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Package UniGene
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<h1 class="epydoc">Source Code for <a href="Bio.UniGene-module.html">Package Bio.UniGene</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright 2006 by Sean Davis. All rights reserved.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-comment"># $Id: __init__.py,v 1.12 2009-04-24 12:03:45 mdehoon Exp $</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-comment"># Sean Davis <sdavis2 at mail dot nih dot gov></tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-comment"># National Cancer Institute</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-comment"># National Institutes of Health</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-comment"># Bethesda, MD, USA</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring">"""Parse Unigene flat file format files such as the Hs.data file.</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring">Here is an overview of the flat file format that this parser deals with:</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring"> Line types/qualifiers:</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring"> ID UniGene cluster ID</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-docstring"> TITLE Title for the cluster</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring"> GENE Gene symbol</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-docstring"> CYTOBAND Cytological band</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-docstring"> EXPRESS Tissues of origin for ESTs in cluster</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring"> RESTR_EXPR Single tissue or development stage contributes </tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring"> more than half the total EST frequency for this gene.</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring"> GNM_TERMINUS genomic confirmation of presence of a 3' terminus; </tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring"> T if a non-templated polyA tail is found among </tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring"> a cluster's sequences; else</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-docstring"> I if templated As are found in genomic sequence or</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-docstring"> S if a canonical polyA signal is found on </tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring"> the genomic sequence</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-docstring"> GENE_ID Entrez gene identifier associated with at least one</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-docstring"> sequence in this cluster; </tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-docstring"> to be used instead of LocusLink. </tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-docstring"> LOCUSLINK LocusLink identifier associated with at least one</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-docstring"> sequence in this cluster; </tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-docstring"> deprecated in favor of GENE_ID</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-docstring"> HOMOL Homology;</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-docstring"> CHROMOSOME Chromosome. For plants, CHROMOSOME refers to mapping</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-docstring"> on the arabidopsis genome.</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-docstring"> STS STS</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"><tt class="py-docstring"> ACC= GenBank/EMBL/DDBJ accession number of STS</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-docstring"> [optional field]</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt class="py-docstring"> UNISTS= identifier in NCBI's UNISTS database</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-docstring"> TXMAP Transcript map interval</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-docstring"> MARKER= Marker found on at least one sequence in this</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-docstring"> cluster</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-docstring"> RHPANEL= Radiation Hybrid panel used to place marker</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"><tt class="py-docstring"> PROTSIM Protein Similarity data for the sequence with</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-docstring"> highest-scoring protein similarity in this cluster</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-docstring"> ORG= Organism</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"><tt class="py-docstring"> PROTGI= Sequence GI of protein</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"><tt class="py-docstring"> PROTID= Sequence ID of protein</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"><tt class="py-docstring"> PCT= Percent alignment</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"><tt class="py-docstring"> ALN= length of aligned region (aa)</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"><tt class="py-docstring"> SCOUNT Number of sequences in the cluster</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"><tt class="py-docstring"> SEQUENCE Sequence</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"><tt class="py-docstring"> ACC= GenBank/EMBL/DDBJ accession number of sequence</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"><tt class="py-docstring"> NID= Unique nucleotide sequence identifier (gi)</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"><tt class="py-docstring"> PID= Unique protein sequence identifier (used for</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"><tt class="py-docstring"> non-ESTs)</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"><tt class="py-docstring"> CLONE= Clone