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        <a href="Bio-module.html">Package&nbsp;Bio</a> ::
        <a href="Bio.Sequencing-module.html">Package&nbsp;Sequencing</a> ::
        Module&nbsp;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"></tt><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L3"></a><tt class="py-lineno">  3</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license.  Please see the LICENSE file that should have been included</tt> </tt>
<a name="L4"></a><tt class="py-lineno">  4</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L5"></a><tt class="py-lineno">  5</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt 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 (new) 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">version 1.3, 05/06/2004</tt> </tt>
<a name="L9"></a><tt class="py-lineno">  9</tt>  <tt class="py-line"><tt class="py-docstring">Written by Frank Kauff (fkauff@duke.edu) and</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt>  <tt class="py-line"><tt class="py-docstring">Cymon J. Cox (cymon@duke.edu)</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt>  <tt class="py-line"><tt class="py-docstring">Uses the Biopython Parser interface: ParserSupport.py</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt>  <tt class="py-line"><tt class="py-docstring">Usage:</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt>  <tt class="py-line"><tt class="py-docstring">There are two ways of reading an ace file: The ACEParser() reads</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt>  <tt class="py-line"><tt class="py-docstring">the whole file at once and the RecordParser() reads contig after</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt>  <tt class="py-line"><tt class="py-docstring">contig.</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt>  <tt class="py-line"><tt class="py-docstring">1) Parse whole ace file at once:</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt>  <tt class="py-line"><tt class="py-docstring">        from Bio.Sequencing import Ace</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt>  <tt class="py-line"><tt class="py-docstring">        aceparser=Ace.ACEParser()</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt>  <tt class="py-line"><tt class="py-docstring">        acefilerecord=aceparser.parse(open('my_ace_file.ace','r'))</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt>  <tt class="py-line"><tt class="py-docstring">This gives you:</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt>  <tt class="py-line"><tt class="py-docstring">        acefilerecord.ncontigs (the number of contigs in the ace file)</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt>  <tt class="py-line"><tt class="py-docstring">        acefilerecord.nreads (the number of reads in the ace file)</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt>  <tt class="py-line"><tt class="py-docstring">        acefilerecord.contigs[] (one instance of the Contig class for each contig)</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</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="L32"></a><tt class="py-lineno"> 32</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="L33"></a><tt class="py-lineno"> 33</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt>  <tt class="py-line"><tt class="py-docstring">        contig3=acefilerecord.contigs[2]</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt>  <tt class="py-line"><tt class="py-docstring">        read4=contig3.reads[3]</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt>  <tt class="py-line"><tt class="py-docstring">        RD_of_read4=read4.rd</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt>  <tt class="py-line"><tt class="py-docstring">        DS_of_read4=read4.ds</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</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="L40"></a><tt class="py-lineno"> 40</tt>  <tt class="py-line"><tt class="py-docstring">sorted into the right place.</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">see _RecordConsumer for details.</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">2) Or you can iterate over the contigs of an ace file one by one in the ususal way:</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt>  <tt class="py-line"><tt class="py-docstring">        from Bio.Sequencing import Ace</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt>  <tt class="py-line"><tt class="py-docstring">        recordparser=Ace.RecordParser()</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt>  <tt class="py-line"><tt class="py-docstring">        iterator=Ace.Iterator(open('my_ace_file.ace','r'),recordparser)</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt>  <tt class="py-line"><tt class="py-docstring">        for contig in iterator :</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt>  <tt class="py-line"><tt class="py-docstring">            print contig.name</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt>  <tt class="py-line"><tt class="py-docstring">            ...</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</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="L54"></a><tt class="py-lineno"> 54</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="L55"></a><tt class="py-lineno"> 55</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="L56"></a><tt class="py-lineno"> 56</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="L57"></a><tt class="py-lineno"> 57</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="L58"></a><tt class="py-lineno"> 58</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="L59"></a><tt class="py-lineno"> 59</tt>  <tt class="py-line"><tt class="py-docstring">are needed, the ACEParser instead of the RecordParser might be appropriate.</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt>  <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">os</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-1" class="py-name" targets="Module Bio.File=Bio.File-module.html"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-1', 'File', 'link-1');">File</a></tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-2" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-2', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-3" class="py-name" targets="Module Bio.ParserSupport=Bio.ParserSupport-module.html"><a title="Bio.ParserSupport" class="py-name" href="#" onclick="return doclink('link-3', 'ParserSupport', 'link-3');">ParserSupport</a></tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-4" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-4', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Package Bio.Alphabet=Bio.Alphabet-module.html,Class Bio.Alphabet.Alphabet=Bio.Alphabet.Alphabet-class.html"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-5', 'Alphabet', 'link-5');">Alphabet</a></tt> <tt class="py-keyword">import</tt> <tt id="link-6" class="py-name" targets="Module Bio.Alphabet.IUPAC=Bio.Alphabet.IUPAC-module.html"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-6', 'IUPAC', 'link-6');">IUPAC</a></tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt>  <tt class="py-line"> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt>  <tt class="py-line"> </tt>
<a name="rd"></a><div id="rd-def"><a name="L67"></a><tt class="py-lineno"> 67</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>
</div><div id="rd-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="rd-expanded"><a name="L68"></a><tt class="py-lineno"> 68</tt>  <tt class="py-line">    <tt class="py-docstring">"""RD (reads), store a read with its name, sequence etc."""</tt> </tt>
<a name="rd.__init__"></a><div id="rd.__init__-def"><a name="L69"></a><tt class="py-lineno"> 69</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="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-7" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.name=Bio.Encodings.IUPACEncoding-module.html#name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-7', 'name', 'link-7');">name</a></tt><tt class="py-op">=</tt><tt class="py-string">''</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</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="L72"></a><tt class="py-lineno"> 72</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="L73"></a><tt class="py-lineno"> 73</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="L74"></a><tt class="py-lineno"> 74</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-8" class="py-name" targets="Method Bio.AlignAce.Parser.AlignAceConsumer.sequence()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#sequence,Variable Bio.Emboss.primer3_format.sequence=Bio.Emboss.primer3_format-module.html#sequence,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.IntelliGenetics._RecordConsumer.sequence()=Bio.IntelliGenetics._RecordConsumer-class.html#sequence,Method Bio.Rebase._RecordConsumer.sequence()=Bio.Rebase._RecordConsumer-class.html#sequence,Function Bio.Std.sequence()=Bio.Std-module.html#sequence,Module Bio.builders.SeqRecord.sequence=Bio.builders.SeqRecord.sequence-module.html,Variable Bio.expressions.fasta.sequence=Bio.expressions.fasta-module.html#sequence,Variable Bio.expressions.genbank.sequence=Bio.expressions.genbank-module.html#sequence,Variable Bio.expressions.swissprot.sprot38.sequence=Bio.expressions.swissprot.sprot38-module.html#sequence,Module Bio.formatdefs.sequence=Bio.formatdefs.sequence-module.html,Variable Bio.formatdefs.sequence.sequence=Bio.formatdefs.sequence-module.html#sequence,Variable Martel.test.test_swissprot38.sequence=Martel.test.test_swissprot38-module.html#sequence,Variable Martel.test.testformats.swissprot38.sequence=Martel.test.testformats.swissprot38-module.html#sequence"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-8', 'sequence', 'link-8');">sequence</a></tt><tt class="py-op">=</tt><tt class="py-string">''</tt> </tt>
</div></div><a name="L75"></a><tt class="py-lineno"> 75</tt>  <tt class="py-line"> </tt>
<a name="qa"></a><div id="qa-def"><a name="L76"></a><tt class="py-lineno"> 76</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>
</div><div id="qa-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="qa-expanded"><a name="L77"></a><tt class="py-lineno"> 77</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="L78"></a><tt class="py-lineno"> 78</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-op">:</tt> </tt>
</div><div id="qa.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="qa.__init__-expanded"><a name="L79"></a><tt class="py-lineno"> 79</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="L80"></a><tt class="py-lineno"> 80</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="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">align_clipping_start</tt><tt class="py-op">=</tt><tt class="py-name">None</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">align_clipping_end</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
</div></div><a name="L83"></a><tt class="py-lineno"> 83</tt>  <tt class="py-line"> </tt>
<a name="ds"></a><div id="ds-def"><a name="L84"></a><tt class="py-lineno"> 84</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>
</div><div id="ds-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="ds-expanded"><a name="L85"></a><tt class="py-lineno"> 85</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="L86"></a><tt class="py-lineno"> 86</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-op">:</tt> </tt>
</div><div id="ds.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ds.__init__-expanded"><a name="L87"></a><tt class="py-lineno"> 87</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Method Bio.Sequencing.Phd._RecordConsumer.chromat_file()=Bio.Sequencing.Phd._RecordConsumer-class.html#chromat_file"><a title="Bio.Sequencing.Phd._RecordConsumer.chromat_file" class="py-name" href="#" onclick="return doclink('link-9', 'chromat_file', 'link-9');">chromat_file</a></tt><tt class="py-op">=</tt><tt class="py-string">''</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</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="L89"></a><tt class="py-lineno"> 89</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-10" class="py-name" targets="Method Bio.Sequencing.Phd._RecordConsumer.time()=Bio.Sequencing.Phd._RecordConsumer-class.html#time"><a title="Bio.Sequencing.Phd._RecordConsumer.time" class="py-name" href="#" onclick="return doclink('link-10', 'time', 'link-10');">time</a></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 id="link-11" class="py-name" targets="Method Bio.Sequencing.Phd._RecordConsumer.chem()=Bio.Sequencing.Phd._RecordConsumer-class.html#chem"><a title="Bio.Sequencing.Phd._RecordConsumer.chem" class="py-name" href="#" onclick="return doclink('link-11', 'chem', 'link-11');">chem</a></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 id="link-12" class="py-name" targets="Method Bio.Sequencing.Phd._RecordConsumer.dye()=Bio.Sequencing.Phd._RecordConsumer-class.html#dye"><a title="Bio.Sequencing.Phd._RecordConsumer.dye" class="py-name" href="#" onclick="return doclink('link-12', 'dye', 'link-12');">dye</a></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">template</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">direction</tt><tt class="py-op">=</tt><tt class="py-string">''</tt> </tt>
</div></div><a name="L94"></a><tt class="py-lineno"> 94</tt>  <tt class="py-line">     </tt>
<a name="af"></a><div id="af-def"><a name="L95"></a><tt class="py-lineno"> 95</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>
</div><div id="af-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="af-expanded"><a name="L96"></a><tt class="py-lineno"> 96</tt>  <tt class="py-line">    <tt class="py-docstring">"""AF lines, define the location of the read within the contig."""</tt> </tt>
<a name="af.__init__"></a><div id="af.__init__-def"><a name="L97"></a><tt class="py-lineno"> 97</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-op">:</tt> </tt>
</div><div id="af.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="af.__init__-expanded"><a name="L98"></a><tt class="py-lineno"> 98</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.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-13', 'name', 'link-7');">name</a></tt><tt class="py-op">=</tt><tt class="py-string">''</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</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="L100"></a><tt class="py-lineno">100</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>
</div></div><a name="L101"></a><tt class="py-lineno">101</tt>  <tt class="py-line"> </tt>
<a name="bs"></a><div id="bs-def"><a name="L102"></a><tt class="py-lineno">102</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>
</div><div id="bs-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="bs-expanded"><a name="L103"></a><tt class="py-lineno">103</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="L104"></a><tt class="py-lineno">104</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-op">:</tt> </tt>
</div><div id="bs.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="bs.__init__-expanded"><a name="L105"></a><tt class="py-lineno">105</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-14" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-14', 'name', 'link-7');">name</a></tt><tt class="py-op">=</tt><tt class="py-string">''</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt>  <tt class="py-line">        <tt class="py-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="L107"></a><tt class="py-lineno">107</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>
</div></div><a name="L108"></a><tt class="py-lineno">108</tt>  <tt class="py-line"> </tt>
<a name="rt"></a><div id="rt-def"><a name="L109"></a><tt class="py-lineno">109</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>
</div><a name="L110"></a><tt class="py-lineno">110</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="L111"></a><tt class="py-lineno">111</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-op">:</tt> </tt>
</div><div id="rt.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="rt.__init__-expanded"><a name="L112"></a><tt class="py-lineno">112</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-15', 'name', 'link-7');">name</a></tt><tt class="py-op">=</tt><tt class="py-string">''</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</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="L114"></a><tt class="py-lineno">114</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="L115"></a><tt class="py-lineno">115</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">padded_start</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<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 class="py-name">padded_end</tt><tt class="py-op">=</tt><tt class="py-name">None</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 id="link-16" 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.Prosite._RecordConsumer.date()=Bio.Prosite._RecordConsumer-class.html#date,Method Bio.SwissProt.SProt._RecordConsumer.date()=Bio.SwissProt.SProt._RecordConsumer-class.html#date,Method Bio.SwissProt.SProt._SequenceConsumer.date()=Bio.SwissProt.SProt._SequenceConsumer-class.html#date,Variable Bio.expressions.embl.embl65.date=Bio.expressions.embl.embl65-module.html#date,Variable Bio.expressions.genbank.date=Bio.expressions.genbank-module.html#date"><a title="Bio.GenBank._FeatureConsumer.date
Bio.GenBank._RecordConsumer.date
Bio.Prosite._RecordConsumer.date
Bio.SwissProt.SProt._RecordConsumer.date
Bio.SwissProt.SProt._SequenceConsumer.date
Bio.expressions.embl.embl65.date
Bio.expressions.genbank.date" class="py-name" href="#" onclick="return doclink('link-16', 'date', 'link-16');">date</a></tt><tt class="py-op">=</tt><tt class="py-string">''</tt> </tt>
</div></div><a name="L118"></a><tt class="py-lineno">118</tt>  <tt class="py-line"> </tt>
<a name="ct"></a><div id="ct-def"><a name="L119"></a><tt class="py-lineno">119</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>
</div><div id="ct-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="ct-expanded"><a name="L120"></a><tt class="py-lineno">120</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="L121"></a><tt class="py-lineno">121</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-op">:</tt> </tt>
</div><div id="ct.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ct.__init__-expanded"><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 id="link-17" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-17', 'name', 'link-7');">name</a></tt><tt class="py-op">=</tt><tt class="py-string">''</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">tag_type</tt><tt class="py-op">=</tt><tt class="py-string">''</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</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="L125"></a><tt class="py-lineno">125</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="L126"></a><tt class="py-lineno">126</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="L127"></a><tt class="py-lineno">127</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name"><a title="Bio.GenBank._FeatureConsumer.date
Bio.GenBank._RecordConsumer.date
Bio.Prosite._RecordConsumer.date
Bio.SwissProt.SProt._RecordConsumer.date
Bio.SwissProt.SProt._SequenceConsumer.date
Bio.expressions.embl.embl65.date
Bio.expressions.genbank.date" class="py-name" href="#" onclick="return doclink('link-18', 'date', 'link-16');">date</a></tt><tt class="py-op">=</tt><tt class="py-string">''</tt> </tt>
<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 class="py-name">notrans</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">info</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
</div></div><a name="L130"></a><tt class="py-lineno">130</tt>  <tt class="py-line"> </tt>
<a name="wa"></a><div id="wa-def"><a name="L131"></a><tt class="py-lineno">131</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>
</div><div id="wa-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="wa-expanded"><a name="L132"></a><tt class="py-lineno">132</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="L133"></a><tt class="py-lineno">133</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-op">:</tt> </tt>
</div><div id="wa.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="wa.__init__-expanded"><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">tag_type</tt><tt class="py-op">=</tt><tt class="py-string">''</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 class="py-name">program</tt><tt class="py-op">=</tt><tt class="py-string">''</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name"><a title="Bio.GenBank._FeatureConsumer.date
Bio.GenBank._RecordConsumer.date
Bio.Prosite._RecordConsumer.date
Bio.SwissProt.SProt._RecordConsumer.date
Bio.SwissProt.SProt._SequenceConsumer.date
Bio.expressions.embl.embl65.date
Bio.expressions.genbank.date" class="py-name" href="#" onclick="return doclink('link-19', 'date', 'link-16');">date</a></tt><tt class="py-op">=</tt><tt class="py-string">''</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</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>
</div></div><a name="L138"></a><tt class="py-lineno">138</tt>  <tt class="py-line"> </tt>
<a name="wr"></a><div id="wr-def"><a name="L139"></a><tt class="py-lineno">139</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>
</div><div id="wr-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="wr-expanded"><a name="L140"></a><tt class="py-lineno">140</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="L141"></a><tt class="py-lineno">141</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-op">:</tt> </tt>
</div><div id="wr.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="wr.__init__-expanded"><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 id="link-20" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-20', 'name', 'link-7');">name</a></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">aligned</tt><tt class="py-op">=</tt><tt class="py-string">''</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">program</tt><tt class="py-op">=</tt><tt class="py-string">''</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-21" class="py-name"><a title="Bio.GenBank._FeatureConsumer.date
Bio.GenBank._RecordConsumer.date
Bio.Prosite._RecordConsumer.date
Bio.SwissProt.SProt._RecordConsumer.date
Bio.SwissProt.SProt._SequenceConsumer.date
Bio.expressions.embl.embl65.date
Bio.expressions.genbank.date" class="py-name" href="#" onclick="return doclink('link-21', 'date', 'link-16');">date</a></tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
</div></div><a name="L146"></a><tt class="py-lineno">146</tt>  <tt class="py-line"> </tt>
<a name="Reads"></a><div id="Reads-def"><a name="L147"></a><tt class="py-lineno">147</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>
</div><div id="Reads-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Reads-expanded"><a name="L148"></a><tt class="py-lineno">148</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="L149"></a><tt class="py-lineno">149</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-op">:</tt> </tt>
</div><div id="Reads.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Reads.__init__-expanded"><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 id="link-22" 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-22', 'rd', 'link-22');">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="L151"></a><tt class="py-lineno">151</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name" targets="Method Bio.Sequencing.Ace._RecordConsumer.qa()=Bio.Sequencing.Ace._RecordConsumer-class.html#qa,Class Bio.Sequencing.Ace.qa=Bio.Sequencing.Ace.qa-class.html"><a title="Bio.Sequencing.Ace._RecordConsumer.qa
Bio.Sequencing.Ace.qa" class="py-name" href="#" onclick="return doclink('link-23', 'qa', 'link-23');">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="L152"></a><tt class="py-lineno">152</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-24" class="py-name" targets="Method Bio.Sequencing.Ace._RecordConsumer.ds()=Bio.Sequencing.Ace._RecordConsumer-class.html#ds,Class Bio.Sequencing.Ace.ds=Bio.Sequencing.Ace.ds-class.html"><a title="Bio.Sequencing.Ace._RecordConsumer.ds
Bio.Sequencing.Ace.ds" class="py-name" href="#" onclick="return doclink('link-24', 'ds', 'link-24');">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="L153"></a><tt class="py-lineno">153</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-25" 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-25', 'rt', 'link-25');">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="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-26" 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-26', 'wr', 'link-26');">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>
</div></div><a name="L155"></a><tt class="py-lineno">155</tt>  <tt class="py-line">         </tt>
<a name="Contig"></a><div id="Contig-def"><a name="L156"></a><tt class="py-lineno">156</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>
</div><div id="Contig-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Contig-expanded"><a name="L157"></a><tt class="py-lineno">157</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="L158"></a><tt class="py-lineno">158</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-op">:</tt> </tt>
