs</tt><tt class="py-op">[</tt><tt id="link-272" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-272', 'i', 'link-221');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-273" class="py-name"><a title="Bio.Sequencing.Ace.ct" class="py-name" href="#" onclick="return doclink('link-273', 'ct', 'link-94');">ct</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L495"></a><tt class="py-lineno">495</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">contigs</tt><tt class="py-op">[</tt><tt id="link-274" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-274', 'i', 'link-221');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-275" class="py-name"><a title="Bio.Sequencing.Ace.ct" class="py-name" href="#" onclick="return doclink('link-275', 'ct', 'link-94');">ct</a></tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L496"></a><tt class="py-lineno">496</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">contigs</tt><tt class="py-op">[</tt><tt id="link-276" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-276', 'i', 'link-221');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-277" class="py-name"><a title="Bio.Sequencing.Ace.ct" class="py-name" href="#" onclick="return doclink('link-277', 'ct', 'link-94');">ct</a></tt><tt class="py-op">.</tt><tt id="link-278" class="py-name"><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-278', 'append', 'link-124');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">ct_tag</tt><tt class="py-op">)</tt> </tt>
<a name="L497"></a><tt class="py-lineno">497</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-279" class="py-name"><a title="Bio.Sequencing.Ace.rt" class="py-name" href="#" onclick="return doclink('link-279', 'rt', 'link-75');">rt</a></tt> <tt class="py-keyword">or</tt> <tt id="link-280" class="py-name"><a title="Bio.Sequencing.Ace.wr" class="py-name" href="#" onclick="return doclink('link-280', 'wr', 'link-76');">wr</a></tt><tt class="py-op">:</tt> </tt>
<a name="L498"></a><tt class="py-lineno">498</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">j</tt> <tt class="py-keyword">in</tt> <tt id="link-281" class="py-name"><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-281', 'range', 'link-222');">range</a></tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">reads</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L499"></a><tt class="py-lineno">499</tt> <tt class="py-line"> <tt class="py-name">r</tt> <tt class="py-op">=</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">reads</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt> </tt>
<a name="L500"></a><tt class="py-lineno">500</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">rt_tag</tt> <tt class="py-keyword">in</tt> <tt id="link-282" class="py-name"><a title="Bio.Sequencing.Ace.rt" class="py-name" href="#" onclick="return doclink('link-282', 'rt', 'link-75');">rt</a></tt><tt class="py-op">:</tt> </tt>
<a name="L501"></a><tt class="py-lineno">501</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">rt_tag</tt><tt class="py-op">.</tt><tt id="link-283" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-283', 'name', 'link-0');">name</a></tt><tt class="py-op">==</tt><tt class="py-name">r</tt><tt class="py-op">.</tt><tt id="link-284" class="py-name"><a title="Bio.Sequencing.Ace.rd" class="py-name" href="#" onclick="return doclink('link-284', 'rd', 'link-72');">rd</a></tt><tt class="py-op">.</tt><tt id="link-285" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-285', 'name', 'link-0');">name</a></tt><tt class="py-op">:</tt> </tt>