identifier (used for ESTs only)</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"><tt class="py-docstring"> END= End (5'/3') of clone insert read (used for</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"><tt class="py-docstring"> ESTs only) </tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"><tt class="py-docstring"> LID= Library ID; see Hs.lib.info for library name</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"><tt class="py-docstring"> and tissue</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"><tt class="py-docstring"> MGC= 5' CDS-completeness indicator; if present, the</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"><tt class="py-docstring"> clone associated with this sequence is believed</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"><tt class="py-docstring"> CDS-complete. A value greater than 511 is the gi</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"><tt class="py-docstring"> of the CDS-complete mRNA matched by the EST,</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"><tt class="py-docstring"> otherwise the value is an indicator of the</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"><tt class="py-docstring"> reliability of the test indicating CDS</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"><tt class="py-docstring"> completeness; higher values indicate more</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"><tt class="py-docstring"> reliable CDS-completeness predictions. </tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"><tt class="py-docstring"> SEQTYPE= Description of the nucleotide sequence.</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"><tt class="py-docstring"> Possible values are mRNA, EST and HTC.</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"><tt class="py-docstring"> TRACE= The Trace ID of the EST sequence, as provided by</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"><tt class="py-docstring"> NCBI Trace Archive</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> </tt>
<a name="SequenceLine"></a><div id="SequenceLine-def"><a name="L81"></a><tt class="py-lineno"> 81</tt> <a class="py-toggle" href="#" id="SequenceLine-toggle" onclick="return toggle('SequenceLine');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.UniGene.SequenceLine-class.html">SequenceLine</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SequenceLine-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="SequenceLine-expanded"><a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-docstring">"""Store the information for one SEQUENCE line from a Unigene file</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"><tt class="py-docstring"> Initialize with the text part of the SEQUENCE line, or nothing.</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"><tt class="py-docstring"> Attributes and descriptions (access as LOWER CASE)</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"><tt class="py-docstring"> ACC= GenBank/EMBL/DDBJ accession number of sequence</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"><tt class="py-docstring"> NID= Unique nucleotide sequence identifier (gi)</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"><tt class="py-docstring"> PID= Unique protein sequence identifier (used for non-ESTs)</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"><tt class="py-docstring"> CLONE= Clone identifier (used for ESTs only)</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"><tt class="py-docstring"> END= End (5'/3') of clone insert read (used for ESTs only) </tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"><tt class="py-docstring"> LID= Library ID; see Hs.lib.info for library name and tissue</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"><tt class="py-docstring"> MGC= 5' CDS-completeness indicator; if present, </tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"><tt class="py-docstring"> the clone associated with this sequence </tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"><tt class="py-docstring"> is believed CDS-complete. A value greater than 511</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"><tt class="py-docstring"> is the gi of the CDS-complete mRNA matched by the EST,</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"><tt class="py-docstring"> otherwise the value is an indicator of the reliability</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"><tt class="py-docstring"> of the test indicating CDS completeness;</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"><tt class="py-docstring"> higher values indicate more reliable CDS-completeness</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"><tt class="py-docstring"> predictions. </tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"><tt class="py-docstring"> SEQTYPE= Description of the nucleotide sequence. Possible values</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"><tt class="py-docstring"> are mRNA, EST and HTC.</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"><tt class="py-docstring"> TRACE= The Trace ID of the EST sequence, as provided by NCBI</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"><tt class="py-docstring"> Trace Archive</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> </tt>
<a name="SequenceLine.__init__"></a><div id="SequenceLine.__init__-def"><a name="L107"></a><tt class="py-lineno">107</tt> <a class="py-toggle" href="#" id="SequenceLine.__init__-toggle" onclick="return toggle('SequenceLine.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene.SequenceLine-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">text</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="SequenceLine.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SequenceLine.__init__-expanded"><a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-0" class="py-name" targets="Variable Bio.FSSP.fssp_rec.align.acc=Bio.FSSP.fssp_rec.align-class.html#acc"><a title="Bio.FSSP.fssp_rec.align.acc" class="py-name" href="#" onclick="return doclink('link-0', 'acc', 'link-0');">acc</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.nid()=Bio.GenBank._FeatureConsumer-class.html#nid,Method Bio.GenBank._RecordConsumer.nid()=Bio.GenBank._RecordConsumer-class.html#nid"><a title="Bio.GenBank._FeatureConsumer.nid