</div><div id="Contig.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Contig.__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-27" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-27', 'name', 'link-7');">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">nbases</tt><tt class="py-op">=</tt><tt class="py-name">None</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">nreads</tt><tt class="py-op">=</tt><tt class="py-name">None</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">nsegments</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">uorc</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-28" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-28', 'sequence', 'link-8');">sequence</a></tt><tt class="py-op">=</tt><tt class="py-name">None</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">quality</tt><tt class="py-op">=</tt><tt class="py-name">None</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 id="link-29" class="py-name" targets="Method Bio.Sequencing.Ace._RecordConsumer.af()=Bio.Sequencing.Ace._RecordConsumer-class.html#af,Class Bio.Sequencing.Ace.af=Bio.Sequencing.Ace.af-class.html"><a title="Bio.Sequencing.Ace._RecordConsumer.af
Bio.Sequencing.Ace.af" class="py-name" href="#" onclick="return doclink('link-29', 'af', 'link-29');">af</a></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-30" class="py-name" targets="Method Bio.Sequencing.Ace._RecordConsumer.bs()=Bio.Sequencing.Ace._RecordConsumer-class.html#bs,Class Bio.Sequencing.Ace.bs=Bio.Sequencing.Ace.bs-class.html"><a title="Bio.Sequencing.Ace._RecordConsumer.bs
Bio.Sequencing.Ace.bs" class="py-name" href="#" onclick="return doclink('link-30', 'bs', 'link-30');">bs</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-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="L169"></a><tt class="py-lineno">169</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-31" 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-31', 'ct', 'link-31');">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="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-32" 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-32', 'wa', 'link-32');">wa</a></tt><tt class="py-op">=</tt><tt class="py-name">None</tt>    <tt class="py-comment"># none or many</tt> </tt>
</div></div><a name="L171"></a><tt class="py-lineno">171</tt>  <tt class="py-line">         </tt>
<a name="Iterator"></a><div id="Iterator-def"><a name="L172"></a><tt class="py-lineno">172</tt> <a class="py-toggle" href="#" id="Iterator-toggle" onclick="return toggle('Iterator');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Sequencing.Ace.Iterator-class.html">Iterator</a><tt class="py-op">:</tt> </tt>
</div><div id="Iterator-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Iterator-expanded"><a name="L173"></a><tt class="py-lineno">173</tt>  <tt class="py-line">    <tt class="py-docstring">"""Iterates over an ACE-file with multiple contigs.</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt>  <tt class="py-line"><tt class="py-docstring">    Methods: </tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt>  <tt class="py-line"><tt class="py-docstring">    next    Return the next record from the stream, or None.</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt>  <tt class="py-line"> </tt>
<a name="Iterator.__init__"></a><div id="Iterator.__init__-def"><a name="L179"></a><tt class="py-lineno">179</tt> <a class="py-toggle" href="#" id="Iterator.__init__-toggle" onclick="return toggle('Iterator.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace.Iterator-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">handle</tt><tt class="py-op">,</tt> <tt class="py-param">parser</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="Iterator.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Iterator.__init__-expanded"><a name="L180"></a><tt class="py-lineno">180</tt>  <tt class="py-line">        <tt class="py-docstring">"""__init__(self, handle, parser=None)</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt>  <tt class="py-line"><tt class="py-docstring">        Create a new iterator.  handle is a file-like object.  parser</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt>  <tt class="py-line"><tt class="py-docstring">        is an optional Parser object to change the results into another form.</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt>  <tt class="py-line"><tt class="py-docstring">        If set to None, then the raw contents of the file will be returned.</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_uhandle</tt> <tt class="py-op">=</tt> <tt id="link-33" class="py-name"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-33', 'File', 'link-1');">File</a></tt><tt class="py-op">.</tt><tt id="link-34" class="py-name" targets="Class Bio.File.UndoHandle=Bio.File.UndoHandle-class.html"><a title="Bio.File.UndoHandle" class="py-name" href="#" onclick="return doclink('link-34', 'UndoHandle', 'link-34');">UndoHandle</a></tt><tt class="py-op">(</tt><tt id="link-35" class="py-name" targets="Variable Bio.LocusLink.web_parse.handle=Bio.LocusLink.web_parse-module.html#handle,Variable Bio.Ndb.handle=Bio.Ndb-module.html#handle"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-35', 'handle', 'link-35');">handle</a></tt><tt class="py-op">)</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parser</tt> <tt class="py-op">=</tt> <tt class="py-name">parser</tt> </tt>
</div><a name="L188"></a><tt class="py-lineno">188</tt>  <tt class="py-line"> </tt>
<a name="Iterator.next"></a><div id="Iterator.next-def"><a name="L189"></a><tt class="py-lineno">189</tt> <a class="py-toggle" href="#" id="Iterator.next-toggle" onclick="return toggle('Iterator.next');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace.Iterator-class.html#next">next</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="Iterator.next-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Iterator.next-expanded"><a name="L190"></a><tt class="py-lineno">190</tt>  <tt class="py-line">        <tt class="py-docstring">"""next(self) -&gt; object</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt>  <tt class="py-line"><tt class="py-docstring">        Return the next contig record from the file. If no more records</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt>  <tt class="py-line"><tt class="py-docstring">        return None.</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt>  <tt class="py-line"> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt>  <tt class="py-line">        <tt class="py-name">lines</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt>  <tt class="py-line">        <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt>  </tt>
<a name="L198"></a><tt class="py-lineno">198</tt>  <tt class="py-line">            <tt class="py-comment"># if at beginning, skip the AS and look for first CO command</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-name">line</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_uhandle</tt><tt class="py-op">.</tt><tt id="link-36" class="py-name" targets="Method Bio.EUtils.ReseekFile.ReseekFile.readline()=Bio.EUtils.ReseekFile.ReseekFile-class.html#readline,Method Bio.File.SGMLHandle.readline()=Bio.File.SGMLHandle-class.html#readline,Method Bio.File.UndoHandle.readline()=Bio.File.UndoHandle-class.html#readline,Method Bio.SGMLExtractor.SGMLExtractorHandle.readline()=Bio.SGMLExtractor.SGMLExtractorHandle-class.html#readline"><a title="Bio.EUtils.ReseekFile.ReseekFile.readline
Bio.File.SGMLHandle.readline
Bio.File.UndoHandle.readline
Bio.SGMLExtractor.SGMLExtractorHandle.readline" class="py-name" href="#" onclick="return doclink('link-36', 'readline', 'link-36');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">line</tt><tt class="py-op">:</tt>                    <tt class="py-comment"># empty or corrupt file</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt>  <tt class="py-line">                <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</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-op">:</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-string">'CO'</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">lines</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name" targets="Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-class.html#append,Method Bio.EUtils.POM.ElementNode.append()=Bio.EUtils.POM.ElementNode-class.html#append,Method Bio.EUtils.sourcegen.SourceFile.append()=Bio.EUtils.sourcegen.SourceFile-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,Method Martel.msre_parse.SubPattern.append()=Martel.msre_parse.SubPattern-class.html#append"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-37', 'append', 'link-37');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt>  <tt class="py-line">                <tt class="py-keyword">break</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt>  <tt class="py-line">        <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt>  <tt class="py-line">            <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_uhandle</tt><tt class="py-op">.</tt><tt id="link-38" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.readline
Bio.File.SGMLHandle.readline
Bio.File.UndoHandle.readline
Bio.SGMLExtractor.SGMLExtractorHandle.readline" class="py-name" href="#" onclick="return doclink('link-38', 'readline', 'link-36');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</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="L208"></a><tt class="py-lineno">208</tt>  <tt class="py-line">                <tt class="py-keyword">break</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt>  <tt class="py-line">            <tt class="py-comment"># If a new record, then put the line back and stop.</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-keyword">if</tt> <tt class="py-name">lines</tt> <tt class="py-keyword">and</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'CO'</tt><tt class="py-op">:</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 class="py-name">_uhandle</tt><tt class="py-op">.</tt><tt id="link-39" class="py-name" targets="Method Bio.File.UndoHandle.saveline()=Bio.File.UndoHandle-class.html#saveline"><a title="Bio.File.UndoHandle.saveline" class="py-name" href="#" onclick="return doclink('link-39', 'saveline', 'link-39');">saveline</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt>  <tt class="py-line">                <tt class="py-keyword">break</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt>  <tt class="py-line">            <tt class="py-name">lines</tt><tt class="py-op">.</tt><tt id="link-40" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-40', 'append', 'link-37');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt>  <tt class="py-line"> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">lines</tt><tt class="py-op">:</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt>  <tt class="py-line"> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt>  <tt class="py-line">        <tt id="link-41" class="py-name" targets="Variable BioSQL.BioSeq.DBSeq.data=BioSQL.BioSeq.DBSeq-class.html#data"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-41', 'data', 'link-41');">data</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">lines</tt><tt class="py-op">)</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</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">_parser</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parser</tt><tt class="py-op">.</tt><tt id="link-42" class="py-name" targets="Method Bio.Affy.CelFile.CelParser.parse()=Bio.Affy.CelFile.CelParser-class.html#parse,Method Bio.AlignAce.Parser.AlignAceParser.parse()=Bio.AlignAce.Parser.AlignAceParser-class.html#parse,Method Bio.AlignAce.Parser.CompareAceParser.parse()=Bio.AlignAce.Parser.CompareAceParser-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,Method Bio.Blast.NCBIWWW.BlastParser.parse()=Bio.Blast.NCBIWWW.BlastParser-class.html#parse,Method Bio.Blast.NCBIXML.BlastParser.parse()=Bio.Blast.NCBIXML.BlastParser-class.html#parse,Function Bio.Blast.NCBIXML.parse()=Bio.Blast.NCBIXML-module.html#parse,Method Bio.CDD.RecordParser.parse()=Bio.CDD.RecordParser-class.html#parse,Method Bio.Compass.RecordParser.parse()=Bio.Compass.RecordParser-class.html#parse,Function Bio.Decode.parse()=Bio.Decode-module.html#parse,Method Bio.ECell.RecordParser.parse()=Bio.ECell.RecordParser-class.html#parse,Method Bio.EUtils.POM.POMDocument.parse()=Bio.EUtils.POM.POMDocument-class.html#parse,Module Bio.EUtils.parse=Bio.EUtils.parse-module.html,Method Bio.Emboss.Primer.Primer3Parser.parse()=Bio.Emboss.Primer.Primer3Parser-class.html#parse,Method Bio.Emboss.Primer.PrimerSearchParser.parse()=Bio.Emboss.Primer.PrimerSearchParser-class.html#parse,Method Bio.Enzyme.RecordParser.parse()=Bio.Enzyme.RecordParser-class.html#parse,Method Bio.Fasta.RecordParser.parse()=Bio.Fasta.RecordParser-class.html#parse,Method Bio.Fasta.SequenceParser.parse()=Bio.Fasta.SequenceParser-class.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,Method Bio.Gobase.RecordParser.parse()=Bio.Gobase.RecordParser-class.html#parse,Method Bio.IntelliGenetics.RecordParser.parse()=Bio.IntelliGenetics.RecordParser-class.html#parse,Method Bio.InterPro.InterProParser.parse()=Bio.InterPro.InterProParser-class.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,Method Bio.LocusLink.RecordParser.parse()=Bio.LocusLink.RecordParser-class.html#parse,Method Bio.LocusLink.web_parse.LocusLinkParser.parse()=Bio.LocusLink.web_parse.LocusLinkParser-class.html#parse,Method Bio.MEME.Parser.MASTParser.parse()=Bio.MEME.Parser.MASTParser-class.html#parse,Method Bio.MEME.Parser.MEMEParser.parse()=Bio.MEME.Parser.MEMEParser-class.html#parse,Method Bio.Medline.RecordParser.parse()=Bio.Medline.RecordParser-class.html#parse,Method Bio.MetaTool.RecordParser.parse()=Bio.MetaTool.RecordParser-class.html#parse,Method Bio.NBRF.RecordParser.parse()=Bio.NBRF.RecordParser-class.html#parse,Method Bio.Ndb.NdbParser.parse()=Bio.Ndb.NdbParser-class.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.PopGen.FDist.RecordParser.parse()=Bio.PopGen.FDist.RecordParser-class.html#parse,Method Bio.PopGen.GenePop.RecordParser.parse()=Bio.PopGen.GenePop.RecordParser-class.html#parse,Function Bio.PopGen.GenePop.parse()=Bio.PopGen.GenePop-module.html#parse,Method Bio.Prosite.Prodoc.RecordParser.parse()=Bio.Prosite.Prodoc.RecordParser-class.html#parse,Function Bio.Prosite.Prodoc.parse()=Bio.Prosite.Prodoc-module.html#parse,Method Bio.Prosite.RecordParser.parse()=Bio.Prosite.RecordParser-class.html#parse,Function Bio.Prosite.parse()=Bio.Prosite-module.html#parse,Method Bio.Rebase.RecordParser.parse()=Bio.Rebase.RecordParser-class.html#parse,Method Bio.SCOP.Cla.Parser.parse()=Bio.SCOP.Cla.Parser-class.html#parse,Function Bio.SCOP.Cla.parse()=Bio.SCOP.Cla-module.html#parse,Method Bio.SCOP.Des.Parser.parse()=Bio.SCOP.Des.Parser-class.html#parse,Function Bio.SCOP.Des.parse()=Bio.SCOP.Des-module.html#parse,Method Bio.SCOP.Dom.Parser.parse()=Bio.SCOP.Dom.Parser-class.html#parse,Function Bio.SCOP.Dom.parse()=Bio.SCOP.Dom-module.html#parse,Method Bio.SCOP.Hie.Parser.parse()=Bio.SCOP.Hie.Parser-class.html#parse,Function Bio.SCOP.Hie.parse()=Bio.SCOP.Hie-module.html#parse,Method Bio.SCOP.Raf.Parser.parse()=Bio.SCOP.Raf.Parser-class.html#parse,Function Bio.SCOP.Raf.parse()=Bio.SCOP.Raf-module.html#parse,Method Bio.Saf.RecordParser.parse()=Bio.Saf.RecordParser-class.html#parse,Function Bio.SeqIO.parse()=Bio.SeqIO-module.html#parse,Method Bio.Sequencing.Ace.ACEParser.parse()=Bio.Sequencing.Ace.ACEParser-class.html#parse,Method Bio.Sequencing.Ace.RecordParser.parse()=Bio.Sequencing.Ace.RecordParser-class.html#parse,Method Bio.Sequencing.Phd.RecordParser.parse()=Bio.Sequencing.Phd.RecordParser-class.html#parse,Method Bio.SwissProt.KeyWList.ListParser.parse()=Bio.SwissProt.KeyWList.ListParser-class.html#parse,Function Bio.SwissProt.KeyWList.parse()=Bio.SwissProt.KeyWList-module.html#parse,Method Bio.SwissProt.SProt.RecordParser.parse()=Bio.SwissProt.SProt.RecordParser-class.html#parse,Method Bio.SwissProt.SProt.SequenceParser.parse()=Bio.SwissProt.SProt.SequenceParser-class.html#parse,Function Bio.SwissProt.parse()=Bio.SwissProt-module.html#parse,Method Bio.UniGene.RecordParser.parse()=Bio.UniGene.RecordParser-class.html#parse,Function Bio.Wise.psw.parse()=Bio.Wise.psw-module.html#parse,Method Martel.Parser.HeaderFooterParser.parse()=Martel.Parser.HeaderFooterParser-class.html#parse,Method Martel.Parser.Parser.parse()=Martel.Parser.Parser-class.html#parse,Method Martel.Parser.RecordParser.parse()=Martel.Parser.RecordParser-class.html#parse,Function Martel.msre_parse.parse()=Martel.msre_parse-module.html#parse"><a title="Bio.Affy.CelFile.CelParser.parse
Bio.AlignAce.Parser.AlignAceParser.parse
Bio.AlignAce.Parser.CompareAceParser.parse
Bio.AlignIO.parse
Bio.Blast.NCBIStandalone.BlastErrorParser.parse
Bio.Blast.NCBIStandalone.BlastParser.parse
Bio.Blast.NCBIStandalone.PSIBlastParser.parse
Bio.Blast.NCBIWWW.BlastParser.parse
Bio.Blast.NCBIXML.BlastParser.parse
Bio.Blast.NCBIXML.parse
Bio.CDD.RecordParser.parse
Bio.Compass.RecordParser.parse
Bio.Decode.parse
Bio.ECell.RecordParser.parse
Bio.EUtils.POM.POMDocument.parse
Bio.EUtils.parse
Bio.Emboss.Primer.Primer3Parser.parse
Bio.Emboss.Primer.PrimerSearchParser.parse
Bio.Enzyme.RecordParser.parse
Bio.Fasta.RecordParser.parse
Bio.Fasta.SequenceParser.parse
Bio.GenBank.FeatureParser.parse
Bio.GenBank.LocationParser.parse
Bio.GenBank.RecordParser.parse
Bio.GenBank.Scanner.InsdcScanner.parse
Bio.Geo.parse
Bio.Gobase.RecordParser.parse
Bio.IntelliGenetics.RecordParser.parse
Bio.InterPro.InterProParser.parse
Bio.KEGG.Compound.parse
Bio.KEGG.Enzyme.parse
Bio.KEGG.Map.parse
Bio.LocusLink.RecordParser.parse
Bio.LocusLink.web_parse.LocusLinkParser.parse
Bio.MEME.Parser.MASTParser.parse
Bio.MEME.Parser.MEMEParser.parse
Bio.Medline.RecordParser.parse
Bio.MetaTool.RecordParser.parse
Bio.NBRF.RecordParser.parse
Bio.Ndb.NdbParser.parse
Bio.ParserSupport.AbstractParser.parse
Bio.Parsers.spark.GenericParser.parse
Bio.PopGen.FDist.RecordParser.parse
Bio.PopGen.GenePop.RecordParser.parse
Bio.PopGen.GenePop.parse
Bio.Prosite.Prodoc.RecordParser.parse
Bio.Prosite.Prodoc.parse
Bio.Prosite.RecordParser.parse
Bio.Prosite.parse
Bio.Rebase.RecordParser.parse
Bio.SCOP.Cla.Parser.parse
Bio.SCOP.Cla.parse
Bio.SCOP.Des.Parser.parse
Bio.SCOP.Des.parse
Bio.SCOP.Dom.Parser.parse
Bio.SCOP.Dom.parse
Bio.SCOP.Hie.Parser.parse
Bio.SCOP.Hie.parse
Bio.SCOP.Raf.Parser.parse
Bio.SCOP.Raf.parse
Bio.Saf.RecordParser.parse
Bio.SeqIO.parse
Bio.Sequencing.Ace.ACEParser.parse
Bio.Sequencing.Ace.RecordParser.parse
Bio.Sequencing.Phd.RecordParser.parse
Bio.SwissProt.KeyWList.ListParser.parse
Bio.SwissProt.KeyWList.parse
Bio.SwissProt.SProt.RecordParser.parse
Bio.SwissProt.SProt.SequenceParser.parse
Bio.SwissProt.parse
Bio.UniGene.RecordParser.parse
Bio.Wise.psw.parse
Martel.Parser.HeaderFooterParser.parse
Martel.Parser.Parser.parse
Martel.Parser.RecordParser.parse
Martel.msre_parse.parse" class="py-name" href="#" onclick="return doclink('link-42', 'parse', 'link-42');">parse</a></tt><tt class="py-op">(</tt><tt id="link-43" class="py-name"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-43', 'File', 'link-1');">File</a></tt><tt class="py-op">.</tt><tt class="py-name">StringHandle</tt><tt class="py-op">(</tt><tt id="link-44" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-44', 'data', 'link-41');">data</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-45" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-45', 'data', 'link-41');">data</a></tt> </tt>
</div><a name="L222"></a><tt class="py-lineno">222</tt>  <tt class="py-line"> </tt>
<a name="Iterator.__iter__"></a><div id="Iterator.__iter__-def"><a name="L223"></a><tt class="py-lineno">223</tt> <a class="py-toggle" href="#" id="Iterator.__iter__-toggle" onclick="return toggle('Iterator.__iter__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace.Iterator-class.html#__iter__">__iter__</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="Iterator.__iter__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Iterator.__iter__-expanded"><a name="L224"></a><tt class="py-lineno">224</tt>  <tt class="py-line">        <tt class="py-docstring">"""Iterate over the ACE file record by record."""</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">iter</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-46" 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.FastaIO.FastaM10Iterator.next()=Bio.AlignIO.FastaIO.FastaM10Iterator-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.CDD.Iterator.next()=Bio.CDD.Iterator-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.ECell.Iterator.next()=Bio.ECell.Iterator-class.html#next,Method Bio.Enzyme.Iterator.next()=Bio.Enzyme.Iterator-class.html#next,Method Bio.Fasta.Iterator.next()=Bio.Fasta.Iterator-class.html#next,Method Bio.GenBank.Iterator.next()=Bio.GenBank.Iterator-class.html#next,Method Bio.Gobase.Iterator.next()=Bio.Gobase.Iterator-class.html#next,Method Bio.IntelliGenetics.IntelliGeneticsReader.next()=Bio.IntelliGenetics.IntelliGeneticsReader-class.html#next,Method Bio.IntelliGenetics.Iterator.next()=Bio.IntelliGenetics.Iterator-class.html#next,Method Bio.LocusLink.Iterator.next()=Bio.LocusLink.Iterator-class.html#next,Method Bio.Medline.Iterator.next()=Bio.Medline.Iterator-class.html#next,Method Bio.MetaTool.Iterator.next()=Bio.MetaTool.Iterator-class.html#next,Method Bio.NBRF.Iterator.next()=Bio.NBRF.Iterator-class.html#next,Method Bio.Nexus.Nexus.CharBuffer.next()=Bio.Nexus.Nexus.CharBuffer-class.html#next,Method Bio.Prosite.Iterator.next()=Bio.Prosite.Iterator-class.html#next,Method Bio.Prosite.Prodoc.Iterator.next()=Bio.Prosite.Prodoc.Iterator-class.html#next,Method Bio.Rebase.Iterator.next()=Bio.Rebase.Iterator-class.html#next,Method Bio.SCOP.Cla.Iterator.next()=Bio.SCOP.Cla.Iterator-class.html#next,Method Bio.SCOP.Des.Iterator.next()=Bio.SCOP.Des.Iterator-class.html#next,Method Bio.SCOP.Dom.Iterator.next()=Bio.SCOP.Dom.Iterator-class.html#next,Method Bio.SCOP.Hie.Iterator.next()=Bio.SCOP.Hie.Iterator-class.html#next,Method Bio.SCOP.Raf.Iterator.next()=Bio.SCOP.Raf.Iterator-class.html#next,Method Bio.Saf.Iterator.next()=Bio.Saf.Iterator-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.Sequencing.Ace.Iterator.next()=Bio.Sequencing.Ace.Iterator-class.html#next,Method Bio.Sequencing.Phd.Iterator.next()=Bio.Sequencing.Phd.Iterator-class.html#next,Method Bio.SwissProt.SProt.Iterator.next()=Bio.SwissProt.SProt.Iterator-class.html#next,Method Bio.UniGene.Iterator.next()=Bio.UniGene.Iterator-class.html#next,Method Martel.Iterator.EventStream.next()=Martel.Iterator.EventStream-class.html#next,Method Martel.Iterator.HeaderFooterEventStream.next()=Martel.Iterator.HeaderFooterEventStream-class.html#next,Method Martel.Iterator.Iterate.next()=Martel.Iterator.Iterate-class.html#next,Method Martel.Iterator.RecordEventStream.next()=Martel.Iterator.RecordEventStream-class.html#next,Method Martel.RecordReader.CountLines.next()=Martel.RecordReader.CountLines-class.html#next,Method Martel.RecordReader.EndsWith.next()=Martel.RecordReader.EndsWith-class.html#next,Method Martel.RecordReader.Everything.next()=Martel.RecordReader.Everything-class.html#next,Method Martel.RecordReader.Nothing.next()=Martel.RecordReader.Nothing-class.html#next,Method Martel.RecordReader.RecordReader.next()=Martel.RecordReader.RecordReader-class.html#next,Method Martel.RecordReader.StartsWith.next()=Martel.RecordReader.StartsWith-class.html#next,Method Martel.RecordReader.Until.next()=Martel.RecordReader.Until-class.html#next"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.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.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-46', 'next', 'link-46');">next</a></tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L226"></a><tt class="py-lineno">226</tt>  <tt class="py-line"> </tt>
<a name="RecordParser"></a><div id="RecordParser-def"><a name="L227"></a><tt class="py-lineno">227</tt> <a class="py-toggle" href="#" id="RecordParser-toggle" onclick="return toggle('RecordParser');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Sequencing.Ace.RecordParser-class.html">RecordParser</a><tt class="py-op">(</tt><tt class="py-base-class">AbstractParser</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="RecordParser-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="RecordParser-expanded"><a name="L228"></a><tt class="py-lineno">228</tt>  <tt class="py-line">    <tt class="py-docstring">"""Parses ACE file data into a Record object."""</tt> </tt>
<a name="RecordParser.__init__"></a><div id="RecordParser.__init__-def"><a name="L229"></a><tt class="py-lineno">229</tt> <a class="py-toggle" href="#" id="RecordParser.__init__-toggle" onclick="return toggle('RecordParser.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace.RecordParser-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="RecordParser.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="RecordParser.__init__-expanded"><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 class="py-name">_scanner</tt> <tt class="py-op">=</tt> <tt id="link-47" class="py-name" targets="Class Bio.Blast.NCBIStandalone._Scanner=Bio.Blast.NCBIStandalone._Scanner-class.html,Class Bio.Blast.NCBIWWW._Scanner=Bio.Blast.NCBIWWW._Scanner-class.html,Class Bio.CDD._Scanner=Bio.CDD._Scanner-class.html,Class Bio.Compass._Scanner=Bio.Compass._Scanner-class.html,Class Bio.ECell._Scanner=Bio.ECell._Scanner-class.html,Class Bio.Enzyme._Scanner=Bio.Enzyme._Scanner-class.html,Class Bio.Gobase._Scanner=Bio.Gobase._Scanner-class.html,Class Bio.IntelliGenetics._Scanner=Bio.IntelliGenetics._Scanner-class.html,Class Bio.LocusLink._Scanner=Bio.LocusLink._Scanner-class.html,Class Bio.Medline._Scanner=Bio.Medline._Scanner-class.html,Class Bio.MetaTool._Scanner=Bio.MetaTool._Scanner-class.html,Class Bio.NBRF._Scanner=Bio.NBRF._Scanner-class.html,Class Bio.PopGen.FDist._Scanner=Bio.PopGen.FDist._Scanner-class.html,Class Bio.PopGen.GenePop._Scanner=Bio.PopGen.GenePop._Scanner-class.html,Class Bio.Prosite.Prodoc._Scanner=Bio.Prosite.Prodoc._Scanner-class.html,Class Bio.Prosite._Scanner=Bio.Prosite._Scanner-class.html,Class Bio.Rebase._Scanner=Bio.Rebase._Scanner-class.html,Class Bio.Saf._Scanner=Bio.Saf._Scanner-class.html,Class Bio.Sequencing.Ace._Scanner=Bio.Sequencing.Ace._Scanner-class.html,Class Bio.Sequencing.Phd._Scanner=Bio.Sequencing.Phd._Scanner-class.html,Class Bio.SwissProt.KeyWList._Scanner=Bio.SwissProt.KeyWList._Scanner-class.html,Class Bio.SwissProt.SProt._Scanner=Bio.SwissProt.SProt._Scanner-class.html,Class Bio.UniGene._Scanner=Bio.UniGene._Scanner-class.html"><a title="Bio.Blast.NCBIStandalone._Scanner