<a name="L502"></a><tt class="py-lineno">502</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">contigs</tt><tt class="py-op">[</tt><tt id="link-286" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-286', 'i', 'link-221');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">reads</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-287" class="py-name"><a title="Bio.Sequencing.Ace.rt" class="py-name" href="#" onclick="return doclink('link-287', 'rt', 'link-75');">rt</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L503"></a><tt class="py-lineno">503</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">contigs</tt><tt class="py-op">[</tt><tt id="link-288" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-288', 'i', 'link-221');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">reads</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-289" class="py-name"><a title="Bio.Sequencing.Ace.rt" class="py-name" href="#" onclick="return doclink('link-289', 'rt', 'link-75');">rt</a></tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L504"></a><tt class="py-lineno">504</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">contigs</tt><tt class="py-op">[</tt><tt id="link-290" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-290', 'i', 'link-221');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">reads</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-291" class="py-name"><a title="Bio.Sequencing.Ace.rt" class="py-name" href="#" onclick="return doclink('link-291', 'rt', 'link-75');">rt</a></tt><tt class="py-op">.</tt><tt id="link-292" class="py-name"><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-292', 'append', 'link-124');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">rt_tag</tt><tt class="py-op">)</tt> </tt>
<a name="L505"></a><tt class="py-lineno">505</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">wr_tag</tt> <tt class="py-keyword">in</tt> <tt id="link-293" class="py-name"><a title="Bio.Sequencing.Ace.wr" class="py-name" href="#" onclick="return doclink('link-293', 'wr', 'link-76');">wr</a></tt><tt class="py-op">:</tt> </tt>
<a name="L506"></a><tt class="py-lineno">506</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">wr_tag</tt><tt class="py-op">.</tt><tt id="link-294" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-294', 'name', 'link-0');">name</a></tt><tt class="py-op">==</tt><tt class="py-name">r</tt><tt class="py-op">.</tt><tt id="link-295" class="py-name"><a title="Bio.Sequencing.Ace.rd" class="py-name" href="#" onclick="return doclink('link-295', 'rd', 'link-72');">rd</a></tt><tt class="py-op">.</tt><tt id="link-296" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-296', 'name', 'link-0');">name</a></tt><tt class="py-op">:</tt> </tt>
<a name="L507"></a><tt class="py-lineno">507</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">contigs</tt><tt class="py-op">[</tt><tt id="link-297" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-297', 'i', 'link-221');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">reads</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-298" class="py-name"><a title="Bio.Sequencing.Ace.wr" class="py-name" href="#" onclick="return doclink('link-298', 'wr', 'link-76');">wr</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L508"></a><tt class="py-lineno">508</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">contigs</tt><tt class="py-op">[</tt><tt id="link-299" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-299', 'i', 'link-221');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">reads</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-300" class="py-name"><a title="Bio.Sequencing.Ace.wr" class="py-name" href="#" onclick="return doclink('link-300', 'wr', 'link-76');">wr</a></tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L509"></a><tt class="py-lineno">509</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">contigs</tt><tt class="py-op">[</tt><tt id="link-301" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-301', 'i', 'link-221');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">reads</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-302" class="py-name"><a title="Bio.Sequencing.Ace.wr" class="py-name" href="#" onclick="return doclink('link-302', 'wr', 'link-76');">wr</a></tt><tt class="py-op">.</tt><tt id="link-303" class="py-name"><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-303', 'append', 'link-124');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">wr_tag</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L510"></a><tt class="py-lineno">510</tt> <tt class="py-line"> </tt>