Bio.GenBank._RecordConsumer.nid" class="py-name" href="#" onclick="return doclink('link-1', 'nid', 'link-1');">nid</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lid</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.pid()=Bio.GenBank._FeatureConsumer-class.html#pid,Method Bio.GenBank._RecordConsumer.pid()=Bio.GenBank._RecordConsumer-class.html#pid"><a title="Bio.GenBank._FeatureConsumer.pid
Bio.GenBank._RecordConsumer.pid" class="py-name" href="#" onclick="return doclink('link-2', 'pid', 'link-2');">pid</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<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 class="py-name">clone</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">image</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">is_image</tt> <tt class="py-op">=</tt> <tt class="py-name">False</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 id="link-3" class="py-name" targets="Variable Bio.SeqFeature.FeatureLocation.end=Bio.SeqFeature.FeatureLocation-class.html#end"><a title="Bio.SeqFeature.FeatureLocation.end" class="py-name" href="#" onclick="return doclink('link-3', 'end', 'link-3');">end</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</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">mgc</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">seqtype</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Method Bio.Nexus.Nodes.Chain.trace()=Bio.Nexus.Nodes.Chain-class.html#trace,Method Bio.Phylo.BaseTree.TreeMixin.trace()=Bio.Phylo.BaseTree.TreeMixin-class.html#trace"><a title="Bio.Nexus.Nodes.Chain.trace
Bio.Phylo.BaseTree.TreeMixin.trace" class="py-name" href="#" onclick="return doclink('link-4', 'trace', 'link-4');">trace</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">text</tt><tt class="py-op">==</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">text</tt><tt class="py-op">=</tt><tt class="py-name">text</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Method Bio.UniGene.ProtsimLine._init_from_text()=Bio.UniGene.ProtsimLine-class.html#_init_from_text,Method Bio.UniGene.STSLine._init_from_text()=Bio.UniGene.STSLine-class.html#_init_from_text,Method Bio.UniGene.SequenceLine._init_from_text()=Bio.UniGene.SequenceLine-class.html#_init_from_text,Method Bio.UniGene.UnigeneProtsimRecord._init_from_text()=Bio.UniGene.UnigeneProtsimRecord-class.html#_init_from_text,Method Bio.UniGene.UnigeneSTSRecord._init_from_text()=Bio.UniGene.UnigeneSTSRecord-class.html#_init_from_text,Method Bio.UniGene.UnigeneSequenceRecord._init_from_text()=Bio.UniGene.UnigeneSequenceRecord-class.html#_init_from_text"><a title="Bio.UniGene.ProtsimLine._init_from_text
Bio.UniGene.STSLine._init_from_text
Bio.UniGene.SequenceLine._init_from_text
Bio.UniGene.UnigeneProtsimRecord._init_from_text
Bio.UniGene.UnigeneSTSRecord._init_from_text
Bio.UniGene.UnigeneSequenceRecord._init_from_text" class="py-name" href="#" onclick="return doclink('link-5', '_init_from_text', 'link-5');">_init_from_text</a></tt><tt class="py-op">(</tt><tt class="py-name">text</tt><tt class="py-op">)</tt> </tt>
</div><a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> </tt>
<a name="SequenceLine._init_from_text"></a><div id="SequenceLine._init_from_text-def"><a name="L123"></a><tt class="py-lineno">123</tt> <a class="py-toggle" href="#" id="SequenceLine._init_from_text-toggle" onclick="return toggle('SequenceLine._init_from_text');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene.SequenceLine-class.html#_init_from_text">_init_from_text</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">text</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SequenceLine._init_from_text-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SequenceLine._init_from_text-expanded"><a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-name">parts</tt> <tt class="py-op">=</tt> <tt class="py-name">text</tt><tt class="py-op">.</tt><tt id="link-6" class="py-name" targets="Method Bio.Nexus.Trees.Tree.split()=Bio.Nexus.Trees.Tree-class.html#split,Method Bio.Phylo.BaseTree.TreeMixin.split()=Bio.Phylo.BaseTree.TreeMixin-class.html#split,Method Bio.Restriction.Restriction.RestrictionBatch.split()=Bio.Restriction.Restriction.RestrictionBatch-class.html#split,Method Bio.Seq.Seq.split()=Bio.Seq.Seq-class.html#split"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.split" class="py-name" href="#" onclick="return doclink('link-6', 'split', 'link-6');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">'; '</tt><tt class="py-op">)</tt><tt class="py-op">;</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">part</tt> <tt class="py-keyword">in</tt> <tt class="py-name">parts</tt><tt class="py-op">:</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt class="py-name">key</tt><tt class="py-op">,</tt> <tt class="py-name">val</tt> <tt class="py-op">=</tt> <tt class="py-name">part</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.split" class="py-name" href="#" onclick="return doclink('link-7', 'split', 'link-6');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">"="</tt><tt class="py-op">)</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">key</tt><tt class="py-op">==</tt><tt class="py-string">'CLONE'</tt><tt class="py-op">:</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">val</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">5</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-string">'IMAGE'</tt><tt class="py-op">:</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">is_image</tt><tt class="py-op">=</tt><tt class="py-name">True</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">image</tt> <tt class="py-op">=</tt> <tt class="py-name">val</tt><tt class="py-op">[</tt><tt class="py-number">6</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-name">setattr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt><tt class="py-name">key</tt><tt class="py-op">.</tt><tt id="link-8" class="py-name" targets="Method Bio.Seq.Seq.lower()=Bio.Seq.Seq-class.html#lower,Method Bio.Seq.UnknownSeq.lower()=Bio.Seq.UnknownSeq-class.html#lower,Method Bio.SeqRecord.SeqRecord.lower()=Bio.SeqRecord.SeqRecord-class.html#lower"><a title="Bio.Seq.Seq.lower