Bio.Blast.NCBIWWW._Scanner
Bio.CDD._Scanner
Bio.Compass._Scanner
Bio.ECell._Scanner
Bio.Enzyme._Scanner
Bio.Gobase._Scanner
Bio.IntelliGenetics._Scanner
Bio.LocusLink._Scanner
Bio.Medline._Scanner
Bio.MetaTool._Scanner
Bio.NBRF._Scanner
Bio.PopGen.FDist._Scanner
Bio.PopGen.GenePop._Scanner
Bio.Prosite.Prodoc._Scanner
Bio.Prosite._Scanner
Bio.Rebase._Scanner
Bio.Saf._Scanner
Bio.Sequencing.Ace._Scanner
Bio.Sequencing.Phd._Scanner
Bio.SwissProt.KeyWList._Scanner
Bio.SwissProt.SProt._Scanner
Bio.UniGene._Scanner" class="py-name" href="#" onclick="return doclink('link-47', '_Scanner', 'link-47');">_Scanner</a></tt><tt class="py-op">(</tt><tt class="py-op">)</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">_consumer</tt> <tt class="py-op">=</tt> <tt id="link-48" class="py-name" targets="Class Bio.CDD._RecordConsumer=Bio.CDD._RecordConsumer-class.html,Class Bio.ECell._RecordConsumer=Bio.ECell._RecordConsumer-class.html,Class Bio.Enzyme._RecordConsumer=Bio.Enzyme._RecordConsumer-class.html,Class Bio.GenBank._RecordConsumer=Bio.GenBank._RecordConsumer-class.html,Class Bio.Gobase._RecordConsumer=Bio.Gobase._RecordConsumer-class.html,Class Bio.IntelliGenetics._RecordConsumer=Bio.IntelliGenetics._RecordConsumer-class.html,Class Bio.LocusLink._RecordConsumer=Bio.LocusLink._RecordConsumer-class.html,Class Bio.Medline._RecordConsumer=Bio.Medline._RecordConsumer-class.html,Class Bio.MetaTool._RecordConsumer=Bio.MetaTool._RecordConsumer-class.html,Class Bio.NBRF._RecordConsumer=Bio.NBRF._RecordConsumer-class.html,Class Bio.PopGen.FDist._RecordConsumer=Bio.PopGen.FDist._RecordConsumer-class.html,Class Bio.PopGen.GenePop._RecordConsumer=Bio.PopGen.GenePop._RecordConsumer-class.html,Class Bio.Prosite.Prodoc._RecordConsumer=Bio.Prosite.Prodoc._RecordConsumer-class.html,Class Bio.Prosite._RecordConsumer=Bio.Prosite._RecordConsumer-class.html,Class Bio.Rebase._RecordConsumer=Bio.Rebase._RecordConsumer-class.html,Class Bio.Saf._RecordConsumer=Bio.Saf._RecordConsumer-class.html,Class Bio.Sequencing.Ace._RecordConsumer=Bio.Sequencing.Ace._RecordConsumer-class.html,Class Bio.Sequencing.Phd._RecordConsumer=Bio.Sequencing.Phd._RecordConsumer-class.html,Class Bio.SwissProt.SProt._RecordConsumer=Bio.SwissProt.SProt._RecordConsumer-class.html,Class Bio.UniGene._RecordConsumer=Bio.UniGene._RecordConsumer-class.html"><a title="Bio.CDD._RecordConsumer
Bio.ECell._RecordConsumer
Bio.Enzyme._RecordConsumer
Bio.GenBank._RecordConsumer
Bio.Gobase._RecordConsumer
Bio.IntelliGenetics._RecordConsumer
Bio.LocusLink._RecordConsumer
Bio.Medline._RecordConsumer
Bio.MetaTool._RecordConsumer
Bio.NBRF._RecordConsumer
Bio.PopGen.FDist._RecordConsumer
Bio.PopGen.GenePop._RecordConsumer
Bio.Prosite.Prodoc._RecordConsumer
Bio.Prosite._RecordConsumer
Bio.Rebase._RecordConsumer
Bio.Saf._RecordConsumer
Bio.Sequencing.Ace._RecordConsumer
Bio.Sequencing.Phd._RecordConsumer
Bio.SwissProt.SProt._RecordConsumer
Bio.UniGene._RecordConsumer" class="py-name" href="#" onclick="return doclink('link-48', '_RecordConsumer', 'link-48');">_RecordConsumer</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L232"></a><tt class="py-lineno">232</tt>  <tt class="py-line"> </tt>
<a name="RecordParser.parse"></a><div id="RecordParser.parse-def"><a name="L233"></a><tt class="py-lineno">233</tt> <a class="py-toggle" href="#" id="RecordParser.parse-toggle" onclick="return toggle('RecordParser.parse');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace.RecordParser-class.html#parse">parse</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">handle</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="RecordParser.parse-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="RecordParser.parse-expanded"><a name="L234"></a><tt class="py-lineno">234</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-49" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-49', 'handle', 'link-35');">handle</a></tt><tt class="py-op">,</tt> <tt id="link-50" class="py-name"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-50', 'File', 'link-1');">File</a></tt><tt class="py-op">.</tt><tt id="link-51" class="py-name"><a title="Bio.File.UndoHandle" class="py-name" href="#" onclick="return doclink('link-51', 'UndoHandle', 'link-34');">UndoHandle</a></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">uhandle</tt> <tt class="py-op">=</tt> <tt id="link-52" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-52', 'handle', 'link-35');">handle</a></tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt>  <tt class="py-line">            <tt class="py-name">uhandle</tt> <tt class="py-op">=</tt> <tt id="link-53" class="py-name"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-53', 'File', 'link-1');">File</a></tt><tt class="py-op">.</tt><tt id="link-54" class="py-name"><a title="Bio.File.UndoHandle" class="py-name" href="#" onclick="return doclink('link-54', 'UndoHandle', 'link-34');">UndoHandle</a></tt><tt class="py-op">(</tt><tt id="link-55" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-55', 'handle', 'link-35');">handle</a></tt><tt class="py-op">)</tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_scanner</tt><tt class="py-op">.</tt><tt id="link-56" class="py-name" targets="Method Bio.Affy.CelFile.CelScanner.feed()=Bio.Affy.CelFile.CelScanner-class.html#feed,Method Bio.AlignAce.Scanner.AlignAceScanner.feed()=Bio.AlignAce.Scanner.AlignAceScanner-class.html#feed,Method Bio.AlignAce.Scanner.CompareAceScanner.feed()=Bio.AlignAce.Scanner.CompareAceScanner-class.html#feed,Method Bio.Blast.NCBIStandalone._Scanner.feed()=Bio.Blast.NCBIStandalone._Scanner-class.html#feed,Method Bio.Blast.NCBIWWW._Scanner.feed()=Bio.Blast.NCBIWWW._Scanner-class.html#feed,Method Bio.CDD._Scanner.feed()=Bio.CDD._Scanner-class.html#feed,Method Bio.Compass._Scanner.feed()=Bio.Compass._Scanner-class.html#feed,Method Bio.ECell._Scanner.feed()=Bio.ECell._Scanner-class.html#feed,Method Bio.Emboss.Primer._Primer3Scanner.feed()=Bio.Emboss.Primer._Primer3Scanner-class.html#feed,Method Bio.Emboss.Primer._PrimerSearchScanner.feed()=Bio.Emboss.Primer._PrimerSearchScanner-class.html#feed,Method Bio.Enzyme._Scanner.feed()=Bio.Enzyme._Scanner-class.html#feed,Method Bio.GenBank.Scanner.InsdcScanner.feed()=Bio.GenBank.Scanner.InsdcScanner-class.html#feed,Method Bio.Gobase._Scanner.feed()=Bio.Gobase._Scanner-class.html#feed,Method Bio.IntelliGenetics._Scanner.feed()=Bio.IntelliGenetics._Scanner-class.html#feed,Method Bio.InterPro.InterProParser.feed()=Bio.InterPro.InterProParser-class.html#feed,Method Bio.LocusLink._Scanner.feed()=Bio.LocusLink._Scanner-class.html#feed,Method Bio.LocusLink.web_parse.LocusLinkParser.feed()=Bio.LocusLink.web_parse.LocusLinkParser-class.html#feed,Method Bio.MEME.Parser._MASTScanner.feed()=Bio.MEME.Parser._MASTScanner-class.html#feed,Method Bio.MEME.Parser._MEMEScanner.feed()=Bio.MEME.Parser._MEMEScanner-class.html#feed,Method Bio.Medline._Scanner.feed()=Bio.Medline._Scanner-class.html#feed,Method Bio.MetaTool._Scanner.feed()=Bio.MetaTool._Scanner-class.html#feed,Method Bio.NBRF._Scanner.feed()=Bio.NBRF._Scanner-class.html#feed,Method Bio.Ndb.NdbParser.feed()=Bio.Ndb.NdbParser-class.html#feed,Method Bio.NetCatch.ExtractUrls.feed()=Bio.NetCatch.ExtractUrls-class.html#feed,Method Bio.PopGen.FDist._Scanner.feed()=Bio.PopGen.FDist._Scanner-class.html#feed,Method Bio.PopGen.GenePop._Scanner.feed()=Bio.PopGen.GenePop._Scanner-class.html#feed,Method Bio.Prosite.Prodoc._Scanner.feed()=Bio.Prosite.Prodoc._Scanner-class.html#feed,Method Bio.Prosite._Scanner.feed()=Bio.Prosite._Scanner-class.html#feed,Method Bio.Rebase._Scanner.feed()=Bio.Rebase._Scanner-class.html#feed,Method Bio.Saf._Scanner.feed()=Bio.Saf._Scanner-class.html#feed,Method Bio.Sequencing.Ace._Scanner.feed()=Bio.Sequencing.Ace._Scanner-class.html#feed,Method Bio.Sequencing.Phd._Scanner.feed()=Bio.Sequencing.Phd._Scanner-class.html#feed,Method Bio.SwissProt.KeyWList._Scanner.feed()=Bio.SwissProt.KeyWList._Scanner-class.html#feed,Method Bio.SwissProt.SProt._Scanner.feed()=Bio.SwissProt.SProt._Scanner-class.html#feed,Method Bio.UniGene._Scanner.feed()=Bio.UniGene._Scanner-class.html#feed"><a title="Bio.Affy.CelFile.CelScanner.feed
Bio.AlignAce.Scanner.AlignAceScanner.feed
Bio.AlignAce.Scanner.CompareAceScanner.feed
Bio.Blast.NCBIStandalone._Scanner.feed
Bio.Blast.NCBIWWW._Scanner.feed
Bio.CDD._Scanner.feed
Bio.Compass._Scanner.feed
Bio.ECell._Scanner.feed
Bio.Emboss.Primer._Primer3Scanner.feed
Bio.Emboss.Primer._PrimerSearchScanner.feed
Bio.Enzyme._Scanner.feed
Bio.GenBank.Scanner.InsdcScanner.feed
Bio.Gobase._Scanner.feed
Bio.IntelliGenetics._Scanner.feed
Bio.InterPro.InterProParser.feed
Bio.LocusLink._Scanner.feed
Bio.LocusLink.web_parse.LocusLinkParser.feed
Bio.MEME.Parser._MASTScanner.feed
Bio.MEME.Parser._MEMEScanner.feed
Bio.Medline._Scanner.feed
Bio.MetaTool._Scanner.feed
Bio.NBRF._Scanner.feed
Bio.Ndb.NdbParser.feed
Bio.NetCatch.ExtractUrls.feed
Bio.PopGen.FDist._Scanner.feed
Bio.PopGen.GenePop._Scanner.feed
Bio.Prosite.Prodoc._Scanner.feed
Bio.Prosite._Scanner.feed
Bio.Rebase._Scanner.feed
Bio.Saf._Scanner.feed
Bio.Sequencing.Ace._Scanner.feed
Bio.Sequencing.Phd._Scanner.feed
Bio.SwissProt.KeyWList._Scanner.feed
Bio.SwissProt.SProt._Scanner.feed
Bio.UniGene._Scanner.feed" class="py-name" href="#" onclick="return doclink('link-56', 'feed', 'link-56');">feed</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_consumer</tt><tt class="py-op">)</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_consumer</tt><tt class="py-op">.</tt><tt id="link-57" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-57', 'data', 'link-41');">data</a></tt> </tt>
</div></div><a name="L240"></a><tt class="py-lineno">240</tt>  <tt class="py-line"> </tt>
<a name="ACEFileRecord"></a><div id="ACEFileRecord-def"><a name="L241"></a><tt class="py-lineno">241</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>
</div><div id="ACEFileRecord-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="ACEFileRecord-expanded"><a name="L242"></a><tt class="py-lineno">242</tt>  <tt class="py-line">    <tt class="py-docstring">"""Holds data of an ACE file.</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="ACEFileRecord.__init__"></a><div id="ACEFileRecord.__init__-def"><a name="L244"></a><tt class="py-lineno">244</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="L245"></a><tt class="py-lineno">245</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="L246"></a><tt class="py-lineno">246</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="L247"></a><tt class="py-lineno">247</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="L248"></a><tt class="py-lineno">248</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-58" class="py-name"><a title="Bio.Sequencing.Ace.wa" class="py-name" href="#" onclick="return doclink('link-58', 'wa', 'link-32');">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="L249"></a><tt class="py-lineno">249</tt>  <tt class="py-line"> </tt>
<a name="ACEFileRecord.sort"></a><div id="ACEFileRecord.sort-def"><a name="L250"></a><tt class="py-lineno">250</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="L251"></a><tt class="py-lineno">251</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="L252"></a><tt class="py-lineno">252</tt>  <tt class="py-line">        </tt>
<a name="L253"></a><tt class="py-lineno">253</tt>  <tt class="py-line">        <tt id="link-59" class="py-name"><a title="Bio.Sequencing.Ace.ct" class="py-name" href="#" onclick="return doclink('link-59', 'ct', 'link-31');">ct</a></tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt>  <tt class="py-line">        <tt id="link-60" class="py-name"><a title="Bio.Sequencing.Ace.rt" class="py-name" href="#" onclick="return doclink('link-60', 'rt', 'link-25');">rt</a></tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt>  <tt class="py-line">        <tt id="link-61" class="py-name"><a title="Bio.Sequencing.Ace.wr" class="py-name" href="#" onclick="return doclink('link-61', 'wr', 'link-26');">wr</a></tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt>  <tt class="py-line">        <tt class="py-comment"># search for tags that aren't in the right position</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-keyword">for</tt> <tt id="link-62" 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-62', 'i', 'link-62');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</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="L258"></a><tt class="py-lineno">258</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-63" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-63', 'i', 'link-62');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</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-64" class="py-name"><a title="Bio.Sequencing.Ace.wa" class="py-name" href="#" onclick="return doclink('link-64', 'wa', 'link-32');">wa</a></tt><tt class="py-op">:</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</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-65" class="py-name"><a title="Bio.Sequencing.Ace.wa" class="py-name" href="#" onclick="return doclink('link-65', 'wa', 'link-32');">wa</a></tt><tt class="py-op">:</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</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.Sequencing.Ace.wa" class="py-name" href="#" onclick="return doclink('link-66', 'wa', 'link-32');">wa</a></tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-67" class="py-name"><a title="Bio.Sequencing.Ace.wa" class="py-name" href="#" onclick="return doclink('link-67', 'wa', 'link-32');">wa</a></tt><tt class="py-op">.</tt><tt id="link-68" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.extend()=Bio.EUtils.POM.ElementNode-class.html#extend,Method Bio.SCOP.Raf.SeqMap.extend()=Bio.SCOP.Raf.SeqMap-class.html#extend,Method Bio.Seq.MutableSeq.extend()=Bio.Seq.MutableSeq-class.html#extend"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-68', 'extend', 'link-68');">extend</a></tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt id="link-69" class="py-name"><a title="Bio.Sequencing.Ace.wa" class="py-name" href="#" onclick="return doclink('link-69', 'wa', 'link-32');">wa</a></tt><tt class="py-op">)</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</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-70" class="py-name"><a title="Bio.Sequencing.Ace.ct" class="py-name" href="#" onclick="return doclink('link-70', 'ct', 'link-31');">ct</a></tt><tt class="py-op">:</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</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-71" class="py-name"><a title="Bio.Sequencing.Ace.ct" class="py-name" href="#" onclick="return doclink('link-71', 'ct', 'link-31');">ct</a></tt> <tt class="py-keyword">if</tt> <tt class="py-name">ct_tag</tt><tt class="py-op">.</tt><tt id="link-72" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-72', 'name', 'link-7');">name</a></tt><tt class="py-op">!=</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt id="link-73" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-73', 'name', 'link-7');">name</a></tt><tt class="py-op">]</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt>  <tt class="py-line">                <tt id="link-74" class="py-name" targets="Method Bio.GFF.FeatureAggregate.map()=Bio.GFF.FeatureAggregate-class.html#map"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-74', 'map', 'link-74');">map</a></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-75" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-75', 'i', 'link-62');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-76" class="py-name"><a title="Bio.Sequencing.Ace.ct" class="py-name" href="#" onclick="return doclink('link-76', 'ct', 'link-31');">ct</a></tt><tt class="py-op">.</tt><tt id="link-77" class="py-name" targets="Method Bio.Crystal.Chain.remove()=Bio.Crystal.Chain-class.html#remove,Method Bio.GFF.GenericTools.TempFile.remove()=Bio.GFF.GenericTools.TempFile-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.GFF.GenericTools.TempFile.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-77', 'remove', 'link-77');">remove</a></tt><tt class="py-op">,</tt><tt class="py-name">newcts</tt><tt class="py-op">)</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt>  <tt class="py-line">                <tt id="link-78" class="py-name"><a title="Bio.Sequencing.Ace.ct" class="py-name" href="#" onclick="return doclink('link-78', 'ct', 'link-31');">ct</a></tt><tt class="py-op">.</tt><tt id="link-79" class="py-name"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-79', 'extend', 'link-68');">extend</a></tt><tt class="py-op">(</tt><tt class="py-name">newcts</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">for</tt> <tt class="py-name">j</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-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="L268"></a><tt class="py-lineno">268</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="L269"></a><tt class="py-lineno">269</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-80" class="py-name"><a title="Bio.Sequencing.Ace.rt" class="py-name" href="#" onclick="return doclink('link-80', 'rt', 'link-25');">rt</a></tt><tt class="py-op">:</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</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-81" class="py-name"><a title="Bio.Sequencing.Ace.rt" class="py-name" href="#" onclick="return doclink('link-81', 'rt', 'link-25');">rt</a></tt> <tt class="py-keyword">if</tt> <tt class="py-name">rt_tag</tt><tt class="py-op">.</tt><tt id="link-82" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-82', 'name', 'link-7');">name</a></tt><tt class="py-op">!=</tt><tt class="py-name">r</tt><tt class="py-op">.</tt><tt id="link-83" class="py-name"><a title="Bio.Sequencing.Ace.rd" class="py-name" href="#" onclick="return doclink('link-83', 'rd', 'link-22');">rd</a></tt><tt class="py-op">.</tt><tt id="link-84" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-84', 'name', 'link-7');">name</a></tt><tt class="py-op">]</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt>  <tt class="py-line">                    <tt id="link-85" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-85', 'map', 'link-74');">map</a></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-86" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-86', 'i', 'link-62');">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-87" class="py-name"><a title="Bio.Sequencing.Ace.rt" class="py-name" href="#" onclick="return doclink('link-87', 'rt', 'link-25');">rt</a></tt><tt class="py-op">.</tt><tt id="link-88" class="py-name"><a title="Bio.Crystal.Chain.remove
Bio.GFF.GenericTools.TempFile.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-88', 'remove', 'link-77');">remove</a></tt><tt class="py-op">,</tt><tt class="py-name">newrts</tt><tt class="py-op">)</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt>  <tt class="py-line">                    <tt id="link-89" class="py-name"><a title="Bio.Sequencing.Ace.rt" class="py-name" href="#" onclick="return doclink('link-89', 'rt', 'link-25');">rt</a></tt><tt class="py-op">.</tt><tt id="link-90" class="py-name"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-90', 'extend', 'link-68');">extend</a></tt><tt class="py-op">(</tt><tt class="py-name">newrts</tt><tt class="py-op">)</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</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-91" class="py-name"><a title="Bio.Sequencing.Ace.wr" class="py-name" href="#" onclick="return doclink('link-91', 'wr', 'link-26');">wr</a></tt><tt class="py-op">:</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</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-92" class="py-name"><a title="Bio.Sequencing.Ace.wr" class="py-name" href="#" onclick="return doclink('link-92', 'wr', 'link-26');">wr</a></tt> <tt class="py-keyword">if</tt> <tt class="py-name">wr_tag</tt><tt class="py-op">.</tt><tt id="link-93" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-93', 'name', 'link-7');">name</a></tt><tt class="py-op">!=</tt><tt class="py-name">r</tt><tt class="py-op">.</tt><tt id="link-94" class="py-name"><a title="Bio.Sequencing.Ace.rd" class="py-name" href="#" onclick="return doclink('link-94', 'rd', 'link-22');">rd</a></tt><tt class="py-op">.</tt><tt id="link-95" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-95', 'name', 'link-7');">name</a></tt><tt class="py-op">]</tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt>  <tt class="py-line">                    <tt id="link-96" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-96', 'map', 'link-74');">map</a></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-97" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-97', 'i', 'link-62');">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-98" class="py-name"><a title="Bio.Sequencing.Ace.wr" class="py-name" href="#" onclick="return doclink('link-98', 'wr', 'link-26');">wr</a></tt><tt class="py-op">.</tt><tt id="link-99" class="py-name"><a title="Bio.Crystal.Chain.remove
Bio.GFF.GenericTools.TempFile.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-99', 'remove', 'link-77');">remove</a></tt><tt class="py-op">,</tt><tt class="py-name">newwrs</tt><tt class="py-op">)</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt>  <tt class="py-line">                    <tt id="link-100" class="py-name"><a title="Bio.Sequencing.Ace.wr" class="py-name" href="#" onclick="return doclink('link-100', 'wr', 'link-26');">wr</a></tt><tt class="py-op">.</tt><tt id="link-101" class="py-name"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-101', 'extend', 'link-68');">extend</a></tt><tt class="py-op">(</tt><tt class="py-name">newwrs</tt><tt class="py-op">)</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt>  <tt class="py-line">        <tt class="py-comment"># now sort them into their proper place</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-keyword">for</tt> <tt id="link-102" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-102', 'i', 'link-62');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</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="L279"></a><tt class="py-lineno">279</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-103" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-103', 'i', 'link-62');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</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-104" class="py-name"><a title="Bio.Sequencing.Ace.ct" class="py-name" href="#" onclick="return doclink('link-104', 'ct', 'link-31');">ct</a></tt><tt class="py-op">:</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</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-105" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-105', 'name', 'link-7');">name</a></tt><tt class="py-op">==</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt id="link-106" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-106', 'name', 'link-7');">name</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">self</tt><tt class="py-op">.</tt><tt class="py-name">contigs</tt><tt class="py-op">[</tt><tt id="link-107" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-107', 'i', 'link-62');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-108" class="py-name"><a title="Bio.Sequencing.Ace.ct" class="py-name" href="#" onclick="return doclink('link-108', 'ct', 'link-31');">ct</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</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-109" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-109', 'i', 'link-62');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-110" class="py-name"><a title="Bio.Sequencing.Ace.ct" class="py-name" href="#" onclick="return doclink('link-110', 'ct', 'link-31');">ct</a></tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</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-111" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-111', 'i', 'link-62');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-112" class="py-name"><a title="Bio.Sequencing.Ace.ct" class="py-name" href="#" onclick="return doclink('link-112', 'ct', 'link-31');">ct</a></tt><tt class="py-op">.</tt><tt id="link-113" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-113', 'append', 'link-37');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">ct_tag</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">if</tt> <tt id="link-114" class="py-name"><a title="Bio.Sequencing.Ace.rt" class="py-name" href="#" onclick="return doclink('link-114', 'rt', 'link-25');">rt</a></tt> <tt class="py-keyword">or</tt> <tt id="link-115" class="py-name"><a title="Bio.Sequencing.Ace.wr" class="py-name" href="#" onclick="return doclink('link-115', 'wr', 'link-26');">wr</a></tt><tt class="py-op">:</tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt>  <tt class="py-line">                <tt class="py-keyword">for</tt> <tt class="py-name">j</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-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="L287"></a><tt class="py-lineno">287</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="L288"></a><tt class="py-lineno">288</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-116" class="py-name"><a title="Bio.Sequencing.Ace.rt" class="py-name" href="#" onclick="return doclink('link-116', 'rt', 'link-25');">rt</a></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">if</tt> <tt class="py-name">rt_tag</tt><tt class="py-op">.