<a name="read"></a><div id="read-def"><a name="L511"></a><tt class="py-lineno">511</tt> <a class="py-toggle" href="#" id="read-toggle" onclick="return toggle('read');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace-module.html#read">read</a><tt class="py-op">(</tt><tt class="py-param">handle</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="read-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="read-expanded"><a name="L512"></a><tt class="py-lineno">512</tt> <tt class="py-line"> <tt class="py-docstring">"""Parses the full ACE file in list of contigs.</tt> </tt>
<a name="L513"></a><tt class="py-lineno">513</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L514"></a><tt class="py-lineno">514</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L515"></a><tt class="py-lineno">515</tt> <tt class="py-line"> </tt>
<a name="L516"></a><tt class="py-lineno">516</tt> <tt class="py-line"> <tt id="link-304" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-304', 'handle', 'link-104');">handle</a></tt> <tt class="py-op">=</tt> <tt class="py-name">iter</tt><tt class="py-op">(</tt><tt id="link-305" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-305', 'handle', 'link-104');">handle</a></tt><tt class="py-op">)</tt> </tt>
<a name="L517"></a><tt class="py-lineno">517</tt> <tt class="py-line"> </tt>
<a name="L518"></a><tt class="py-lineno">518</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">=</tt><tt id="link-306" class="py-name" targets="Class Bio.Sequencing.Ace.ACEFileRecord=Bio.Sequencing.Ace.ACEFileRecord-class.html"><a title="Bio.Sequencing.Ace.ACEFileRecord" class="py-name" href="#" onclick="return doclink('link-306', 'ACEFileRecord', 'link-306');">ACEFileRecord</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L519"></a><tt class="py-lineno">519</tt> <tt class="py-line"> </tt>
<a name="L520"></a><tt class="py-lineno">520</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L521"></a><tt class="py-lineno">521</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt id="link-307" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-307', 'handle', 'link-104');">handle</a></tt><tt class="py-op">.</tt><tt id="link-308" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.File.UndoHandle.next
Bio.GenBank.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.PopGen.GenePop.Controller._FileIterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.UniGene.Iterator.next" class="py-name" href="#" onclick="return doclink('link-308', 'next', 'link-108');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L522"></a><tt class="py-lineno">522</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">StopIteration</tt><tt class="py-op">:</tt> </tt>
<a name="L523"></a><tt class="py-lineno">523</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">"Premature end of file"</tt><tt class="py-op">)</tt> </tt>
<a name="L524"></a><tt class="py-lineno">524</tt> <tt class="py-line"> </tt>
<a name="L525"></a><tt class="py-lineno">525</tt> <tt class="py-line"> <tt class="py-comment"># check if the file starts correctly</tt> </tt>
<a name="L526"></a><tt class="py-lineno">526</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 id="link-309" class="py-name"><a title="Bio.Seq.Seq.startswith" class="py-name" href="#" onclick="return doclink('link-309', 'startswith', 'link-106');">startswith</a></tt><tt class="py-op">(</tt><tt class="py-string">'AS'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L527"></a><tt class="py-lineno">527</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">"File does not start with 'AS'."</tt><tt class="py-op">)</tt> </tt>
<a name="L528"></a><tt class="py-lineno">528</tt> <tt class="py-line"> </tt>