Bio.Seq.UnknownSeq.lower
Bio.SeqRecord.SeqRecord.lower" class="py-name" href="#" onclick="return doclink('link-8', 'lower', 'link-8');">lower</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">val</tt><tt class="py-op">)</tt> </tt>
</div><a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> </tt>
<a name="SequenceLine.__repr__"></a><div id="SequenceLine.__repr__-def"><a name="L133"></a><tt class="py-lineno">133</tt> <a class="py-toggle" href="#" id="SequenceLine.__repr__-toggle" onclick="return toggle('SequenceLine.__repr__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene.SequenceLine-class.html#__repr__">__repr__</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="SequenceLine.__repr__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SequenceLine.__repr__-expanded"><a name="L134"></a><tt class="py-lineno">134</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">text</tt> </tt>
</div></div><a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> </tt>
<a name="ProtsimLine"></a><div id="ProtsimLine-def"><a name="L137"></a><tt class="py-lineno">137</tt> <a class="py-toggle" href="#" id="ProtsimLine-toggle" onclick="return toggle('ProtsimLine');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.UniGene.ProtsimLine-class.html">ProtsimLine</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ProtsimLine-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="ProtsimLine-expanded"><a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-docstring">"""Store the information for one PROTSIM line from a Unigene file</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"><tt class="py-docstring"> Initialize with the text part of the PROTSIM line, or nothing.</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"><tt class="py-docstring"> Attributes and descriptions (access as LOWER CASE)</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"><tt class="py-docstring"> ORG= Organism</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"><tt class="py-docstring"> PROTGI= Sequence GI of protein</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"><tt class="py-docstring"> PROTID= Sequence ID of protein</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"><tt class="py-docstring"> PCT= Percent alignment</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"><tt class="py-docstring"> ALN= length of aligned region (aa)</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> </tt>
<a name="ProtsimLine.__init__"></a><div id="ProtsimLine.__init__-def"><a name="L150"></a><tt class="py-lineno">150</tt> <a class="py-toggle" href="#" id="ProtsimLine.__init__-toggle" onclick="return toggle('ProtsimLine.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene.ProtsimLine-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">text</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="ProtsimLine.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ProtsimLine.__init__-expanded"><a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">org</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">protgi</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">protid</tt> <tt class="py-op">=</tt> <tt class="py-string">''</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 class="py-name">pct</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">aln</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">text</tt><tt class="py-op">==</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">text</tt><tt class="py-op">=</tt><tt class="py-name">text</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name"><a title="Bio.UniGene.ProtsimLine._init_from_text
Bio.UniGene.STSLine._init_from_text
Bio.UniGene.SequenceLine._init_from_text
Bio.UniGene.UnigeneProtsimRecord._init_from_text
Bio.UniGene.UnigeneSTSRecord._init_from_text
Bio.UniGene.UnigeneSequenceRecord._init_from_text" class="py-name" href="#" onclick="return doclink('link-9', '_init_from_text', 'link-5');">_init_from_text</a></tt><tt class="py-op">(</tt><tt class="py-name">text</tt><tt class="py-op">)</tt> </tt>
</div><a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> </tt>
<a name="ProtsimLine._init_from_text"></a><div id="ProtsimLine._init_from_text-def"><a name="L160"></a><tt class="py-lineno">160</tt> <a class="py-toggle" href="#" id="ProtsimLine._init_from_text-toggle" onclick="return toggle('ProtsimLine._init_from_text');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene.ProtsimLine-class.html#_init_from_text">_init_from_text</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">text</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ProtsimLine._init_from_text-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ProtsimLine._init_from_text-expanded"><a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-name">parts</tt> <tt class="py-op">=</tt> <tt class="py-name">text</tt><tt class="py-op">.</tt><tt id="link-10" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.split" class="py-name" href="#" onclick="return doclink('link-10', 'split', 'link-6');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">'; '</tt><tt class="py-op">)</tt><tt class="py-op">;</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">part</tt> <tt class="py-keyword">in</tt> <tt class="py-name">parts</tt><tt class="py-op">:</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-name">key</tt><tt class="py-op">,</tt> <tt class="py-name">val</tt> <tt class="py-op">=</tt> <tt class="py-name">part</tt><tt class="py-op">.</tt><tt id="link-11" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.split" class="py-name" href="#" onclick="return doclink('link-11', 'split', 'link-6');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">"="</tt><tt class="py-op">)</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-name">setattr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt><tt class="py-name">key</tt><tt class="py-op">.</tt><tt id="link-12" class="py-name"><a title="Bio.Seq.Seq.lower