</tt><tt id="link-117" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-117', 'name', 'link-7');">name</a></tt><tt class="py-op">==</tt><tt class="py-name">r</tt><tt class="py-op">.</tt><tt id="link-118" class="py-name"><a title="Bio.Sequencing.Ace.rd" class="py-name" href="#" onclick="return doclink('link-118', 'rd', 'link-22');">rd</a></tt><tt class="py-op">.</tt><tt id="link-119" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-119', 'name', 'link-7');">name</a></tt><tt class="py-op">:</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</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-120" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-120', 'i', 'link-62');">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-121" class="py-name"><a title="Bio.Sequencing.Ace.rt" class="py-name" href="#" onclick="return doclink('link-121', 'rt', 'link-25');">rt</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</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-122" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-122', 'i', 'link-62');">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-123" class="py-name"><a title="Bio.Sequencing.Ace.rt" class="py-name" href="#" onclick="return doclink('link-123', 'rt', 'link-25');">rt</a></tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</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-124" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-124', 'i', 'link-62');">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-125" class="py-name"><a title="Bio.Sequencing.Ace.rt" class="py-name" href="#" onclick="return doclink('link-125', 'rt', 'link-25');">rt</a></tt><tt class="py-op">.</tt><tt id="link-126" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-126', 'append', 'link-37');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">rt_tag</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">for</tt> <tt class="py-name">wr_tag</tt> <tt class="py-keyword">in</tt> <tt id="link-127" class="py-name"><a title="Bio.Sequencing.Ace.wr" class="py-name" href="#" onclick="return doclink('link-127', 'wr', 'link-26');">wr</a></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">if</tt> <tt class="py-name">wr_tag</tt><tt class="py-op">.</tt><tt id="link-128" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-128', 'name', 'link-7');">name</a></tt><tt class="py-op">==</tt><tt class="py-name">r</tt><tt class="py-op">.</tt><tt id="link-129" class="py-name"><a title="Bio.Sequencing.Ace.rd" class="py-name" href="#" onclick="return doclink('link-129', 'rd', 'link-22');">rd</a></tt><tt class="py-op">.</tt><tt id="link-130" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-130', 'name', 'link-7');">name</a></tt><tt class="py-op">:</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</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-131" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-131', 'i', 'link-62');">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-132" class="py-name"><a title="Bio.Sequencing.Ace.wr" class="py-name" href="#" onclick="return doclink('link-132', 'wr', 'link-26');">wr</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</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-133" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-133', 'i', 'link-62');">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-134" class="py-name"><a title="Bio.Sequencing.Ace.wr" class="py-name" href="#" onclick="return doclink('link-134', 'wr', 'link-26');">wr</a></tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</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-135" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-135', 'i', 'link-62');">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-136" class="py-name"><a title="Bio.Sequencing.Ace.wr" class="py-name" href="#" onclick="return doclink('link-136', 'wr', 'link-26');">wr</a></tt><tt class="py-op">.</tt><tt id="link-137" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-137', 'append', 'link-37');">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="L298"></a><tt class="py-lineno">298</tt>  <tt class="py-line">        </tt>
<a name="ACEParser"></a><div id="ACEParser-def"><a name="L299"></a><tt class="py-lineno">299</tt> <a class="py-toggle" href="#" id="ACEParser-toggle" onclick="return toggle('ACEParser');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Sequencing.Ace.ACEParser-class.html">ACEParser</a><tt class="py-op">(</tt><tt class="py-base-class">AbstractParser</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ACEParser-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="ACEParser-expanded"><a name="L300"></a><tt class="py-lineno">300</tt>  <tt class="py-line">    <tt class="py-docstring">"""Parses full ACE file in list of contigs.</tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt>  <tt class="py-line"> </tt>
<a name="ACEParser.__init__"></a><div id="ACEParser.__init__-def"><a name="L304"></a><tt class="py-lineno">304</tt> <a class="py-toggle" href="#" id="ACEParser.__init__-toggle" onclick="return toggle('ACEParser.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace.ACEParser-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="ACEParser.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ACEParser.__init__-expanded"><a name="L305"></a><tt class="py-lineno">305</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-138" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-138', 'data', 'link-41');">data</a></tt><tt class="py-op">=</tt><tt id="link-139" 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-139', 'ACEFileRecord', 'link-139');">ACEFileRecord</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L306"></a><tt class="py-lineno">306</tt>  <tt class="py-line">         </tt>
<a name="ACEParser.parse"></a><div id="ACEParser.parse-def"><a name="L307"></a><tt class="py-lineno">307</tt> <a class="py-toggle" href="#" id="ACEParser.parse-toggle" onclick="return toggle('ACEParser.parse');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace.ACEParser-class.html#parse">parse</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">handle</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ACEParser.parse-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ACEParser.parse-expanded"><a name="L308"></a><tt class="py-lineno">308</tt>  <tt class="py-line">        <tt class="py-name">firstline</tt><tt class="py-op">=</tt><tt id="link-140" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-140', 'handle', 'link-35');">handle</a></tt><tt class="py-op">.</tt><tt id="link-141" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.readline
Bio.File.SGMLHandle.readline
Bio.File.UndoHandle.readline
Bio.SGMLExtractor.SGMLExtractorHandle.readline" class="py-name" href="#" onclick="return doclink('link-141', 'readline', 'link-36');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt>  <tt class="py-line">        <tt class="py-comment"># check if the file starts correctly</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-keyword">if</tt> <tt class="py-name">firstline</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">!=</tt><tt class="py-string">'AS'</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">"File does not start with 'AS'."</tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-142" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-142', 'data', 'link-41');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">ncontigs</tt><tt class="py-op">=</tt><tt class="py-name">eval</tt><tt class="py-op">(</tt><tt class="py-name">firstline</tt><tt class="py-op">.</tt><tt id="link-143" class="py-name" targets="Method Bio.Nexus.Trees.Tree.split()=Bio.Nexus.Trees.Tree-class.html#split,Method Bio.Restriction.Restriction.RestrictionBatch.split()=Bio.Restriction.Restriction.RestrictionBatch-class.html#split"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-143', 'split', 'link-143');">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>
<a name="L313"></a><tt class="py-lineno">313</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-144" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-144', 'data', 'link-41');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">nreads</tt><tt class="py-op">=</tt><tt class="py-name">eval</tt><tt class="py-op">(</tt><tt class="py-name">firstline</tt><tt class="py-op">.</tt><tt id="link-145" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-145', 'split', 'link-143');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt>  <tt class="py-line">        <tt class="py-comment"># now read all the records</tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-name">recparser</tt><tt class="py-op">=</tt><tt id="link-146" class="py-name" targets="Class Bio.CDD.RecordParser=Bio.CDD.RecordParser-class.html,Class Bio.Compass.RecordParser=Bio.Compass.RecordParser-class.html,Class Bio.ECell.RecordParser=Bio.ECell.RecordParser-class.html,Class Bio.Enzyme.RecordParser=Bio.Enzyme.RecordParser-class.html,Class Bio.Fasta.RecordParser=Bio.Fasta.RecordParser-class.html,Class Bio.GenBank.RecordParser=Bio.GenBank.RecordParser-class.html,Class Bio.Gobase.RecordParser=Bio.Gobase.RecordParser-class.html,Class Bio.IntelliGenetics.RecordParser=Bio.IntelliGenetics.RecordParser-class.html,Class Bio.LocusLink.RecordParser=Bio.LocusLink.RecordParser-class.html,Class Bio.Medline.RecordParser=Bio.Medline.RecordParser-class.html,Class Bio.MetaTool.RecordParser=Bio.MetaTool.RecordParser-class.html,Class Bio.NBRF.RecordParser=Bio.NBRF.RecordParser-class.html,Class Bio.PopGen.FDist.RecordParser=Bio.PopGen.FDist.RecordParser-class.html,Class Bio.PopGen.GenePop.RecordParser=Bio.PopGen.GenePop.RecordParser-class.html,Class Bio.Prosite.Prodoc.RecordParser=Bio.Prosite.Prodoc.RecordParser-class.html,Class Bio.Prosite.RecordParser=Bio.Prosite.RecordParser-class.html,Class Bio.Rebase.RecordParser=Bio.Rebase.RecordParser-class.html,Class Bio.Saf.RecordParser=Bio.Saf.RecordParser-class.html,Class Bio.Sequencing.Ace.RecordParser=Bio.Sequencing.Ace.RecordParser-class.html,Class Bio.Sequencing.Phd.RecordParser=Bio.Sequencing.Phd.RecordParser-class.html,Class Bio.SwissProt.SProt.RecordParser=Bio.SwissProt.SProt.RecordParser-class.html,Class Bio.UniGene.RecordParser=Bio.UniGene.RecordParser-class.html,Class Martel.Parser.RecordParser=Martel.Parser.RecordParser-class.html"><a title="Bio.CDD.RecordParser
Bio.Compass.RecordParser
Bio.ECell.RecordParser
Bio.Enzyme.RecordParser
Bio.Fasta.RecordParser
Bio.GenBank.RecordParser
Bio.Gobase.RecordParser
Bio.IntelliGenetics.RecordParser
Bio.LocusLink.RecordParser
Bio.Medline.RecordParser
Bio.MetaTool.RecordParser
Bio.NBRF.RecordParser
Bio.PopGen.FDist.RecordParser
Bio.PopGen.GenePop.RecordParser
Bio.Prosite.Prodoc.RecordParser
Bio.Prosite.RecordParser
Bio.Rebase.RecordParser
Bio.Saf.RecordParser
Bio.Sequencing.Ace.RecordParser
Bio.Sequencing.Phd.RecordParser
Bio.SwissProt.SProt.RecordParser
Bio.UniGene.RecordParser
Martel.Parser.RecordParser" class="py-name" href="#" onclick="return doclink('link-146', 'RecordParser', 'link-146');">RecordParser</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt>  <tt class="py-line">        <tt class="py-name">iter</tt><tt class="py-op">=</tt><tt id="link-147" class="py-name" targets="Class Bio.Blast.NCBIStandalone.Iterator=Bio.Blast.NCBIStandalone.Iterator-class.html,Class Bio.CDD.Iterator=Bio.CDD.Iterator-class.html,Class Bio.Compass.Iterator=Bio.Compass.Iterator-class.html,Class Bio.ECell.Iterator=Bio.ECell.Iterator-class.html,Class Bio.Enzyme.Iterator=Bio.Enzyme.Iterator-class.html,Class Bio.Fasta.Iterator=Bio.Fasta.Iterator-class.html,Class Bio.GenBank.Iterator=Bio.GenBank.Iterator-class.html,Class Bio.Gobase.Iterator=Bio.Gobase.Iterator-class.html,Class Bio.IntelliGenetics.Iterator=Bio.IntelliGenetics.Iterator-class.html,Class Bio.LocusLink.Iterator=Bio.LocusLink.Iterator-class.html,Class Bio.Medline.Iterator=Bio.Medline.Iterator-class.html,Class Bio.MetaTool.Iterator=Bio.MetaTool.Iterator-class.html,Class Bio.NBRF.Iterator=Bio.NBRF.Iterator-class.html,Class Bio.Prosite.Iterator=Bio.Prosite.Iterator-class.html,Class Bio.Prosite.Prodoc.Iterator=Bio.Prosite.Prodoc.Iterator-class.html,Class Bio.Rebase.Iterator=Bio.Rebase.Iterator-class.html,Class Bio.SCOP.Cla.Iterator=Bio.SCOP.Cla.Iterator-class.html,Class Bio.SCOP.Des.Iterator=Bio.SCOP.Des.Iterator-class.html,Class Bio.SCOP.Dom.Iterator=Bio.SCOP.Dom.Iterator-class.html,Class Bio.SCOP.Hie.Iterator=Bio.SCOP.Hie.Iterator-class.html,Class Bio.SCOP.Raf.Iterator=Bio.SCOP.Raf.Iterator-class.html,Class Bio.Saf.Iterator=Bio.Saf.Iterator-class.html,Class Bio.Sequencing.Ace.Iterator=Bio.Sequencing.Ace.Iterator-class.html,Class Bio.Sequencing.Phd.Iterator=Bio.Sequencing.Phd.Iterator-class.html,Class Bio.SwissProt.SProt.Iterator=Bio.SwissProt.SProt.Iterator-class.html,Class Bio.UniGene.Iterator=Bio.UniGene.Iterator-class.html,Module Martel.Iterator=Martel.Iterator-module.html,Class Martel.Iterator.Iterator=Martel.Iterator.Iterator-class.html"><a title="Bio.Blast.NCBIStandalone.Iterator
Bio.CDD.Iterator
Bio.Compass.Iterator
Bio.ECell.Iterator
Bio.Enzyme.Iterator
Bio.Fasta.Iterator
Bio.GenBank.Iterator
Bio.Gobase.Iterator
Bio.IntelliGenetics.Iterator
Bio.LocusLink.Iterator
Bio.Medline.Iterator
Bio.MetaTool.Iterator
Bio.NBRF.Iterator
Bio.Prosite.Iterator
Bio.Prosite.Prodoc.Iterator
Bio.Rebase.Iterator
Bio.SCOP.Cla.Iterator
Bio.SCOP.Des.Iterator
Bio.SCOP.Dom.Iterator
Bio.SCOP.Hie.Iterator
Bio.SCOP.Raf.Iterator
Bio.Saf.Iterator
Bio.Sequencing.Ace.Iterator
Bio.Sequencing.Phd.Iterator
Bio.SwissProt.SProt.Iterator
Bio.UniGene.Iterator
Martel.Iterator
Martel.Iterator.Iterator" class="py-name" href="#" onclick="return doclink('link-147', 'Iterator', 'link-147');">Iterator</a></tt><tt class="py-op">(</tt><tt id="link-148" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-148', 'handle', 'link-35');">handle</a></tt><tt class="py-op">,</tt><tt class="py-name">recparser</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">while</tt> <tt class="py-number">1</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">rec</tt><tt class="py-op">=</tt><tt class="py-name">iter</tt><tt class="py-op">.</tt><tt id="link-149" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.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.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-149', 'next', 'link-46');">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">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">rec</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">break</tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-150" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-150', 'data', 'link-41');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">contigs</tt><tt class="py-op">.</tt><tt id="link-151" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-151', 'append', 'link-37');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">rec</tt><tt class="py-op">)</tt> </tt>
<a name="L322"></a><tt class="py-lineno">322</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="L323"></a><tt class="py-lineno">323</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <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="L324"></a><tt class="py-lineno">324</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <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="L325"></a><tt class="py-lineno">325</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment"># iterator leaves no other choice. But if the user uses the ACEParser, we can check</tt> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment"># them and put them into the appropriate contig/read instance.</tt> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment"># Conclusion: An ACE file is not a filetype for which iteration is 100% suitable...</tt> </tt>
<a name="L328"></a><tt class="py-lineno">328</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-152" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-152', 'data', 'link-41');">data</a></tt><tt class="py-op">.</tt><tt id="link-153" class="py-name" targets="Method Bio.PDB.Residue.DisorderedResidue.sort()=Bio.PDB.Residue.DisorderedResidue-class.html#sort,Method Bio.PDB.Residue.Residue.sort()=Bio.PDB.Residue.Residue-class.html#sort,Method Bio.Sequencing.Ace.ACEFileRecord.sort()=Bio.Sequencing.Ace.ACEFileRecord-class.html#sort"><a title="Bio.PDB.Residue.DisorderedResidue.sort
Bio.PDB.Residue.Residue.sort
Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-153', 'sort', 'link-153');">sort</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L329"></a><tt class="py-lineno">329</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-154" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-154', 'data', 'link-41');">data</a></tt> </tt>
</div></div><a name="L330"></a><tt class="py-lineno">330</tt>  <tt class="py-line"> </tt>
<a name="_Scanner"></a><div id="_Scanner-def"><a name="L331"></a><tt class="py-lineno">331</tt> <a class="py-toggle" href="#" id="_Scanner-toggle" onclick="return toggle('_Scanner');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Sequencing.Ace._Scanner-class.html">_Scanner</a><tt class="py-op">:</tt> </tt>
</div><div id="_Scanner-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_Scanner-expanded"><a name="L332"></a><tt class="py-lineno">332</tt>  <tt class="py-line">    <tt class="py-docstring">"""Scans an ACE-formatted file.</tt> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt>  <tt class="py-line"><tt class="py-docstring">    Methods:</tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt>  <tt class="py-line"><tt class="py-docstring">    feed - Feed one ACE record.</tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="_Scanner.feed"></a><div id="_Scanner.feed-def"><a name="L337"></a><tt class="py-lineno">337</tt> <a class="py-toggle" href="#" id="_Scanner.feed-toggle" onclick="return toggle('_Scanner.feed');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace._Scanner-class.html#feed">feed</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">handle</tt><tt class="py-op">,</tt> <tt class="py-param">consumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Scanner.feed-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Scanner.feed-expanded"><a name="L338"></a><tt class="py-lineno">338</tt>  <tt class="py-line">        <tt class="py-docstring">"""feed(self, handle, consumer)</tt> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L340"></a><tt class="py-lineno">340</tt>  <tt class="py-line"><tt class="py-docstring">        Feed in ACE data for scanning.  handle is a file-like object</tt> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt>  <tt class="py-line"><tt class="py-docstring">        containing ACE data.  consumer is a Consumer object that will</tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt>  <tt class="py-line"><tt class="py-docstring">        receive events as the ACE data is scanned.</tt> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt>  <tt class="py-line">        <tt class="py-keyword">assert</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-155" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-155', 'handle', 'link-35');">handle</a></tt><tt class="py-op">,</tt> <tt id="link-156" class="py-name"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-156', 'File', 'link-1');">File</a></tt><tt class="py-op">.</tt><tt id="link-157" class="py-name"><a title="Bio.File.UndoHandle" class="py-name" href="#" onclick="return doclink('link-157', 'UndoHandle', 'link-34');">UndoHandle</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> \ </tt>
<a name="L345"></a><tt class="py-lineno">345</tt>  <tt class="py-line">            <tt class="py-string">"handle must be an UndoHandle"</tt> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt id="link-158" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-158', 'handle', 'link-35');">handle</a></tt><tt class="py-op">.</tt><tt id="link-159" class="py-name" targets="Method Bio.File.UndoHandle.peekline()=Bio.File.UndoHandle-class.html#peekline"><a title="Bio.File.UndoHandle.peekline" class="py-name" href="#" onclick="return doclink('link-159', 'peekline', 'link-159');">peekline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-160" class="py-name" targets="Method Bio.Compass._Scanner._scan_record()=Bio.Compass._Scanner-class.html#_scan_record,Method Bio.Enzyme._Scanner._scan_record()=Bio.Enzyme._Scanner-class.html#_scan_record,Method Bio.Gobase._Scanner._scan_record()=Bio.Gobase._Scanner-class.html#_scan_record,Method Bio.Medline._Scanner._scan_record()=Bio.Medline._Scanner-class.html#_scan_record,Method Bio.Prosite.Prodoc._Scanner._scan_record()=Bio.Prosite.Prodoc._Scanner-class.html#_scan_record,Method Bio.Prosite._Scanner._scan_record()=Bio.Prosite._Scanner-class.html#_scan_record,Method Bio.Rebase._Scanner._scan_record()=Bio.Rebase._Scanner-class.html#_scan_record,Method Bio.Sequencing.Ace._Scanner._scan_record()=Bio.Sequencing.Ace._Scanner-class.html#_scan_record,Method Bio.Sequencing.Phd._Scanner._scan_record()=Bio.Sequencing.Phd._Scanner-class.html#_scan_record,Method Bio.SwissProt.SProt._Scanner._scan_record()=Bio.SwissProt.SProt._Scanner-class.html#_scan_record"><a title="Bio.Compass._Scanner._scan_record
Bio.Enzyme._Scanner._scan_record
Bio.Gobase._Scanner._scan_record
Bio.Medline._Scanner._scan_record
Bio.Prosite.Prodoc._Scanner._scan_record
Bio.Prosite._Scanner._scan_record
Bio.Rebase._Scanner._scan_record
Bio.Sequencing.Ace._Scanner._scan_record
Bio.Sequencing.Phd._Scanner._scan_record
Bio.SwissProt.SProt._Scanner._scan_record" class="py-name" href="#" onclick="return doclink('link-160', '_scan_record', 'link-160');">_scan_record</a></tt><tt class="py-op">(</tt><tt id="link-161" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-161', 'handle', 'link-35');">handle</a></tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">)</tt> </tt>
</div><a name="L348"></a><tt class="py-lineno">348</tt>  <tt class="py-line"> </tt>
<a name="_Scanner._scan_record"></a><div id="_Scanner._scan_record-def"><a name="L349"></a><tt class="py-lineno">349</tt> <a class="py-toggle" href="#" id="_Scanner._scan_record-toggle" onclick="return toggle('_Scanner._scan_record');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace._Scanner-class.html#_scan_record">_scan_record</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">uhandle</tt><tt class="py-op">,</tt> <tt class="py-param">consumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Scanner._scan_record-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Scanner._scan_record-expanded"><a name="L350"></a><tt class="py-lineno">350</tt>  <tt class="py-line">        <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-162" class="py-name" targets="Method Bio.Sequencing.Ace._RecordConsumer.begin_contig()=Bio.Sequencing.Ace._RecordConsumer-class.html#begin_contig"><a title="Bio.Sequencing.Ace._RecordConsumer.begin_contig" class="py-name" href="#" onclick="return doclink('link-162', 'begin_contig', 'link-162');">begin_contig</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt>  <tt class="py-line">        <tt id="link-163" class="py-name" targets="Function Bio.ParserSupport.read_and_call()=Bio.ParserSupport-module.html#read_and_call"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-163', 'read_and_call', 'link-163');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt><tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-164" class="py-name" targets="Method Bio.Sequencing.Ace._RecordConsumer.co_header()=Bio.Sequencing.Ace._RecordConsumer-class.html#co_header"><a title="Bio.Sequencing.Ace._RecordConsumer.co_header" class="py-name" href="#" onclick="return doclink('link-164', 'co_header', 'link-164');">co_header</a></tt><tt class="py-op">,</tt><tt id="link-165" class="py-name" targets="Method Bio.GFF.easy.Location.start()=Bio.GFF.easy.Location-class.html#start,Method Bio.Prosite.Pattern.PrositeMatch.start()=Bio.Prosite.Pattern.PrositeMatch-class.html#start,Variable Bio.Restriction._Update.RestrictionCompiler.start=Bio.Restriction._Update.RestrictionCompiler-module.html#start,Method Martel.LAX.LAX.start()=Martel.LAX.LAX-class.html#start"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-165', 'start', 'link-165');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'CO '</tt><tt class="py-op">)</tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt>  <tt class="py-line">        <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-166" class="py-name" targets="Method Bio.Sequencing.Ace._RecordConsumer.co_data()=Bio.Sequencing.Ace._RecordConsumer-class.html#co_data"><a title="Bio.Sequencing.Ace._RecordConsumer.co_data" class="py-name" href="#" onclick="return doclink('link-166', 'co_data', 'link-166');">co_data</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-167" class="py-name" targets="Method Bio.Sequencing.Ace._Scanner._scan_sequence_data()=Bio.Sequencing.Ace._Scanner-class.html#_scan_sequence_data,Method Bio.SwissProt.SProt._Scanner._scan_sequence_data()=Bio.SwissProt.SProt._Scanner-class.html#_scan_sequence_data"><a title="Bio.Sequencing.Ace._Scanner._scan_sequence_data