<a name="L529"></a><tt class="py-lineno">529</tt> <tt class="py-line"> <tt class="py-name">words</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-310" 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-310', 'split', 'link-3');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L530"></a><tt class="py-lineno">530</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt class="py-name">ncontigs</tt><tt class="py-op">,</tt> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt class="py-name">nreads</tt> <tt class="py-op">=</tt> <tt class="py-name">map</tt><tt class="py-op">(</tt><tt class="py-name">int</tt><tt class="py-op">,</tt> <tt class="py-name">words</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L531"></a><tt class="py-lineno">531</tt> <tt class="py-line"> </tt>
<a name="L532"></a><tt class="py-lineno">532</tt> <tt class="py-line"> <tt class="py-comment"># now read all the records</tt> </tt>
<a name="L533"></a><tt class="py-lineno">533</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt class="py-name">contigs</tt> <tt class="py-op">=</tt> <tt id="link-311" 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-311', 'list', 'link-311');">list</a></tt><tt class="py-op">(</tt><tt id="link-312" class="py-name" targets="Method Bio.Affy.CelFile.CelParser.parse()=Bio.Affy.CelFile.CelParser-class.html#parse,Function Bio.AlignIO.parse()=Bio.AlignIO-module.html#parse,Method Bio.Blast.NCBIStandalone.BlastErrorParser.parse()=Bio.Blast.NCBIStandalone.BlastErrorParser-class.html#parse,Method Bio.Blast.NCBIStandalone.BlastParser.parse()=Bio.Blast.NCBIStandalone.BlastParser-class.html#parse,Method Bio.Blast.NCBIStandalone.PSIBlastParser.parse()=Bio.Blast.NCBIStandalone.PSIBlastParser-class.html#parse,Function Bio.Blast.NCBIXML.parse()=Bio.Blast.NCBIXML-module.html#parse,Method Bio.Compass.RecordParser.parse()=Bio.Compass.RecordParser-class.html#parse,Function Bio.Compass.parse()=Bio.Compass-module.html#parse,Function Bio.Emboss.Primer3.parse()=Bio.Emboss.Primer3-module.html#parse,Method Bio.Entrez.Parser.DataHandler.parse()=Bio.Entrez.Parser.DataHandler-class.html#parse,Function Bio.Entrez.parse()=Bio.Entrez-module.html#parse,Function Bio.ExPASy.Enzyme.parse()=Bio.ExPASy.Enzyme-module.html#parse,Function Bio.ExPASy.Prodoc.parse()=Bio.ExPASy.Prodoc-module.html#parse,Function Bio.ExPASy.Prosite.parse()=Bio.ExPASy.Prosite-module.html#parse,Method Bio.GenBank.FeatureParser.parse()=Bio.GenBank.FeatureParser-class.html#parse,Function Bio.GenBank.LocationParser.parse()=Bio.GenBank.LocationParser-module.html#parse,Method Bio.GenBank.RecordParser.parse()=Bio.GenBank.RecordParser-class.html#parse,Method Bio.GenBank.Scanner.InsdcScanner.parse()=Bio.GenBank.Scanner.InsdcScanner-class.html#parse,Function Bio.Geo.parse()=Bio.Geo-module.html#parse,Function Bio.KEGG.Compound.parse()=Bio.KEGG.Compound-module.html#parse,Function Bio.KEGG.Enzyme.parse()=Bio.KEGG.Enzyme-module.html#parse,Function Bio.KEGG.Map.parse()=Bio.KEGG.Map-module.html#parse,Function Bio.Medline.parse()=Bio.Medline-module.html#parse,Function Bio.Motif.parse()=Bio.Motif-module.html#parse,Method Bio.ParserSupport.AbstractParser.parse()=Bio.ParserSupport.AbstractParser-class.html#parse,Method Bio.Parsers.spark.GenericParser.parse()=Bio.Parsers.spark.GenericParser-class.html#parse,Method Bio.Phylo.NewickIO.Parser.parse()=Bio.Phylo.NewickIO.Parser-class.html#parse,Function Bio.Phylo.NewickIO.parse()=Bio.Phylo.NewickIO-module.html#parse,Function Bio.Phylo.NexusIO.parse()=Bio.Phylo.NexusIO-module.html#parse,Method Bio.Phylo.PhyloXMLIO.Parser.parse()=Bio.Phylo.PhyloXMLIO.Parser-class.html#parse,Function Bio.Phylo.PhyloXMLIO.parse()=Bio.Phylo.PhyloXMLIO-module.html#parse,Function Bio.Phylo._io.parse()=Bio.Phylo._io-module.html#parse,Function Bio.SCOP.Cla.parse()=Bio.SCOP.Cla-module.html#parse,Function Bio.SCOP.Des.parse()=Bio.SCOP.Des-module.html#parse,Function Bio.SCOP.Dom.parse()=Bio.SCOP.Dom-module.html#parse,Function Bio.SCOP.Hie.parse()=Bio.SCOP.Hie-module.html#parse,Function Bio.SCOP.Raf.parse()=Bio.SCOP.Raf-module.html#parse,Method Bio.SeqIO.UniprotIO.Parser.parse()=Bio.SeqIO.UniprotIO.Parser-class.html#parse,Function Bio.SeqIO.parse()=Bio.SeqIO-module.html#parse,Function Bio.Sequencing.Ace.parse()=Bio.Sequencing.Ace-module.html#parse,Function Bio.Sequencing.Phd.parse()=Bio.Sequencing.Phd-module.html#parse,Function Bio.SwissProt.KeyWList.parse()=Bio.SwissProt.KeyWList-module.html#parse,Function Bio.SwissProt.parse()=Bio.SwissProt-module.html#parse,Method Bio.UniGene.RecordParser.parse()=Bio.UniGene.RecordParser-class.html#parse,Method Bio.UniGene.UniGene.UniGeneParser.parse()=Bio.UniGene.UniGene.UniGeneParser-class.html#parse,Function Bio.UniGene.parse()=Bio.UniGene-module.html#parse,Function Bio.Wise.psw.parse()=Bio.Wise.psw-module.html#parse"><a title="Bio.Affy.CelFile.CelParser.parse
Bio.AlignIO.parse
Bio.Blast.NCBIStandalone.BlastErrorParser.parse
Bio.Blast.NCBIStandalone.BlastParser.parse
Bio.Blast.NCBIStandalone.PSIBlastParser.parse
Bio.Blast.NCBIXML.parse
Bio.Compass.RecordParser.parse
Bio.Compass.parse
Bio.Emboss.Primer3.parse
Bio.Entrez.Parser.DataHandler.parse
Bio.Entrez.parse
Bio.ExPASy.Enzyme.parse
Bio.ExPASy.Prodoc.parse
Bio.ExPASy.Prosite.parse
Bio.GenBank.FeatureParser.parse
Bio.GenBank.LocationParser.parse
Bio.GenBank.RecordParser.parse
Bio.GenBank.Scanner.InsdcScanner.parse
Bio.Geo.parse
Bio.KEGG.Compound.parse
Bio.KEGG.Enzyme.parse
Bio.KEGG.Map.parse
Bio.Medline.parse
Bio.Motif.parse
Bio.ParserSupport.AbstractParser.parse
Bio.Parsers.spark.GenericParser.parse
Bio.Phylo.NewickIO.Parser.parse
Bio.Phylo.NewickIO.parse
Bio.Phylo.NexusIO.parse
Bio.Phylo.PhyloXMLIO.Parser.parse
Bio.Phylo.PhyloXMLIO.parse
Bio.Phylo._io.parse
Bio.SCOP.Cla.parse
Bio.SCOP.Des.parse
Bio.SCOP.Dom.parse
Bio.SCOP.Hie.parse
Bio.SCOP.Raf.parse
Bio.SeqIO.UniprotIO.Parser.parse
Bio.SeqIO.parse
Bio.Sequencing.Ace.parse
Bio.Sequencing.Phd.parse
Bio.SwissProt.KeyWList.parse
Bio.SwissProt.parse
Bio.UniGene.RecordParser.parse
Bio.UniGene.UniGene.UniGeneParser.parse
Bio.UniGene.parse
Bio.Wise.psw.parse" class="py-name" href="#" onclick="return doclink('link-312', 'parse', 'link-312');">parse</a></tt><tt class="py-op">(</tt><tt id="link-313" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-313', 'handle', 'link-104');">handle</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L534"></a><tt class="py-lineno">534</tt> <tt class="py-line"> <tt class="py-comment"># wa, ct, rt rags are usually at the end of the file, but not necessarily (correct?).</tt> </tt>
<a name="L535"></a><tt class="py-lineno">535</tt> <tt class="py-line"> <tt class="py-comment"># If the iterator is used, the tags are returned with the contig or the read after which they appear,</tt> </tt>
<a name="L536"></a><tt class="py-lineno">536</tt> <tt class="py-line"> <tt class="py-comment"># if all tags are at the end, they are read with the last contig. The concept of an</tt> </tt>
<a name="L537"></a><tt class="py-lineno">537</tt> <tt class="py-line"> <tt class="py-comment"># iterator leaves no other choice. But if the user uses the ACEParser, we can check</tt> </tt>
<a name="L538"></a><tt class="py-lineno">538</tt> <tt class="py-line"> <tt class="py-comment"># them and put them into the appropriate contig/read instance.</tt> </tt>
<a name="L539"></a><tt class="py-lineno">539</tt> <tt class="py-line"> <tt class="py-comment"># Conclusion: An ACE file is not a filetype for which iteration is 100% suitable...</tt> </tt>
<a name="L540"></a><tt class="py-lineno">540</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-314" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.sort
Bio.PDB.Residue.DisorderedResidue.sort
Bio.PDB.Residue.Residue.sort
Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-314', 'sort', 'link-10');">sort</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L541"></a><tt class="py-lineno">541</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">record</tt> </tt>
</div><a name="L542"></a><tt class="py-lineno">542</tt> <tt class="py-line"> </tt><script type="text/javascript">
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