Bio.SwissProt.SProt._Scanner._scan_sequence_data" class="py-name" href="#" onclick="return doclink('link-167', '_scan_sequence_data', 'link-167');">_scan_sequence_data</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt>  <tt class="py-line">        <tt id="link-168" class="py-name" targets="Function Bio.ParserSupport.read_and_call_while()=Bio.ParserSupport-module.html#read_and_call_while"><a title="Bio.ParserSupport.read_and_call_while" class="py-name" href="#" onclick="return doclink('link-168', 'read_and_call_while', 'link-168');">read_and_call_while</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt><tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-169" class="py-name" targets="Method Bio.AlignAce.Parser.AlignAceConsumer.noevent()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#noevent,Method Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent()=Bio.Blast.NCBIStandalone._BlastErrorConsumer-class.html#noevent,Method Bio.MEME.Parser._MASTConsumer.noevent()=Bio.MEME.Parser._MASTConsumer-class.html#noevent,Method Bio.MEME.Parser._MEMEConsumer.noevent()=Bio.MEME.Parser._MEMEConsumer-class.html#noevent"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-169', 'noevent', 'link-169');">noevent</a></tt><tt class="py-op">,</tt><tt id="link-170" class="py-name" targets="Variable Bio.MetaTool.metatool_format.blank=Bio.MetaTool.metatool_format-module.html#blank"><a title="Bio.MetaTool.metatool_format.blank" class="py-name" href="#" onclick="return doclink('link-170', 'blank', 'link-170');">blank</a></tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt>  <tt class="py-line">        <tt id="link-171" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-171', 'read_and_call', 'link-163');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt><tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-172" class="py-name" targets="Method Bio.Sequencing.Ace._RecordConsumer.bq_header()=Bio.Sequencing.Ace._RecordConsumer-class.html#bq_header"><a title="Bio.Sequencing.Ace._RecordConsumer.bq_header" class="py-name" href="#" onclick="return doclink('link-172', 'bq_header', 'link-172');">bq_header</a></tt><tt class="py-op">,</tt><tt id="link-173" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-173', 'start', 'link-165');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'BQ'</tt><tt class="py-op">)</tt> </tt>
<a name="L355"></a><tt class="py-lineno">355</tt>  <tt class="py-line">        <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-174" class="py-name" targets="Method Bio.Sequencing.Ace._RecordConsumer.bq_data()=Bio.Sequencing.Ace._RecordConsumer-class.html#bq_data"><a title="Bio.Sequencing.Ace._RecordConsumer.bq_data" class="py-name" href="#" onclick="return doclink('link-174', 'bq_data', 'link-174');">bq_data</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-175" class="py-name" targets="Method Bio.Sequencing.Ace._Scanner._scan_bq_data()=Bio.Sequencing.Ace._Scanner-class.html#_scan_bq_data"><a title="Bio.Sequencing.Ace._Scanner._scan_bq_data" class="py-name" href="#" onclick="return doclink('link-175', '_scan_bq_data', 'link-175');">_scan_bq_data</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L356"></a><tt class="py-lineno">356</tt>  <tt class="py-line">        <tt id="link-176" class="py-name"><a title="Bio.ParserSupport.read_and_call_while" class="py-name" href="#" onclick="return doclink('link-176', 'read_and_call_while', 'link-168');">read_and_call_while</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt><tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-177" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-177', 'noevent', 'link-169');">noevent</a></tt><tt class="py-op">,</tt><tt id="link-178" class="py-name"><a title="Bio.MetaTool.metatool_format.blank" class="py-name" href="#" onclick="return doclink('link-178', 'blank', 'link-170');">blank</a></tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L357"></a><tt class="py-lineno">357</tt>  <tt class="py-line">        <tt id="link-179" class="py-name"><a title="Bio.ParserSupport.read_and_call_while" class="py-name" href="#" onclick="return doclink('link-179', 'read_and_call_while', 'link-168');">read_and_call_while</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt><tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-180" class="py-name"><a title="Bio.Sequencing.Ace._RecordConsumer.af
Bio.Sequencing.Ace.af" class="py-name" href="#" onclick="return doclink('link-180', 'af', 'link-29');">af</a></tt><tt class="py-op">,</tt><tt id="link-181" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-181', 'start', 'link-165');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'AF '</tt><tt class="py-op">)</tt> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt>  <tt class="py-line">        <tt id="link-182" class="py-name"><a title="Bio.ParserSupport.read_and_call_while" class="py-name" href="#" onclick="return doclink('link-182', 'read_and_call_while', 'link-168');">read_and_call_while</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt><tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-183" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-183', 'noevent', 'link-169');">noevent</a></tt><tt class="py-op">,</tt><tt id="link-184" class="py-name"><a title="Bio.MetaTool.metatool_format.blank" class="py-name" href="#" onclick="return doclink('link-184', 'blank', 'link-170');">blank</a></tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt>  <tt class="py-line">        <tt id="link-185" class="py-name"><a title="Bio.ParserSupport.read_and_call_while" class="py-name" href="#" onclick="return doclink('link-185', 'read_and_call_while', 'link-168');">read_and_call_while</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt><tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-186" class="py-name"><a title="Bio.Sequencing.Ace._RecordConsumer.bs
Bio.Sequencing.Ace.bs" class="py-name" href="#" onclick="return doclink('link-186', 'bs', 'link-30');">bs</a></tt><tt class="py-op">,</tt><tt id="link-187" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-187', 'start', 'link-165');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'BS '</tt><tt class="py-op">)</tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt>  <tt class="py-line">        <tt class="py-comment"># now read all the read data</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment"># it starts with a 'RD', and then a mandatory QA</tt> </tt>
<a name="L362"></a><tt class="py-lineno">362</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment"># then follows an optional DS</tt> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment"># CT,RT,WA,WR may or may not be there in unlimited quantity. They might refer to the actial read or contig,</tt> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <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="L365"></a><tt class="py-lineno">365</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment"># with that later.</tt> </tt>
<a name="L366"></a><tt class="py-lineno">366</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt>  <tt class="py-line">            <tt class="py-comment"># each read must have a rd and qa</tt> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt id="link-188" class="py-name" targets="Function Bio.ParserSupport.read_and_call_until()=Bio.ParserSupport-module.html#read_and_call_until"><a title="Bio.ParserSupport.read_and_call_until" class="py-name" href="#" onclick="return doclink('link-188', 'read_and_call_until', 'link-188');">read_and_call_until</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt><tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-189" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-189', 'noevent', 'link-169');">noevent</a></tt><tt class="py-op">,</tt><tt id="link-190" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-190', 'start', 'link-165');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'RD '</tt><tt class="py-op">)</tt> </tt>
<a name="L369"></a><tt class="py-lineno">369</tt>  <tt class="py-line">            <tt id="link-191" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-191', 'read_and_call', 'link-163');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt><tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-192" class="py-name" targets="Method Bio.Sequencing.Ace._RecordConsumer.rd_header()=Bio.Sequencing.Ace._RecordConsumer-class.html#rd_header"><a title="Bio.Sequencing.Ace._RecordConsumer.rd_header" class="py-name" href="#" onclick="return doclink('link-192', 'rd_header', 'link-192');">rd_header</a></tt><tt class="py-op">,</tt><tt id="link-193" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-193', 'start', 'link-165');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'RD '</tt><tt class="py-op">)</tt> </tt>
<a name="L370"></a><tt class="py-lineno">370</tt>  <tt class="py-line">            <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-194" class="py-name" targets="Method Bio.Sequencing.Ace._RecordConsumer.rd_data()=Bio.Sequencing.Ace._RecordConsumer-class.html#rd_data"><a title="Bio.Sequencing.Ace._RecordConsumer.rd_data" class="py-name" href="#" onclick="return doclink('link-194', 'rd_data', 'link-194');">rd_data</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-195" class="py-name"><a title="Bio.Sequencing.Ace._Scanner._scan_sequence_data
Bio.SwissProt.SProt._Scanner._scan_sequence_data" class="py-name" href="#" onclick="return doclink('link-195', '_scan_sequence_data', 'link-167');">_scan_sequence_data</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L371"></a><tt class="py-lineno">371</tt>  <tt class="py-line">            <tt id="link-196" class="py-name"><a title="Bio.ParserSupport.read_and_call_while" class="py-name" href="#" onclick="return doclink('link-196', 'read_and_call_while', 'link-168');">read_and_call_while</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt><tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-197" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-197', 'noevent', 'link-169');">noevent</a></tt><tt class="py-op">,</tt><tt id="link-198" class="py-name"><a title="Bio.MetaTool.metatool_format.blank" class="py-name" href="#" onclick="return doclink('link-198', 'blank', 'link-170');">blank</a></tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L372"></a><tt class="py-lineno">372</tt>  <tt class="py-line">            <tt id="link-199" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-199', 'read_and_call', 'link-163');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt><tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-200" class="py-name"><a title="Bio.Sequencing.Ace._RecordConsumer.qa
Bio.Sequencing.Ace.qa" class="py-name" href="#" onclick="return doclink('link-200', 'qa', 'link-23');">qa</a></tt><tt class="py-op">,</tt><tt id="link-201" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-201', 'start', 'link-165');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'QA '</tt><tt class="py-op">)</tt> </tt>
<a name="L373"></a><tt class="py-lineno">373</tt>  <tt class="py-line">            <tt class="py-comment"># now one ds can follow</tt> </tt>
<a name="L374"></a><tt class="py-lineno">374</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L375"></a><tt class="py-lineno">375</tt>  <tt class="py-line">                <tt id="link-202" class="py-name"><a title="Bio.ParserSupport.read_and_call_while" class="py-name" href="#" onclick="return doclink('link-202', 'read_and_call_while', 'link-168');">read_and_call_while</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt><tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-203" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-203', 'noevent', 'link-169');">noevent</a></tt><tt class="py-op">,</tt><tt id="link-204" class="py-name"><a title="Bio.MetaTool.metatool_format.blank" class="py-name" href="#" onclick="return doclink('link-204', 'blank', 'link-170');">blank</a></tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L376"></a><tt class="py-lineno">376</tt>  <tt class="py-line">                <tt id="link-205" class="py-name" targets="Function Bio.ParserSupport.attempt_read_and_call()=Bio.ParserSupport-module.html#attempt_read_and_call"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-205', 'attempt_read_and_call', 'link-205');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt><tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-206" class="py-name"><a title="Bio.Sequencing.Ace._RecordConsumer.ds
Bio.Sequencing.Ace.ds" class="py-name" href="#" onclick="return doclink('link-206', 'ds', 'link-24');">ds</a></tt><tt class="py-op">,</tt><tt id="link-207" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-207', 'start', 'link-165');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'DS '</tt><tt class="py-op">)</tt> </tt>
<a name="L377"></a><tt class="py-lineno">377</tt>  <tt class="py-line">            <tt class="py-keyword">except</tt> <tt class="py-name">ValueError</tt><tt class="py-op">:</tt> </tt>
<a name="L378"></a><tt class="py-lineno">378</tt>  <tt class="py-line">                <tt class="py-comment"># file ends</tt> </tt>
<a name="L379"></a><tt class="py-lineno">379</tt>  <tt class="py-line"><tt class="py-comment"></tt>                <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-208" class="py-name" targets="Method Bio.Sequencing.Ace._RecordConsumer.end_contig()=Bio.Sequencing.Ace._RecordConsumer-class.html#end_contig"><a title="Bio.Sequencing.Ace._RecordConsumer.end_contig" class="py-name" href="#" onclick="return doclink('link-208', 'end_contig', 'link-208');">end_contig</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L380"></a><tt class="py-lineno">380</tt>  <tt class="py-line">                <tt class="py-keyword">return</tt> </tt>
<a name="L381"></a><tt class="py-lineno">381</tt>  <tt class="py-line">            <tt class="py-comment"># the file could just end, or there's some more stuff. In ace files, everything can happen.</tt> </tt>
<a name="L382"></a><tt class="py-lineno">382</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-comment"># the following tags are interspersed between reads and can ap[pear multiple times. </tt> </tt>
<a name="L383"></a><tt class="py-lineno">383</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt>  <tt class="py-line">                <tt class="py-comment"># something left </tt> </tt>
<a name="L385"></a><tt class="py-lineno">385</tt>  <tt class="py-line"><tt class="py-comment"></tt>                <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L386"></a><tt class="py-lineno">386</tt>  <tt class="py-line">                    <tt id="link-209" class="py-name"><a title="Bio.ParserSupport.read_and_call_while" class="py-name" href="#" onclick="return doclink('link-209', 'read_and_call_while', 'link-168');">read_and_call_while</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt><tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-210" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-210', 'noevent', 'link-169');">noevent</a></tt><tt class="py-op">,</tt><tt id="link-211" class="py-name"><a title="Bio.MetaTool.metatool_format.blank" class="py-name" href="#" onclick="return doclink('link-211', 'blank', 'link-170');">blank</a></tt><tt class="py-op">=</tt><tt class="py-number">1</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">except</tt> <tt class="py-name">ValueError</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"># file ends here</tt> </tt>
<a name="L389"></a><tt class="py-lineno">389</tt>  <tt class="py-line"><tt class="py-comment"></tt>                    <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-212" class="py-name"><a title="Bio.Sequencing.Ace._RecordConsumer.end_contig" class="py-name" href="#" onclick="return doclink('link-212', 'end_contig', 'link-208');">end_contig</a></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">return</tt> </tt>
<a name="L391"></a><tt class="py-lineno">391</tt>  <tt class="py-line">                <tt class="py-keyword">else</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 id="link-213" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-213', 'attempt_read_and_call', 'link-205');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt><tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-214" class="py-name" targets="Method Bio.Sequencing.Ace._RecordConsumer.rt_start()=Bio.Sequencing.Ace._RecordConsumer-class.html#rt_start"><a title="Bio.Sequencing.Ace._RecordConsumer.rt_start" class="py-name" href="#" onclick="return doclink('link-214', 'rt_start', 'link-214');">rt_start</a></tt><tt class="py-op">,</tt><tt id="link-215" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-215', 'start', 'link-165');">start</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="L393"></a><tt class="py-lineno">393</tt>  <tt class="py-line">                        <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-216" class="py-name" targets="Method Bio.Sequencing.Ace._RecordConsumer.rt_data()=Bio.Sequencing.Ace._RecordConsumer-class.html#rt_data"><a title="Bio.Sequencing.Ace._RecordConsumer.rt_data" class="py-name" href="#" onclick="return doclink('link-216', 'rt_data', 'link-216');">rt_data</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-217" class="py-name" targets="Method Bio.Sequencing.Ace._Scanner._scan_bracket_tags()=Bio.Sequencing.Ace._Scanner-class.html#_scan_bracket_tags"><a title="Bio.Sequencing.Ace._Scanner._scan_bracket_tags" class="py-name" href="#" onclick="return doclink('link-217', '_scan_bracket_tags', 'link-217');">_scan_bracket_tags</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L394"></a><tt class="py-lineno">394</tt>  <tt class="py-line">                    <tt class="py-keyword">elif</tt> <tt id="link-218" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-218', 'attempt_read_and_call', 'link-205');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt><tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-219" class="py-name" targets="Method Bio.Sequencing.Ace._RecordConsumer.wr_start()=Bio.Sequencing.Ace._RecordConsumer-class.html#wr_start"><a title="Bio.Sequencing.Ace._RecordConsumer.wr_start" class="py-name" href="#" onclick="return doclink('link-219', 'wr_start', 'link-219');">wr_start</a></tt><tt class="py-op">,</tt><tt id="link-220" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-220', 'start', 'link-165');">start</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="L395"></a><tt class="py-lineno">395</tt>  <tt class="py-line">                        <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-221" class="py-name" targets="Method Bio.Sequencing.Ace._RecordConsumer.wr_data()=Bio.Sequencing.Ace._RecordConsumer-class.html#wr_data"><a title="Bio.Sequencing.Ace._RecordConsumer.wr_data" class="py-name" href="#" onclick="return doclink('link-221', 'wr_data', 'link-221');">wr_data</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-222" class="py-name"><a title="Bio.Sequencing.Ace._Scanner._scan_bracket_tags" class="py-name" href="#" onclick="return doclink('link-222', '_scan_bracket_tags', 'link-217');">_scan_bracket_tags</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">)</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">elif</tt> <tt id="link-223" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-223', 'attempt_read_and_call', 'link-205');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt><tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-224" class="py-name" targets="Method Bio.Sequencing.Ace._RecordConsumer.wa_start()=Bio.Sequencing.Ace._RecordConsumer-class.html#wa_start"><a title="Bio.Sequencing.Ace._RecordConsumer.wa_start" class="py-name" href="#" onclick="return doclink('link-224', 'wa_start', 'link-224');">wa_start</a></tt><tt class="py-op">,</tt><tt id="link-225" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-225', 'start', 'link-165');">start</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="L397"></a><tt class="py-lineno">397</tt>  <tt class="py-line">                        <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-226" class="py-name" targets="Method Bio.Sequencing.Ace._RecordConsumer.wa_data()=Bio.Sequencing.Ace._RecordConsumer-class.html#wa_data"><a title="Bio.Sequencing.Ace._RecordConsumer.wa_data" class="py-name" href="#" onclick="return doclink('link-226', 'wa_data', 'link-226');">wa_data</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-227" class="py-name"><a title="Bio.Sequencing.Ace._Scanner._scan_bracket_tags" class="py-name" href="#" onclick="return doclink('link-227', '_scan_bracket_tags', 'link-217');">_scan_bracket_tags</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L398"></a><tt class="py-lineno">398</tt>  <tt class="py-line">                    <tt class="py-keyword">elif</tt> <tt id="link-228" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-228', 'attempt_read_and_call', 'link-205');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt><tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-229" class="py-name" targets="Method Bio.Sequencing.Ace._RecordConsumer.ct_start()=Bio.Sequencing.Ace._RecordConsumer-class.html#ct_start"><a title="Bio.Sequencing.Ace._RecordConsumer.ct_start" class="py-name" href="#" onclick="return doclink('link-229', 'ct_start', 'link-229');">ct_start</a></tt><tt class="py-op">,</tt><tt id="link-230" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-230', 'start', 'link-165');">start</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="L399"></a><tt class="py-lineno">399</tt>  <tt class="py-line">                        <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-231" class="py-name" targets="Method Bio.Sequencing.Ace._RecordConsumer.ct_data()=Bio.Sequencing.Ace._RecordConsumer-class.html#ct_data"><a title="Bio.Sequencing.Ace._RecordConsumer.ct_data" class="py-name" href="#" onclick="return doclink('link-231', 'ct_data', 'link-231');">ct_data</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-232" class="py-name"><a title="Bio.Sequencing.Ace._Scanner._scan_bracket_tags" class="py-name" href="#" onclick="return doclink('link-232', '_scan_bracket_tags', 'link-217');">_scan_bracket_tags</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L400"></a><tt class="py-lineno">400</tt>  <tt class="py-line">                    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L401"></a><tt class="py-lineno">401</tt>  <tt class="py-line">                        <tt class="py-name">line</tt><tt class="py-op">=</tt><tt id="link-233" class="py-name" targets="Function Bio.ParserSupport.safe_peekline()=Bio.ParserSupport-module.html#safe_peekline"><a title="Bio.ParserSupport.safe_peekline" class="py-name" href="#" onclick="return doclink('link-233', 'safe_peekline', 'link-233');">safe_peekline</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">)</tt> </tt>
<a name="L402"></a><tt class="py-lineno">402</tt>  <tt class="py-line">                        <tt class="py-keyword">break</tt> </tt>
<a name="L403"></a><tt class="py-lineno">403</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">startswith</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="L404"></a><tt class="py-lineno">404</tt>  <tt class="py-line">                <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-234" class="py-name"><a title="Bio.Sequencing.Ace._RecordConsumer.end_contig" class="py-name" href="#" onclick="return doclink('link-234', 'end_contig', 'link-208');">end_contig</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">break</tt>     </tt>
</div><a name="L406"></a><tt class="py-lineno">406</tt>  <tt class="py-line">     </tt>
<a name="_Scanner._scan_bq_data"></a><div id="_Scanner._scan_bq_data-def"><a name="L407"></a><tt class="py-lineno">407</tt> <a class="py-toggle" href="#" id="_Scanner._scan_bq_data-toggle" onclick="return toggle('_Scanner._scan_bq_data');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace._Scanner-class.html#_scan_bq_data">_scan_bq_data</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">uhandle</tt><tt class="py-op">,</tt> <tt class="py-param">consumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Scanner._scan_bq_data-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Scanner._scan_bq_data-expanded"><a name="L408"></a><tt class="py-lineno">408</tt>  <tt class="py-line">        <tt class="py-docstring">"""Scans multiple lines of quality data and concatenates them."""</tt> </tt>
<a name="L409"></a><tt class="py-lineno">409</tt>  <tt class="py-line">         </tt>
<a name="L410"></a><tt class="py-lineno">410</tt>  <tt class="py-line">        <tt class="py-name">qual</tt><tt class="py-op">=</tt><tt class="py-string">''</tt> </tt>
<a name="L411"></a><tt class="py-lineno">411</tt>  <tt class="py-line">        <tt class="py-keyword">while</tt> <tt class="py-number">1</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 class="py-name">uhandle</tt><tt class="py-op">.</tt><tt id="link-235" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.readline
Bio.File.SGMLHandle.readline
Bio.File.UndoHandle.readline
Bio.SGMLExtractor.SGMLExtractorHandle.readline" class="py-name" href="#" onclick="return doclink('link-235', 'readline', 'link-36');">readline</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">if</tt> <tt id="link-236" class="py-name" targets="Function Bio.ParserSupport.is_blank_line()=Bio.ParserSupport-module.html#is_blank_line"><a title="Bio.ParserSupport.is_blank_line" class="py-name" href="#" onclick="return doclink('link-236', 'is_blank_line', 'link-236');">is_blank_line</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="L414"></a><tt class="py-lineno">414</tt>  <tt class="py-line">                <tt class="py-name">uhandle</tt><tt class="py-op">.</tt><tt id="link-237" class="py-name"><a title="Bio.File.UndoHandle.saveline" class="py-name" href="#" onclick="return doclink('link-237', 'saveline', 'link-39');">saveline</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L415"></a><tt class="py-lineno">415</tt>  <tt class="py-line">                <tt class="py-keyword">break</tt> </tt>
<a name="L416"></a><tt class="py-lineno">416</tt>  <tt class="py-line">            <tt class="py-name">qual</tt><tt class="py-op">+=</tt><tt class="py-string">' '</tt><tt class="py-op">+</tt><tt class="py-name">line</tt> </tt>
<a name="L417"></a><tt class="py-lineno">417</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">qual</tt> </tt>
</div><a name="L418"></a><tt class="py-lineno">418</tt>  <tt class="py-line">    </tt>
<a name="_Scanner._scan_sequence_data"></a><div id="_Scanner._scan_sequence_data-def"><a name="L419"></a><tt class="py-lineno">419</tt> <a class="py-toggle" href="#" id="_Scanner._scan_sequence_data-toggle" onclick="return toggle('_Scanner._scan_sequence_data');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace._Scanner-class.html#_scan_sequence_data">_scan_sequence_data</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">uhandle</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Scanner._scan_sequence_data-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Scanner._scan_sequence_data-expanded"><a name="L420"></a><tt class="py-lineno">420</tt>  <tt class="py-line">        <tt class="py-docstring">"""Scans multiple lines of sequence data and concatenates them."""</tt> </tt>
<a name="L421"></a><tt class="py-lineno">421</tt>  <tt class="py-line">         </tt>
<a name="L422"></a><tt class="py-lineno">422</tt>  <tt class="py-line">        <tt id="link-238" class="py-name" targets="Method Bio.GFF.Feature.seq()=Bio.GFF.Feature-class.html#seq,Method Bio.GFF.FeatureAggregate.seq()=Bio.GFF.FeatureAggregate-class.html#seq,Variable BioSQL.BioSeq.DBSeqRecord.seq=BioSQL.BioSeq.DBSeqRecord-class.html#seq"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-238', 'seq', 'link-238');">seq</a></tt><tt class="py-op">=</tt><tt class="py-string">''</tt> </tt>
<a name="L423"></a><tt class="py-lineno">423</tt>  <tt class="py-line">        <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L424"></a><tt class="py-lineno">424</tt>  <tt class="py-line">            <tt class="py-name">line</tt><tt class="py-op">=</tt><tt class="py-name">uhandle</tt><tt class="py-op">.</tt><tt id="link-239" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.readline
Bio.File.SGMLHandle.readline
Bio.File.UndoHandle.readline
Bio.SGMLExtractor.SGMLExtractorHandle.readline" class="py-name" href="#" onclick="return doclink('link-239', 'readline', 'link-36');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L425"></a><tt class="py-lineno">425</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt id="link-240" class="py-name"><a title="Bio.ParserSupport.is_blank_line" class="py-name" href="#" onclick="return doclink('link-240', 'is_blank_line', 'link-236');">is_blank_line</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="L426"></a><tt class="py-lineno">426</tt>  <tt class="py-line">                <tt class="py-name">uhandle</tt><tt class="py-op">.</tt><tt id="link-241" class="py-name"><a title="Bio.File.UndoHandle.saveline" class="py-name" href="#" onclick="return doclink('link-241', 'saveline', 'link-39');">saveline</a></tt><tt class="py-op">(</tt><tt class="py-name">line</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">break</tt> </tt>
<a name="L428"></a><tt class="py-lineno">428</tt>  <tt class="py-line">            <tt id="link-242" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-242', 'seq', 'link-238');">seq</a></tt><tt class="py-op">+=</tt><tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-243" class="py-name" targets="Class Bio.EUtils.DTDs.LinkOut.strip=Bio.EUtils.DTDs.LinkOut.strip-class.html,Method Bio.File.SGMLStripper.strip()=Bio.File.SGMLStripper-class.html#strip,Method Bio.SGMLExtractor.SGMLExtractor.strip()=Bio.SGMLExtractor.SGMLExtractor-class.html#strip"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-243', 'strip', 'link-243');">strip</a></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">return</tt> <tt id="link-244" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-244', 'seq', 'link-238');">seq</a></tt> </tt>
</div><a name="L430"></a><tt class="py-lineno">430</tt>  <tt class="py-line">      </tt>
<a name="_Scanner._scan_bracket_tags"></a><div id="_Scanner._scan_bracket_tags-def"><a name="L431"></a><tt class="py-lineno">431</tt> <a class="py-toggle" href="#" id="_Scanner._scan_bracket_tags-toggle" onclick="return toggle('_Scanner._scan_bracket_tags');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace._Scanner-class.html#_scan_bracket_tags">_scan_bracket_tags</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">uhandle</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Scanner._scan_bracket_tags-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Scanner._scan_bracket_tags-expanded"><a name="L432"></a><tt class="py-lineno">432</tt>  <tt class="py-line">        <tt class="py-docstring">"""Reads the data lines of a {} tag."""</tt> </tt>
<a name="L433"></a><tt class="py-lineno">433</tt>  <tt class="py-line">         </tt>
<a name="L434"></a><tt class="py-lineno">434</tt>  <tt class="py-line">        <tt class="py-name">fulltag</tt><tt class="py-op">=</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">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L436"></a><tt class="py-lineno">436</tt>  <tt class="py-line">            <tt class="py-name">line</tt><tt class="py-op">=</tt><tt class="py-name">uhandle</tt><tt class="py-op">.</tt><tt id="link-245" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.readline
Bio.File.SGMLHandle.readline
Bio.File.UndoHandle.readline
Bio.SGMLExtractor.SGMLExtractorHandle.readline" class="py-name" href="#" onclick="return doclink('link-245', 'readline', 'link-36');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-246" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-246', 'strip', 'link-243');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L437"></a><tt class="py-lineno">437</tt>  <tt class="py-line">            <tt class="py-name">fulltag</tt><tt class="py-op">.</tt><tt id="link-247" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-247', 'append', 'link-37');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">line</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">if</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">endswith</tt><tt class="py-op">(</tt><tt class="py-string">'}'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L439"></a><tt class="py-lineno">439</tt>  <tt class="py-line">                <tt class="py-name">fulltag</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">fulltag</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 class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt>    <tt class="py-comment"># delete the ending }</tt> </tt>
<a name="L440"></a><tt class="py-lineno">440</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">fulltag</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-string">''</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">fulltag</tt><tt class="py-op">=</tt><tt class="py-name">fulltag</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-comment"># delete empty line</tt> </tt>
<a name="L442"></a><tt class="py-lineno">442</tt>  <tt class="py-line">                <tt class="py-keyword">break</tt> </tt>
<a name="L443"></a><tt class="py-lineno">443</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">fulltag</tt> </tt>
</div></div><a name="L444"></a><tt class="py-lineno">444</tt>  <tt class="py-line">             </tt>
<a name="_RecordConsumer"></a><div id="_RecordConsumer-def"><a name="L445"></a><tt class="py-lineno">445</tt> <a class="py-toggle" href="#" id="_RecordConsumer-toggle" onclick="return toggle('_RecordConsumer');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Sequencing.Ace._RecordConsumer-class.html">_RecordConsumer</a><tt class="py-op">(</tt><tt class="py-base-class">AbstractConsumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_RecordConsumer-expanded"><a name="L446"></a><tt class="py-lineno">446</tt>  <tt class="py-line">    <tt class="py-docstring">"""Reads the ace tags into data records."""</tt> </tt>
<a name="L447"></a><tt class="py-lineno">447</tt>  <tt class="py-line">     </tt>
<a name="_RecordConsumer.__init__"></a><div id="_RecordConsumer.__init__-def"><a name="L448"></a><tt class="py-lineno">448</tt> <a class="py-toggle" href="#" id="_RecordConsumer.__init__-toggle" onclick="return toggle('_RecordConsumer.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace._RecordConsumer-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="_RecordConsumer.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.__init__-expanded"><a name="L449"></a><tt class="py-lineno">449</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-248" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-248', 'data', 'link-41');">data</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
</div><a name="L450"></a><tt class="py-lineno">450</tt>  <tt class="py-line"> </tt>
<a name="_RecordConsumer.begin_contig"></a><div id="_RecordConsumer.begin_contig-def"><a name="L451"></a><tt class="py-lineno">451</tt> <a class="py-toggle" href="#" id="_RecordConsumer.begin_contig-toggle" onclick="return toggle('_RecordConsumer.begin_contig');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace._RecordConsumer-class.html#begin_contig">begin_contig</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="_RecordConsumer.begin_contig-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.begin_contig-expanded"><a name="L452"></a><tt class="py-lineno">452</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-249" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-249', 'data', 'link-41');">data</a></tt> <tt class="py-op">=</tt> <tt id="link-250" 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-250', 'Contig', 'link-250');">Contig</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L453"></a><tt class="py-lineno">453</tt>  <tt class="py-line"> </tt>
<a name="_RecordConsumer.end_contig"></a><div id="_RecordConsumer.end_contig-def"><a name="L454"></a><tt class="py-lineno">454</tt> <a class="py-toggle" href="#" id="_RecordConsumer.end_contig-toggle" onclick="return toggle('_RecordConsumer.end_contig');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace._RecordConsumer-class.html#end_contig">end_contig</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="_RecordConsumer.end_contig-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.end_contig-expanded"><a name="L455"></a><tt class="py-lineno">455</tt>  <tt class="py-line">        <tt class="py-keyword">pass</tt> </tt>
</div><a name="L456"></a><tt class="py-lineno">456</tt>  <tt class="py-line"> </tt>
<a name="_RecordConsumer.co_header"></a><div id="_RecordConsumer.co_header-def"><a name="L457"></a><tt class="py-lineno">457</tt> <a class="py-toggle" href="#" id="_RecordConsumer.co_header-toggle" onclick="return toggle('_RecordConsumer.co_header');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace._RecordConsumer-class.html#co_header">co_header</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-op">:</tt> </tt>
</div><div id="_RecordConsumer.co_header-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.co_header-expanded"><a name="L458"></a><tt class="py-lineno">458</tt>  <tt class="py-line">        <tt id="link-251" class="py-name" targets="Variable Bio.Wise.dnal.Statistics.header=Bio.Wise.dnal.Statistics-class.html#header,Variable Bio.expressions.blast.ncbiblast.header=Bio.expressions.blast.ncbiblast-module.html#header,Variable Bio.expressions.blast.wublast.header=Bio.expressions.blast.wublast-module.html#header,Variable Bio.expressions.blocks.header=Bio.expressions.blocks-module.html#header,Variable Bio.expressions.genbank.header=Bio.expressions.genbank-module.html#header,Variable Bio.expressions.hmmpfam.header=Bio.expressions.hmmpfam-module.html#header"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-251', 'header', 'link-251');">header</a></tt><tt class="py-op">=</tt><tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-252" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-252', 'split', 'link-143');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L459"></a><tt class="py-lineno">459</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-253" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-253', 'data', 'link-41');">data</a></tt><tt class="py-op">.</tt><tt id="link-254" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-254', 'name', 'link-7');">name</a></tt><tt class="py-op">=</tt><tt id="link-255" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-255', 'header', 'link-251');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L460"></a><tt class="py-lineno">460</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-256" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-256', 'data', 'link-41');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">nbases</tt><tt class="py-op">=</tt><tt class="py-name">eval</tt><tt class="py-op">(</tt><tt id="link-257" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-257', 'header', 'link-251');">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="L461"></a><tt class="py-lineno">461</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-258" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-258', 'data', 'link-41');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">nreads</tt><tt class="py-op">=</tt><tt class="py-name">eval</tt><tt class="py-op">(</tt><tt id="link-259" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-259', 'header', 'link-251');">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="L462"></a><tt class="py-lineno">462</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-260" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-260', 'data', 'link-41');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">nsegments</tt><tt class="py-op">=</tt><tt class="py-name">eval</tt><tt class="py-op">(</tt><tt id="link-261" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-261', 'header', 'link-251');">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="L463"></a><tt class="py-lineno">463</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-262" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-262', 'data', 'link-41');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">uorc</tt><tt class="py-op">=</tt><tt id="link-263" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-263', 'header', 'link-251');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">5</tt><tt class="py-op">]</tt> </tt>
</div><a name="L464"></a><tt class="py-lineno">464</tt>  <tt class="py-line"> </tt>
<a name="_RecordConsumer.co_data"></a><div id="_RecordConsumer.co_data-def"><a name="L465"></a><tt class="py-lineno">465</tt> <a class="py-toggle" href="#" id="_RecordConsumer.co_data-toggle" onclick="return toggle('_RecordConsumer.co_data');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace._RecordConsumer-class.html#co_data">co_data</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">seq</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.co_data-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.co_data-expanded"><a name="L466"></a><tt class="py-lineno">466</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-264" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-264', 'data', 'link-41');">data</a></tt><tt class="py-op">.</tt><tt id="link-265" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-265', 'sequence', 'link-8');">sequence</a></tt><tt class="py-op">=</tt><tt id="link-266" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-266', 'seq', 'link-238');">seq</a></tt> </tt>
</div><a name="L467"></a><tt class="py-lineno">467</tt>  <tt class="py-line">     </tt>
<a name="_RecordConsumer.bq_header"></a><div id="_RecordConsumer.bq_header-def"><a name="L468"></a><tt class="py-lineno">468</tt> <a class="py-toggle" href="#" id="_RecordConsumer.bq_header-toggle" onclick="return toggle('_RecordConsumer.bq_header');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace._RecordConsumer-class.html#bq_header">bq_header</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-op">:</tt> </tt>
</div><div id="_RecordConsumer.bq_header-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.bq_header-expanded"><a name="L469"></a><tt class="py-lineno">469</tt>  <tt class="py-line">        <tt class="py-keyword">pass</tt> </tt>
</div><a name="L470"></a><tt class="py-lineno">470</tt>  <tt class="py-line">     </tt>
<a name="_RecordConsumer.bq_data"></a><div id="_RecordConsumer.bq_data-def"><a name="L471"></a><tt class="py-lineno">471</tt> <a class="py-toggle" href="#" id="_RecordConsumer.bq_data-toggle" onclick="return toggle('_RecordConsumer.bq_data');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace._RecordConsumer-class.html#bq_data">bq_data</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">qual</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.bq_data-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.bq_data-expanded"><a name="L472"></a><tt class="py-lineno">472</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-267" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-267', 'data', 'link-41');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">quality</tt><tt class="py-op">=</tt><tt id="link-268" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-268', 'map', 'link-74');">map</a></tt><tt class="py-op">(</tt><tt class="py-name">eval</tt><tt class="py-op">,</tt><tt class="py-name">qual</tt><tt class="py-op">.</tt><tt id="link-269" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-269', 'split', 'link-143');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L473"></a><tt class="py-lineno">473</tt>  <tt class="py-line"> </tt>
<a name="_RecordConsumer.af"></a><div id="_RecordConsumer.af-def"><a name="L474"></a><tt class="py-lineno">474</tt> <a class="py-toggle" href="#" id="_RecordConsumer.af-toggle" onclick="return toggle('_RecordConsumer.af');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace._RecordConsumer-class.html#af">af</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-op">:</tt> </tt>
</div><div id="_RecordConsumer.af-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.af-expanded"><a name="L475"></a><tt class="py-lineno">475</tt>  <tt class="py-line">        <tt id="link-270" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-270', 'header', 'link-251');">header</a></tt><tt class="py-op">=</tt><tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-271" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-271', 'split', 'link-143');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L476"></a><tt class="py-lineno">476</tt>  <tt class="py-line">        <tt class="py-name">afdata</tt><tt class="py-op">=</tt><tt id="link-272" class="py-name"><a title="Bio.Sequencing.Ace._RecordConsumer.af
Bio.Sequencing.Ace.af" class="py-name" href="#" onclick="return doclink('link-272', 'af', 'link-29');">af</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L477"></a><tt class="py-lineno">477</tt>  <tt class="py-line">        <tt class="py-name">afdata</tt><tt class="py-op">.</tt><tt id="link-273" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-273', 'name', 'link-7');">name</a></tt><tt class="py-op">=</tt><tt id="link-274" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-274', 'header', 'link-251');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">1</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">afdata</tt><tt class="py-op">.</tt><tt class="py-name">coru</tt><tt class="py-op">=</tt><tt id="link-275" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-275', 'header', 'link-251');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> </tt>
<a name="L479"></a><tt class="py-lineno">479</tt>  <tt class="py-line">        <tt class="py-name">afdata</tt><tt class="py-op">.</tt><tt class="py-name">padded_start</tt><tt class="py-op">=</tt><tt class="py-name">eval</tt><tt class="py-op">(</tt><tt id="link-276" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-276', 'header', 'link-251');">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="L480"></a><tt class="py-lineno">480</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-277" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-277', 'data', 'link-41');">data</a></tt><tt class="py-op">.</tt><tt id="link-278" class="py-name"><a title="Bio.Sequencing.Ace._RecordConsumer.af
Bio.Sequencing.Ace.af" class="py-name" href="#" onclick="return doclink('link-278', 'af', 'link-29');">af</a></tt><tt class="py-op">.</tt><tt id="link-279" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-279', 'append', 'link-37');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">afdata</tt><tt class="py-op">)</tt> </tt>
</div><a name="L481"></a><tt class="py-lineno">481</tt>  <tt class="py-line">         </tt>
<a name="_RecordConsumer.bs"></a><div id="_RecordConsumer.bs-def"><a name="L482"></a><tt class="py-lineno">482</tt> <a class="py-toggle" href="#" id="_RecordConsumer.bs-toggle" onclick="return toggle('_RecordConsumer.bs');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace._RecordConsumer-class.html#bs">bs</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-op">:</tt> </tt>
</div><div id="_RecordConsumer.bs-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.bs-expanded"><a name="L483"></a><tt class="py-lineno">483</tt>  <tt class="py-line">        <tt id="link-280" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-280', 'header', 'link-251');">header</a></tt><tt class="py-op">=</tt><tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-281" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-281', 'split', 'link-143');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L484"></a><tt class="py-lineno">484</tt>  <tt class="py-line">        <tt class="py-name">bsdata</tt><tt class="py-op">=</tt><tt id="link-282" class="py-name"><a title="Bio.Sequencing.Ace._RecordConsumer.bs
Bio.Sequencing.Ace.bs" class="py-name" href="#" onclick="return doclink('link-282', 'bs', 'link-30');">bs</a></tt><tt class="py-op">(</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">bsdata</tt><tt class="py-op">.</tt><tt class="py-name">padded_start</tt><tt class="py-op">=</tt><tt class="py-name">eval</tt><tt class="py-op">(</tt><tt id="link-283" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-283', 'header', 'link-251');">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="L486"></a><tt class="py-lineno">486</tt>  <tt class="py-line">        <tt class="py-name">bsdata</tt><tt class="py-op">.</tt><tt class="py-name">padded_end</tt><tt class="py-op">=</tt><tt class="py-name">eval</tt><tt class="py-op">(</tt><tt id="link-284" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-284', 'header', 'link-251');">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="L487"></a><tt class="py-lineno">487</tt>  <tt class="py-line">        <tt class="py-name">bsdata</tt><tt class="py-op">.</tt><tt id="link-285" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-285', 'name', 'link-7');">name</a></tt><tt class="py-op">=</tt><tt id="link-286" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-286', 'header', 'link-251');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt> </tt>
<a name="L488"></a><tt class="py-lineno">488</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-287" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-287', 'data', 'link-41');">data</a></tt><tt class="py-op">.</tt><tt id="link-288" class="py-name"><a title="Bio.Sequencing.Ace._RecordConsumer.bs
Bio.Sequencing.Ace.bs" class="py-name" href="#" onclick="return doclink('link-288', 'bs', 'link-30');">bs</a></tt><tt class="py-op">.</tt><tt id="link-289" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-289', 'append', 'link-37');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">bsdata</tt><tt class="py-op">)</tt> </tt>
</div><a name="L489"></a><tt class="py-lineno">489</tt>  <tt class="py-line">         </tt>
<a name="_RecordConsumer.rd_header"></a><div id="_RecordConsumer.rd_header-def"><a name="L490"></a><tt class="py-lineno">490</tt> <a class="py-toggle" href="#" id="_RecordConsumer.rd_header-toggle" onclick="return toggle('_RecordConsumer.rd_header');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace._RecordConsumer-class.html#rd_header">rd_header</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-op">:</tt> </tt>
</div><div id="_RecordConsumer.rd_header-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.rd_header-expanded"><a name="L491"></a><tt class="py-lineno">491</tt>  <tt class="py-line">        <tt id="link-290" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-290', 'header', 'link-251');">header</a></tt><tt class="py-op">=</tt><tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-291" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-291', 'split', 'link-143');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L492"></a><tt class="py-lineno">492</tt>  <tt class="py-line">        <tt class="py-comment"># Reads start with rd, so we create a new read record here</tt> </tt>
<a name="L493"></a><tt class="py-lineno">493</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-292" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-292', 'data', 'link-41');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">reads</tt><tt class="py-op">.</tt><tt id="link-293" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-293', 'append', 'link-37');">append</a></tt><tt class="py-op">(</tt><tt id="link-294" 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-294', 'Reads', 'link-294');">Reads</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L494"></a><tt class="py-lineno">494</tt>  <tt class="py-line">        <tt class="py-name">rddata</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-22');">rd</a></tt><tt class="py-op">(</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">rddata</tt><tt class="py-op">.</tt><tt id="link-296" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-296', 'name', 'link-7');">name</a></tt><tt class="py-op">=</tt><tt id="link-297" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-297', 'header', 'link-251');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">1</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">rddata</tt><tt class="py-op">.</tt><tt class="py-name">padded_bases</tt><tt class="py-op">=</tt><tt class="py-name">eval</tt><tt class="py-op">(</tt><tt id="link-298" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-298', 'header', 'link-251');">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="L497"></a><tt class="py-lineno">497</tt>  <tt class="py-line">        <tt class="py-name">rddata</tt><tt class="py-op">.</tt><tt class="py-name">info_items</tt><tt class="py-op">=</tt><tt class="py-name">eval</tt><tt class="py-op">(</tt><tt id="link-299" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-299', 'header', 'link-251');">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="L498"></a><tt class="py-lineno">498</tt>  <tt class="py-line">        <tt class="py-name">rddata</tt><tt class="py-op">.</tt><tt class="py-name">read_tags</tt><tt class="py-op">=</tt><tt class="py-name">eval</tt><tt class="py-op">(</tt><tt id="link-300" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-300', 'header', 'link-251');">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="L499"></a><tt class="py-lineno">499</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-301" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-301', 'data', 'link-41');">data</a></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-302" class="py-name"><a title="Bio.Sequencing.Ace.rd" class="py-name" href="#" onclick="return doclink('link-302', 'rd', 'link-22');">rd</a></tt><tt class="py-op">=</tt><tt class="py-name">rddata</tt> </tt>
</div><a name="L500"></a><tt class="py-lineno">500</tt>  <tt class="py-line"> </tt>
<a name="_RecordConsumer.rd_data"></a><div id="_RecordConsumer.rd_data-def"><a name="L501"></a><tt class="py-lineno">501</tt> <a class="py-toggle" href="#" id="_RecordConsumer.rd_data-toggle" onclick="return toggle('_RecordConsumer.rd_data');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace._RecordConsumer-class.html#rd_data">rd_data</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">seq</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.rd_data-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.rd_data-expanded"><a name="L502"></a><tt class="py-lineno">502</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-303" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-303', 'data', 'link-41');">data</a></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-304" class="py-name"><a title="Bio.Sequencing.Ace.rd" class="py-name" href="#" onclick="return doclink('link-304', 'rd', 'link-22');">rd</a></tt><tt class="py-op">.</tt><tt id="link-305" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-305', 'sequence', 'link-8');">sequence</a></tt><tt class="py-op">=</tt><tt id="link-306" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-306', 'seq', 'link-238');">seq</a></tt> </tt>
</div><a name="L503"></a><tt class="py-lineno">503</tt>  <tt class="py-line">         </tt>
<a name="_RecordConsumer.qa"></a><div id="_RecordConsumer.qa-def"><a name="L504"></a><tt class="py-lineno">504</tt> <a class="py-toggle" href="#" id="_RecordConsumer.qa-toggle" onclick="return toggle('_RecordConsumer.qa');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace._RecordConsumer-class.html#qa">qa</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-op">:</tt> </tt>
</div><div id="_RecordConsumer.qa-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.qa-expanded"><a name="L505"></a><tt class="py-lineno">505</tt>  <tt class="py-line">        <tt id="link-307" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-307', 'header', 'link-251');">header</a></tt><tt class="py-op">=</tt><tt id="link-308" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-308', 'map', 'link-74');">map</a></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-309" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-309', 'split', 'link-143');">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="L506"></a><tt class="py-lineno">506</tt>  <tt class="py-line">        <tt class="py-name">qadata</tt><tt class="py-op">=</tt><tt id="link-310" class="py-name"><a title="Bio.Sequencing.Ace._RecordConsumer.qa
Bio.Sequencing.Ace.qa" class="py-name" href="#" onclick="return doclink('link-310', 'qa', 'link-23');">qa</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L507"></a><tt class="py-lineno">507</tt>  <tt class="py-line">        <tt class="py-name">qadata</tt><tt class="py-op">.</tt><tt class="py-name">qual_clipping_start</tt><tt class="py-op">=</tt><tt id="link-311" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-311', 'header', 'link-251');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">0</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">qadata</tt><tt class="py-op">.</tt><tt class="py-name">qual_clipping_end</tt><tt class="py-op">=</tt><tt id="link-312" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-312', 'header', 'link-251');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">1</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">qadata</tt><tt class="py-op">.</tt><tt class="py-name">align_clipping_start</tt><tt class="py-op">=</tt><tt id="link-313" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-313', 'header', 'link-251');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> </tt>
<a name="L510"></a><tt class="py-lineno">510</tt>  <tt class="py-line">        <tt class="py-name">qadata</tt><tt class="py-op">.</tt><tt class="py-name">align_clipping_end</tt><tt class="py-op">=</tt><tt id="link-314" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-314', 'header', 'link-251');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt> </tt>
<a name="L511"></a><tt class="py-lineno">511</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-315" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-315', 'data', 'link-41');">data</a></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-316" class="py-name"><a title="Bio.Sequencing.Ace._RecordConsumer.qa
Bio.Sequencing.Ace.qa" class="py-name" href="#" onclick="return doclink('link-316', 'qa', 'link-23');">qa</a></tt><tt class="py-op">=</tt><tt class="py-name">qadata</tt> </tt>
</div><a name="L512"></a><tt class="py-lineno">512</tt>  <tt class="py-line"> </tt>
<a name="_RecordConsumer.ds"></a><div id="_RecordConsumer.ds-def"><a name="L513"></a><tt class="py-lineno">513</tt> <a class="py-toggle" href="#" id="_RecordConsumer.ds-toggle" onclick="return toggle('_RecordConsumer.ds');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace._RecordConsumer-class.html#ds">ds</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-op">:</tt> </tt>
</div><div id="_RecordConsumer.ds-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.ds-expanded"><a name="L514"></a><tt class="py-lineno">514</tt>  <tt class="py-line">        <tt class="py-name">dsdata</tt><tt class="py-op">=</tt><tt id="link-317" class="py-name"><a title="Bio.Sequencing.Ace._RecordConsumer.ds
Bio.Sequencing.Ace.ds" class="py-name" href="#" onclick="return doclink('link-317', 'ds', 'link-24');">ds</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L515"></a><tt class="py-lineno">515</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="L516"></a><tt class="py-lineno">516</tt>  <tt class="py-line">        <tt class="py-name">poss</tt><tt class="py-op">=</tt><tt id="link-318" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-318', 'map', 'link-74');">map</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-319" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.find()=Bio.EUtils.POM.ElementNode-class.html#find,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.biblio.Biblio.find()=Bio.biblio.Biblio-class.html#find,Function Bio.triefind.find()=Bio.triefind-module.html#find"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-319', 'find', 'link-319');">find</a></tt><tt class="py-op">,</tt><tt class="py-name">tags</tt><tt class="py-op">)</tt> </tt>
<a name="L517"></a><tt class="py-lineno">517</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="L518"></a><tt class="py-lineno">518</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">tagpos</tt><tt class="py-op">.</tt><tt id="link-320" class="py-name" targets="Method Bio.Crystal.Crystal.has_key()=Bio.Crystal.Crystal-class.html#has_key,Method Bio.EUtils.POM.ElementNode.has_key()=Bio.EUtils.POM.ElementNode-class.html#has_key,Method Bio.GenBank.NCBIDictionary.has_key()=Bio.GenBank.NCBIDictionary-class.html#has_key,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#has_key,Method Bio.PDB.FragmentMapper'.FragmentMapper.has_key()=Bio.PDB.FragmentMapper%27.FragmentMapper-class.html#has_key,Method Bio.Prosite.ExPASyDictionary.has_key()=Bio.Prosite.ExPASyDictionary-class.html#has_key,Method Bio.Prosite.Prodoc.ExPASyDictionary.has_key()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#has_key,Method Bio.PubMed.Dictionary.has_key()=Bio.PubMed.Dictionary-class.html#has_key,Method Bio.SwissProt.SProt.ExPASyDictionary.has_key()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#has_key,Method Martel.Parser.MartelAttributeList.has_key()=Martel.Parser.MartelAttributeList-class.html#has_key"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-320', 'has_key', 'link-320');">has_key</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>
<a name="L519"></a><tt class="py-lineno">519</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="L520"></a><tt class="py-lineno">520</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-321" class="py-name" targets="Method Bio.Crystal.Crystal.keys()=Bio.Crystal.Crystal-class.html#keys,Method Bio.EUtils.MultiDict._BaseMultiDict.keys()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#keys,Method Bio.GenBank.NCBIDictionary.keys()=Bio.GenBank.NCBIDictionary-class.html#keys,Method Bio.Mindy.BaseDB.DictLookup.keys()=Bio.Mindy.BaseDB.DictLookup-class.html#keys,Method Bio.Mindy.BaseDB.OpenDB.keys()=Bio.Mindy.BaseDB.OpenDB-class.html#keys,Method Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys()=Bio.Mindy.BerkeleyDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys()=Bio.Mindy.BerkeleyDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryNamespace.keys()=Bio.Mindy.FlatDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryTable.keys()=Bio.Mindy.FlatDB.PrimaryTable-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryNamespace.keys()=Bio.Mindy.FlatDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryTable.keys()=Bio.Mindy.FlatDB.SecondaryTable-class.html#keys,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#keys,Method Bio.Prosite.ExPASyDictionary.keys()=Bio.Prosite.ExPASyDictionary-class.html#keys,Method Bio.Prosite.Prodoc.ExPASyDictionary.keys()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#keys,Method Bio.PubMed.Dictionary.keys()=Bio.PubMed.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.Dictionary.keys()=Bio.SwissProt.SProt.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.ExPASyDictionary.keys()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#keys,Method Bio.config.Registry.Registry.keys()=Bio.config.Registry.Registry-class.html#keys,Method BioSQL.BioSeqDatabase.BioSeqDatabase.keys()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#keys,Method BioSQL.BioSeqDatabase.DBServer.keys()=BioSQL.BioSeqDatabase.DBServer-class.html#keys,Method Martel.Parser.MartelAttributeList.keys()=Martel.Parser.MartelAttributeList-class.html#keys"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-321', 'keys', 'link-321');">keys</a></tt><tt class="py-op">(</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">ps</tt><tt class="py-op">.</tt><tt id="link-322" class="py-name"><a title="Bio.PDB.Residue.DisorderedResidue.sort
Bio.PDB.Residue.Residue.sort
Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-322', 'sort', 'link-153');">sort</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">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="L523"></a><tt class="py-lineno">523</tt>  <tt class="py-line">            <tt class="py-name">setattr</tt><tt class="py-op">(</tt><tt class="py-name">dsdata</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-name">lower</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-323" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-323', 'strip', 'link-243');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt>    </tt>
<a name="L524"></a><tt class="py-lineno">524</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-324" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-324', 'data', 'link-41');">data</a></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-325" class="py-name"><a title="Bio.Sequencing.Ace._RecordConsumer.ds
Bio.Sequencing.Ace.ds" class="py-name" href="#" onclick="return doclink('link-325', 'ds', 'link-24');">ds</a></tt><tt class="py-op">=</tt><tt class="py-name">dsdata</tt> </tt>
</div><a name="L525"></a><tt class="py-lineno">525</tt>  <tt class="py-line"> </tt>
<a name="_RecordConsumer.ct_start"></a><div id="_RecordConsumer.ct_start-def"><a name="L526"></a><tt class="py-lineno">526</tt> <a class="py-toggle" href="#" id="_RecordConsumer.ct_start-toggle" onclick="return toggle('_RecordConsumer.ct_start');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace._RecordConsumer-class.html#ct_start">ct_start</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-op">:</tt> </tt>
</div><div id="_RecordConsumer.ct_start-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.ct_start-expanded"><a name="L527"></a><tt class="py-lineno">527</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-326" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-326', 'strip', 'link-243');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">endswith</tt><tt class="py-op">(</tt><tt class="py-string">'{'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L528"></a><tt class="py-lineno">528</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> <tt class="py-name">line</tt> </tt>
<a name="L529"></a><tt class="py-lineno">529</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">'CT tag does not start with CT{'</tt> </tt>
<a name="L530"></a><tt class="py-lineno">530</tt>  <tt class="py-line">        <tt class="py-name">ctdata</tt><tt class="py-op">=</tt><tt id="link-327" class="py-name"><a title="Bio.Sequencing.Ace.ct" class="py-name" href="#" onclick="return doclink('link-327', 'ct', 'link-31');">ct</a></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 class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-328" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-328', 'data', 'link-41');">data</a></tt><tt class="py-op">.</tt><tt id="link-329" class="py-name"><a title="Bio.Sequencing.Ace.ct" class="py-name" href="#" onclick="return doclink('link-329', 'ct', 'link-31');">ct</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L532"></a><tt class="py-lineno">532</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-330" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-330', 'data', 'link-41');">data</a></tt><tt class="py-op">.</tt><tt id="link-331" class="py-name"><a title="Bio.Sequencing.Ace.ct" class="py-name" href="#" onclick="return doclink('link-331', 'ct', 'link-31');">ct</a></tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L533"></a><tt class="py-lineno">533</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-332" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-332', 'data', 'link-41');">data</a></tt><tt class="py-op">.</tt><tt id="link-333" class="py-name"><a title="Bio.Sequencing.Ace.ct" class="py-name" href="#" onclick="return doclink('link-333', 'ct', 'link-31');">ct</a></tt><tt class="py-op">.</tt><tt id="link-334" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-334', 'append', 'link-37');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">ctdata</tt><tt class="py-op">)</tt>    </tt>
</div><a name="L534"></a><tt class="py-lineno">534</tt>  <tt class="py-line">     </tt>
<a name="_RecordConsumer.ct_data"></a><div id="_RecordConsumer.ct_data-def"><a name="L535"></a><tt class="py-lineno">535</tt> <a class="py-toggle" href="#" id="_RecordConsumer.ct_data-toggle" onclick="return toggle('_RecordConsumer.ct_data');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace._RecordConsumer-class.html#ct_data">ct_data</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">taglines</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.ct_data-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.ct_data-expanded"><a name="L536"></a><tt class="py-lineno">536</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">taglines</tt><tt class="py-op">)</tt><tt class="py-op">&lt;</tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L537"></a><tt class="py-lineno">537</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">'Missing header line in CT tag'</tt> </tt>
<a name="L538"></a><tt class="py-lineno">538</tt>  <tt class="py-line">        <tt id="link-335" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-335', 'header', 'link-251');">header</a></tt><tt class="py-op">=</tt><tt class="py-name">taglines</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-336" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-336', 'split', 'link-143');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L539"></a><tt class="py-lineno">539</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-337" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-337', 'data', 'link-41');">data</a></tt><tt class="py-op">.</tt><tt id="link-338" class="py-name"><a title="Bio.Sequencing.Ace.ct" class="py-name" href="#" onclick="return doclink('link-338', 'ct', 'link-31');">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-339" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-339', 'name', 'link-7');">name</a></tt><tt class="py-op">=</tt><tt id="link-340" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-340', 'header', 'link-251');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L540"></a><tt class="py-lineno">540</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-341" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-341', 'data', 'link-41');">data</a></tt><tt class="py-op">.</tt><tt id="link-342" class="py-name"><a title="Bio.Sequencing.Ace.ct" class="py-name" href="#" onclick="return doclink('link-342', 'ct', 'link-31');">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">tag_type</tt><tt class="py-op">=</tt><tt id="link-343" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-343', 'header', 'link-251');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L541"></a><tt class="py-lineno">541</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-344" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-344', 'data', 'link-41');">data</a></tt><tt class="py-op">.</tt><tt id="link-345" class="py-name"><a title="Bio.Sequencing.Ace.ct" class="py-name" href="#" onclick="return doclink('link-345', 'ct', 'link-31');">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">program</tt><tt class="py-op">=</tt><tt id="link-346" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-346', 'header', 'link-251');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> </tt>
<a name="L542"></a><tt class="py-lineno">542</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-347" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-347', 'data', 'link-41');">data</a></tt><tt class="py-op">.</tt><tt id="link-348" class="py-name"><a title="Bio.Sequencing.Ace.ct" class="py-name" href="#" onclick="return doclink('link-348', 'ct', 'link-31');">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">padded_start</tt><tt class="py-op">=</tt><tt class="py-name">eval</tt><tt class="py-op">(</tt><tt id="link-349" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-349', 'header', 'link-251');">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="L543"></a><tt class="py-lineno">543</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-350" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-350', 'data', 'link-41');">data</a></tt><tt class="py-op">.</tt><tt id="link-351" class="py-name"><a title="Bio.Sequencing.Ace.ct" class="py-name" href="#" onclick="return doclink('link-351', 'ct', 'link-31');">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">padded_end</tt><tt class="py-op">=</tt><tt class="py-name">eval</tt><tt class="py-op">(</tt><tt id="link-352" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-352', 'header', 'link-251');">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="L544"></a><tt class="py-lineno">544</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-353" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-353', 'data', 'link-41');">data</a></tt><tt class="py-op">.</tt><tt id="link-354" class="py-name"><a title="Bio.Sequencing.Ace.ct" class="py-name" href="#" onclick="return doclink('link-354', 'ct', 'link-31');">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-355" class="py-name"><a title="Bio.GenBank._FeatureConsumer.date
Bio.GenBank._RecordConsumer.date
Bio.Prosite._RecordConsumer.date
Bio.SwissProt.SProt._RecordConsumer.date
Bio.SwissProt.SProt._SequenceConsumer.date
Bio.expressions.embl.embl65.date
Bio.expressions.genbank.date" class="py-name" href="#" onclick="return doclink('link-355', 'date', 'link-16');">date</a></tt><tt class="py-op">=</tt><tt id="link-356" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-356', 'header', 'link-251');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">5</tt><tt class="py-op">]</tt> </tt>
<a name="L545"></a><tt class="py-lineno">545</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-357" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-357', 'header', 'link-251');">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="L546"></a><tt class="py-lineno">546</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-358" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-358', 'data', 'link-41');">data</a></tt><tt class="py-op">.</tt><tt id="link-359" class="py-name"><a title="Bio.Sequencing.Ace.ct" class="py-name" href="#" onclick="return doclink('link-359', 'ct', 'link-31');">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">notrans</tt><tt class="py-op">=</tt><tt id="link-360" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-360', 'header', 'link-251');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">6</tt><tt class="py-op">]</tt> </tt>
<a name="L547"></a><tt class="py-lineno">547</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-361" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-361', 'data', 'link-41');">data</a></tt><tt class="py-op">.</tt><tt id="link-362" class="py-name"><a title="Bio.Sequencing.Ace.ct" class="py-name" href="#" onclick="return doclink('link-362', 'ct', 'link-31');">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 class="py-name">taglines</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt>  </tt>
</div><a name="L548"></a><tt class="py-lineno">548</tt>  <tt class="py-line"> </tt>
<a name="_RecordConsumer.rt_start"></a><div id="_RecordConsumer.rt_start-def"><a name="L549"></a><tt class="py-lineno">549</tt> <a class="py-toggle" href="#" id="_RecordConsumer.rt_start-toggle" onclick="return toggle('_RecordConsumer.rt_start');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace._RecordConsumer-class.html#rt_start">rt_start</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-op">:</tt> </tt>
</div><div id="_RecordConsumer.rt_start-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.rt_start-expanded"><a name="L550"></a><tt class="py-lineno">550</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-363" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-363', 'strip', 'link-243');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">endswith</tt><tt class="py-op">(</tt><tt class="py-string">'{'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L551"></a><tt class="py-lineno">551</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">'RT tag does not start with RT{'</tt> </tt>
<a name="L552"></a><tt class="py-lineno">552</tt>  <tt class="py-line">        <tt class="py-name">rtdata</tt><tt class="py-op">=</tt><tt id="link-364" class="py-name"><a title="Bio.Sequencing.Ace.rt" class="py-name" href="#" onclick="return doclink('link-364', 'rt', 'link-25');">rt</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L553"></a><tt class="py-lineno">553</tt>  <tt class="py-line">        <tt class="py-comment"># now if we're at the end of the file, this rt could belong to a previous read, not the actual one</tt> </tt>
<a name="L554"></a><tt class="py-lineno">554</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment"># we store it here were it appears, the user can sort later. </tt> </tt>
<a name="L555"></a><tt class="py-lineno">555</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-365" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-365', 'data', 'link-41');">data</a></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-366" class="py-name"><a title="Bio.Sequencing.Ace.rt" class="py-name" href="#" onclick="return doclink('link-366', 'rt', 'link-25');">rt</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L556"></a><tt class="py-lineno">556</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-367" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-367', 'data', 'link-41');">data</a></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-368" class="py-name"><a title="Bio.Sequencing.Ace.rt" class="py-name" href="#" onclick="return doclink('link-368', 'rt', 'link-25');">rt</a></tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L557"></a><tt class="py-lineno">557</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-369" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-369', 'data', 'link-41');">data</a></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-370" class="py-name"><a title="Bio.Sequencing.Ace.rt" class="py-name" href="#" onclick="return doclink('link-370', 'rt', 'link-25');">rt</a></tt><tt class="py-op">.</tt><tt id="link-371" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-371', 'append', 'link-37');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">rtdata</tt><tt class="py-op">)</tt> </tt>
</div><a name="L558"></a><tt class="py-lineno">558</tt>  <tt class="py-line">    </tt>
<a name="_RecordConsumer.rt_data"></a><div id="_RecordConsumer.rt_data-def"><a name="L559"></a><tt class="py-lineno">559</tt> <a class="py-toggle" href="#" id="_RecordConsumer.rt_data-toggle" onclick="return toggle('_RecordConsumer.rt_data');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace._RecordConsumer-class.html#rt_data">rt_data</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">taglines</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.rt_data-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.rt_data-expanded"><a name="L560"></a><tt class="py-lineno">560</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">taglines</tt><tt class="py-op">)</tt><tt class="py-op">&lt;</tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L561"></a><tt class="py-lineno">561</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">'Missing header line in RT tag'</tt> </tt>
<a name="L562"></a><tt class="py-lineno">562</tt>  <tt class="py-line">        <tt id="link-372" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-372', 'header', 'link-251');">header</a></tt><tt class="py-op">=</tt><tt class="py-name">taglines</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-373" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-373', 'split', 'link-143');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L563"></a><tt class="py-lineno">563</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-374" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-374', 'data', 'link-41');">data</a></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-375" class="py-name"><a title="Bio.Sequencing.Ace.rt" class="py-name" href="#" onclick="return doclink('link-375', 'rt', 'link-25');">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-376" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-376', 'name', 'link-7');">name</a></tt><tt class="py-op">=</tt><tt id="link-377" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-377', 'header', 'link-251');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L564"></a><tt class="py-lineno">564</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-378" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-378', 'data', 'link-41');">data</a></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-379" class="py-name"><a title="Bio.Sequencing.Ace.rt" class="py-name" href="#" onclick="return doclink('link-379', 'rt', 'link-25');">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 class="py-name">tag_type</tt><tt class="py-op">=</tt><tt id="link-380" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-380', 'header', 'link-251');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L565"></a><tt class="py-lineno">565</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-381" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-381', 'data', 'link-41');">data</a></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-382" class="py-name"><a title="Bio.Sequencing.Ace.rt" class="py-name" href="#" onclick="return doclink('link-382', 'rt', 'link-25');">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 class="py-name">program</tt><tt class="py-op">=</tt><tt id="link-383" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-383', 'header', 'link-251');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> </tt>
<a name="L566"></a><tt class="py-lineno">566</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-384" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-384', 'data', 'link-41');">data</a></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-385" class="py-name"><a title="Bio.Sequencing.Ace.rt" class="py-name" href="#" onclick="return doclink('link-385', 'rt', 'link-25');">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 class="py-name">padded_start</tt><tt class="py-op">=</tt><tt class="py-name">eval</tt><tt class="py-op">(</tt><tt id="link-386" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-386', 'header', 'link-251');">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="L567"></a><tt class="py-lineno">567</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-387" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-387', 'data', 'link-41');">data</a></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-388" class="py-name"><a title="Bio.Sequencing.Ace.rt" class="py-name" href="#" onclick="return doclink('link-388', 'rt', 'link-25');">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 class="py-name">padded_end</tt><tt class="py-op">=</tt><tt class="py-name">eval</tt><tt class="py-op">(</tt><tt id="link-389" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-389', 'header', 'link-251');">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="L568"></a><tt class="py-lineno">568</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-390" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-390', 'data', 'link-41');">data</a></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-391" class="py-name"><a title="Bio.Sequencing.Ace.rt" class="py-name" href="#" onclick="return doclink('link-391', 'rt', 'link-25');">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-392" class="py-name"><a title="Bio.GenBank._FeatureConsumer.date
Bio.GenBank._RecordConsumer.date
Bio.Prosite._RecordConsumer.date
Bio.SwissProt.SProt._RecordConsumer.date
Bio.SwissProt.SProt._SequenceConsumer.date
Bio.expressions.embl.embl65.date
Bio.expressions.genbank.date" class="py-name" href="#" onclick="return doclink('link-392', 'date', 'link-16');">date</a></tt><tt class="py-op">=</tt><tt id="link-393" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-393', 'header', 'link-251');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">5</tt><tt class="py-op">]</tt> </tt>
</div><a name="L569"></a><tt class="py-lineno">569</tt>  <tt class="py-line">     </tt>
<a name="_RecordConsumer.wa_start"></a><div id="_RecordConsumer.wa_start-def"><a name="L570"></a><tt class="py-lineno">570</tt> <a class="py-toggle" href="#" id="_RecordConsumer.wa_start-toggle" onclick="return toggle('_RecordConsumer.wa_start');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace._RecordConsumer-class.html#wa_start">wa_start</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-op">:</tt> </tt>
</div><div id="_RecordConsumer.wa_start-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.wa_start-expanded"><a name="L571"></a><tt class="py-lineno">571</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-394" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-394', 'strip', 'link-243');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">endswith</tt><tt class="py-op">(</tt><tt class="py-string">'{'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L572"></a><tt class="py-lineno">572</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">'WA tag does not start with WA{'</tt> </tt>
<a name="L573"></a><tt class="py-lineno">573</tt>  <tt class="py-line">        <tt class="py-name">wadata</tt><tt class="py-op">=</tt><tt id="link-395" class="py-name"><a title="Bio.Sequencing.Ace.wa" class="py-name" href="#" onclick="return doclink('link-395', 'wa', 'link-32');">wa</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L574"></a><tt class="py-lineno">574</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-396" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-396', 'data', 'link-41');">data</a></tt><tt class="py-op">.</tt><tt id="link-397" class="py-name"><a title="Bio.Sequencing.Ace.wa" class="py-name" href="#" onclick="return doclink('link-397', 'wa', 'link-32');">wa</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L575"></a><tt class="py-lineno">575</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-398" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-398', 'data', 'link-41');">data</a></tt><tt class="py-op">.</tt><tt id="link-399" class="py-name"><a title="Bio.Sequencing.Ace.wa" class="py-name" href="#" onclick="return doclink('link-399', 'wa', 'link-32');">wa</a></tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L576"></a><tt class="py-lineno">576</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-400" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-400', 'data', 'link-41');">data</a></tt><tt class="py-op">.</tt><tt id="link-401" class="py-name"><a title="Bio.Sequencing.Ace.wa" class="py-name" href="#" onclick="return doclink('link-401', 'wa', 'link-32');">wa</a></tt><tt class="py-op">.</tt><tt id="link-402" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-402', 'append', 'link-37');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">wadata</tt><tt class="py-op">)</tt> </tt>
</div><a name="L577"></a><tt class="py-lineno">577</tt>  <tt class="py-line">     </tt>
<a name="_RecordConsumer.wa_data"></a><div id="_RecordConsumer.wa_data-def"><a name="L578"></a><tt class="py-lineno">578</tt> <a class="py-toggle" href="#" id="_RecordConsumer.wa_data-toggle" onclick="return toggle('_RecordConsumer.wa_data');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace._RecordConsumer-class.html#wa_data">wa_data</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">taglines</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.wa_data-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.wa_data-expanded"><a name="L579"></a><tt class="py-lineno">579</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">taglines</tt><tt class="py-op">)</tt><tt class="py-op">&lt;</tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L580"></a><tt class="py-lineno">580</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">'Missing header line in WA tag'</tt> </tt>
<a name="L581"></a><tt class="py-lineno">581</tt>  <tt class="py-line">        <tt id="link-403" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-403', 'header', 'link-251');">header</a></tt><tt class="py-op">=</tt><tt class="py-name">taglines</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-404" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-404', 'split', 'link-143');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L582"></a><tt class="py-lineno">582</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-405" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-405', 'data', 'link-41');">data</a></tt><tt class="py-op">.</tt><tt id="link-406" class="py-name"><a title="Bio.Sequencing.Ace.wa" class="py-name" href="#" onclick="return doclink('link-406', 'wa', 'link-32');">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">tag_type</tt><tt class="py-op">=</tt><tt id="link-407" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-407', 'header', 'link-251');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L583"></a><tt class="py-lineno">583</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-408" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-408', 'data', 'link-41');">data</a></tt><tt class="py-op">.</tt><tt id="link-409" class="py-name"><a title="Bio.Sequencing.Ace.wa" class="py-name" href="#" onclick="return doclink('link-409', 'wa', 'link-32');">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">program</tt><tt class="py-op">=</tt><tt id="link-410" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-410', 'header', 'link-251');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L584"></a><tt class="py-lineno">584</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-411" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-411', 'data', 'link-41');">data</a></tt><tt class="py-op">.</tt><tt id="link-412" class="py-name"><a title="Bio.Sequencing.Ace.wa" class="py-name" href="#" onclick="return doclink('link-412', 'wa', 'link-32');">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 id="link-413" class="py-name"><a title="Bio.GenBank._FeatureConsumer.date
Bio.GenBank._RecordConsumer.date
Bio.Prosite._RecordConsumer.date
Bio.SwissProt.SProt._RecordConsumer.date
Bio.SwissProt.SProt._SequenceConsumer.date
Bio.expressions.embl.embl65.date
Bio.expressions.genbank.date" class="py-name" href="#" onclick="return doclink('link-413', 'date', 'link-16');">date</a></tt><tt class="py-op">=</tt><tt id="link-414" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-414', 'header', 'link-251');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> </tt>
<a name="L585"></a><tt class="py-lineno">585</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-415" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-415', 'data', 'link-41');">data</a></tt><tt class="py-op">.</tt><tt id="link-416" class="py-name"><a title="Bio.Sequencing.Ace.wa" class="py-name" href="#" onclick="return doclink('link-416', 'wa', 'link-32');">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 class="py-name">taglines</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt>  </tt>
</div><a name="L586"></a><tt class="py-lineno">586</tt>  <tt class="py-line">     </tt>
<a name="_RecordConsumer.wr_start"></a><div id="_RecordConsumer.wr_start-def"><a name="L587"></a><tt class="py-lineno">587</tt> <a class="py-toggle" href="#" id="_RecordConsumer.wr_start-toggle" onclick="return toggle('_RecordConsumer.wr_start');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace._RecordConsumer-class.html#wr_start">wr_start</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-op">:</tt> </tt>
</div><div id="_RecordConsumer.wr_start-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.wr_start-expanded"><a name="L588"></a><tt class="py-lineno">588</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-417" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-417', 'strip', 'link-243');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">endswith</tt><tt class="py-op">(</tt><tt class="py-string">'{'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L589"></a><tt class="py-lineno">589</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">'WR tag does not start with WR{'</tt> </tt>
<a name="L590"></a><tt class="py-lineno">590</tt>  <tt class="py-line">        <tt class="py-name">wrdata</tt><tt class="py-op">=</tt><tt id="link-418" class="py-name"><a title="Bio.Sequencing.Ace.wr" class="py-name" href="#" onclick="return doclink('link-418', 'wr', 'link-26');">wr</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L591"></a><tt class="py-lineno">591</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-419" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-419', 'data', 'link-41');">data</a></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-420" class="py-name"><a title="Bio.Sequencing.Ace.wr" class="py-name" href="#" onclick="return doclink('link-420', 'wr', 'link-26');">wr</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L592"></a><tt class="py-lineno">592</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-421" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-421', 'data', 'link-41');">data</a></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-422" class="py-name"><a title="Bio.Sequencing.Ace.wr" class="py-name" href="#" onclick="return doclink('link-422', 'wr', 'link-26');">wr</a></tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L593"></a><tt class="py-lineno">593</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-423" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-423', 'data', 'link-41');">data</a></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-424" class="py-name"><a title="Bio.Sequencing.Ace.wr" class="py-name" href="#" onclick="return doclink('link-424', 'wr', 'link-26');">wr</a></tt><tt class="py-op">.</tt><tt id="link-425" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-425', 'append', 'link-37');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">wrdata</tt><tt class="py-op">)</tt> </tt>
</div><a name="L594"></a><tt class="py-lineno">594</tt>  <tt class="py-line">     </tt>
<a name="_RecordConsumer.wr_data"></a><div id="_RecordConsumer.wr_data-def"><a name="L595"></a><tt class="py-lineno">595</tt> <a class="py-toggle" href="#" id="_RecordConsumer.wr_data-toggle" onclick="return toggle('_RecordConsumer.wr_data');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Sequencing.Ace._RecordConsumer-class.html#wr_data">wr_data</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">taglines</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.wr_data-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.wr_data-expanded"><a name="L596"></a><tt class="py-lineno">596</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">taglines</tt><tt class="py-op">)</tt><tt class="py-op">&lt;</tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L597"></a><tt class="py-lineno">597</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">'Missing header line in WR tag'</tt> </tt>
<a name="L598"></a><tt class="py-lineno">598</tt>  <tt class="py-line">        <tt id="link-426" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-426', 'header', 'link-251');">header</a></tt><tt class="py-op">=</tt><tt class="py-name">taglines</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-427" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-427', 'split', 'link-143');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L599"></a><tt class="py-lineno">599</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-428" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-428', 'data', 'link-41');">data</a></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-429" class="py-name"><a title="Bio.Sequencing.Ace.wr" class="py-name" href="#" onclick="return doclink('link-429', 'wr', 'link-26');">wr</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-430" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-430', 'name', 'link-7');">name</a></tt><tt class="py-op">=</tt><tt id="link-431" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-431', 'header', 'link-251');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L600"></a><tt class="py-lineno">600</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-432" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-432', 'data', 'link-41');">data</a></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-433" class="py-name"><a title="Bio.Sequencing.Ace.wr" class="py-name" href="#" onclick="return doclink('link-433', 'wr', 'link-26');">wr</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">aligned</tt><tt class="py-op">=</tt><tt id="link-434" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-434', 'header', 'link-251');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L601"></a><tt class="py-lineno">601</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-435" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-435', 'data', 'link-41');">data</a></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-436" class="py-name"><a title="Bio.Sequencing.Ace.wr" class="py-name" href="#" onclick="return doclink('link-436', 'wr', 'link-26');">wr</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">program</tt><tt class="py-op">=</tt><tt id="link-437" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-437', 'header', 'link-251');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> </tt>
<a name="L602"></a><tt class="py-lineno">602</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-438" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-438', 'data', 'link-41');">data</a></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-439" class="py-name"><a title="Bio.Sequencing.Ace.wr" class="py-name" href="#" onclick="return doclink('link-439', 'wr', 'link-26');">wr</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-440" class="py-name"><a title="Bio.GenBank._FeatureConsumer.date
Bio.GenBank._RecordConsumer.date
Bio.Prosite._RecordConsumer.date
Bio.SwissProt.SProt._RecordConsumer.date
Bio.SwissProt.SProt._SequenceConsumer.date
Bio.expressions.embl.embl65.date
Bio.expressions.genbank.date" class="py-name" href="#" onclick="return doclink('link-440', 'date', 'link-16');">date</a></tt><tt class="py-op">=</tt><tt id="link-441" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-441', 'header', 'link-251');">header</a></tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt> </tt>
</div></div><a name="L603"></a><tt class="py-lineno">603</tt>  <tt class="py-line">     </tt>
<a name="L604"></a><tt class="py-lineno">604</tt>  <tt class="py-line"><tt class="py-keyword">if</tt> <tt class="py-name">__name__</tt> <tt class="py-op">==</tt> <tt class="py-string">"__main__"</tt> <tt class="py-op">:</tt> </tt>
<a name="L605"></a><tt class="py-lineno">605</tt>  <tt class="py-line">    <tt class="py-keyword">print</tt> <tt class="py-string">"Quick self test"</tt> </tt>
<a name="L606"></a><tt class="py-lineno">606</tt>  <tt class="py-line">    <tt class="py-comment">#Test the iterator,</tt> </tt>
<a name="L607"></a><tt class="py-lineno">607</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt id="link-442" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-442', 'handle', 'link-35');">handle</a></tt> <tt class="py-op">=</tt> <tt id="link-443" class="py-name" targets="Function Bio.Mindy.FlatDB.open()=Bio.Mindy.FlatDB-module.html#open,Function Bio.Mindy.open()=Bio.Mindy-module.html#open"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-443', 'open', 'link-443');">open</a></tt><tt class="py-op">(</tt><tt class="py-string">"../../Tests/Ace/contig1.ace"</tt><tt class="py-op">)</tt> </tt>
<a name="L608"></a><tt class="py-lineno">608</tt>  <tt class="py-line">    <tt class="py-name">recordparser</tt> <tt class="py-op">=</tt> <tt id="link-444" class="py-name"><a title="Bio.CDD.RecordParser
Bio.Compass.RecordParser
Bio.ECell.RecordParser
Bio.Enzyme.RecordParser
Bio.Fasta.RecordParser
Bio.GenBank.RecordParser
Bio.Gobase.RecordParser
Bio.IntelliGenetics.RecordParser
Bio.LocusLink.RecordParser
Bio.Medline.RecordParser
Bio.MetaTool.RecordParser
Bio.NBRF.RecordParser
Bio.PopGen.FDist.RecordParser
Bio.PopGen.GenePop.RecordParser
Bio.Prosite.Prodoc.RecordParser
Bio.Prosite.RecordParser
Bio.Rebase.RecordParser
Bio.Saf.RecordParser
Bio.Sequencing.Ace.RecordParser
Bio.Sequencing.Phd.RecordParser
Bio.SwissProt.SProt.RecordParser
Bio.UniGene.RecordParser
Martel.Parser.RecordParser" class="py-name" href="#" onclick="return doclink('link-444', 'RecordParser', 'link-146');">RecordParser</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L609"></a><tt class="py-lineno">609</tt>  <tt class="py-line">    <tt class="py-name">iterator</tt> <tt class="py-op">=</tt> <tt id="link-445" class="py-name"><a title="Bio.Blast.NCBIStandalone.Iterator
Bio.CDD.Iterator
Bio.Compass.Iterator
Bio.ECell.Iterator
Bio.Enzyme.Iterator
Bio.Fasta.Iterator
Bio.GenBank.Iterator
Bio.Gobase.Iterator
Bio.IntelliGenetics.Iterator
Bio.LocusLink.Iterator
Bio.Medline.Iterator
Bio.MetaTool.Iterator
Bio.NBRF.Iterator
Bio.Prosite.Iterator
Bio.Prosite.Prodoc.Iterator
Bio.Rebase.Iterator
Bio.SCOP.Cla.Iterator
Bio.SCOP.Des.Iterator
Bio.SCOP.Dom.Iterator
Bio.SCOP.Hie.Iterator
Bio.SCOP.Raf.Iterator
Bio.Saf.Iterator
Bio.Sequencing.Ace.Iterator
Bio.Sequencing.Phd.Iterator
Bio.SwissProt.SProt.Iterator
Bio.UniGene.Iterator
Martel.Iterator
Martel.Iterator.Iterator" class="py-name" href="#" onclick="return doclink('link-445', 'Iterator', 'link-147');">Iterator</a></tt><tt class="py-op">(</tt><tt id="link-446" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-446', 'handle', 'link-35');">handle</a></tt><tt class="py-op">,</tt><tt class="py-name">recordparser</tt><tt class="py-op">)</tt> </tt>
<a name="L610"></a><tt class="py-lineno">610</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">contig</tt> <tt class="py-keyword">in</tt> <tt class="py-name">iterator</tt> <tt class="py-op">:</tt> </tt>
<a name="L611"></a><tt class="py-lineno">611</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-name">contig</tt><tt class="py-op">.</tt><tt id="link-447" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-447', 'name', 'link-7');">name</a></tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">contig</tt><tt class="py-op">.</tt><tt id="link-448" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-448', 'sequence', 'link-8');">sequence</a></tt><tt class="py-op">)</tt> </tt>
<a name="L612"></a><tt class="py-lineno">612</tt>  <tt class="py-line">    <tt id="link-449" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-449', 'handle', 'link-35');">handle</a></tt><tt class="py-op">.</tt><tt id="link-450" class="py-name" targets="Method Bio.FilteredReader.FilteredReader.close()=Bio.FilteredReader.FilteredReader-class.html#close,Method Bio.Mindy.BerkeleyDB.BerkeleyDB.close()=Bio.Mindy.BerkeleyDB.BerkeleyDB-class.html#close,Method Bio.Mindy.FlatDB.MemoryFlatDB.close()=Bio.Mindy.FlatDB.MemoryFlatDB-class.html#close,Method BioSQL.BioSeqDatabase.Adaptor.close()=BioSQL.BioSeqDatabase.Adaptor-class.html#close,Method Martel.Parser.Parser.close()=Martel.Parser.Parser-class.html#close,Method Martel.Parser.RecordParser.close()=Martel.Parser.RecordParser-class.html#close"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-450', 'close', 'link-450');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L613"></a><tt class="py-lineno">613</tt>  <tt class="py-line">    <tt class="py-keyword">print</tt> <tt class="py-string">"Done"</tt> </tt>
<a name="L614"></a><tt class="py-lineno">614</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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