Bio.Seq.UnknownSeq.lower
Bio.SeqRecord.SeqRecord.lower" class="py-name" href="#" onclick="return doclink('link-12', 'lower', 'link-8');">lower</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">val</tt><tt class="py-op">)</tt> </tt>
</div><a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> </tt>
<a name="ProtsimLine.__repr__"></a><div id="ProtsimLine.__repr__-def"><a name="L167"></a><tt class="py-lineno">167</tt> <a class="py-toggle" href="#" id="ProtsimLine.__repr__-toggle" onclick="return toggle('ProtsimLine.__repr__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene.ProtsimLine-class.html#__repr__">__repr__</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="ProtsimLine.__repr__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ProtsimLine.__repr__-expanded"><a name="L168"></a><tt class="py-lineno">168</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">text</tt> </tt>
</div></div><a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> </tt>
<a name="STSLine"></a><div id="STSLine-def"><a name="L171"></a><tt class="py-lineno">171</tt> <a class="py-toggle" href="#" id="STSLine-toggle" onclick="return toggle('STSLine');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.UniGene.STSLine-class.html">STSLine</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="STSLine-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="STSLine-expanded"><a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt class="py-docstring">"""Store the information for one STS line from a Unigene file</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"><tt class="py-docstring"> Initialize with the text part of the STS line, or nothing.</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"><tt class="py-docstring"> Attributes and descriptions (access as LOWER CASE)</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"><tt class="py-docstring"> ACC= GenBank/EMBL/DDBJ accession number of STS [optional field]</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"><tt class="py-docstring"> UNISTS= identifier in NCBI's UNISTS database</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> </tt>
<a name="STSLine.__init__"></a><div id="STSLine.__init__-def"><a name="L182"></a><tt class="py-lineno">182</tt> <a class="py-toggle" href="#" id="STSLine.__init__-toggle" onclick="return toggle('STSLine.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene.STSLine-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">text</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="STSLine.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="STSLine.__init__-expanded"><a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-13" class="py-name"><a title="Bio.FSSP.fssp_rec.align.acc" class="py-name" href="#" onclick="return doclink('link-13', 'acc', 'link-0');">acc</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">unists</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">text</tt><tt class="py-op">==</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">text</tt><tt class="py-op">=</tt><tt class="py-name">text</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 id="link-14" class="py-name"><a title="Bio.UniGene.ProtsimLine._init_from_text
Bio.UniGene.STSLine._init_from_text
Bio.UniGene.SequenceLine._init_from_text
Bio.UniGene.UnigeneProtsimRecord._init_from_text
Bio.UniGene.UnigeneSTSRecord._init_from_text
Bio.UniGene.UnigeneSequenceRecord._init_from_text" class="py-name" href="#" onclick="return doclink('link-14', '_init_from_text', 'link-5');">_init_from_text</a></tt><tt class="py-op">(</tt><tt class="py-name">text</tt><tt class="py-op">)</tt> </tt>
</div><a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> </tt>
<a name="STSLine._init_from_text"></a><div id="STSLine._init_from_text-def"><a name="L189"></a><tt class="py-lineno">189</tt> <a class="py-toggle" href="#" id="STSLine._init_from_text-toggle" onclick="return toggle('STSLine._init_from_text');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene.STSLine-class.html#_init_from_text">_init_from_text</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">text</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="STSLine._init_from_text-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="STSLine._init_from_text-expanded"><a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt class="py-name">parts</tt> <tt class="py-op">=</tt> <tt class="py-name">text</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.split" class="py-name" href="#" onclick="return doclink('link-15', 'split', 'link-6');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">' '</tt><tt class="py-op">)</tt><tt class="py-op">;</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">part</tt> <tt class="py-keyword">in</tt> <tt class="py-name">parts</tt><tt class="py-op">:</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-name">key</tt><tt class="py-op">,</tt> <tt class="py-name">val</tt> <tt class="py-op">=</tt> <tt class="py-name">part</tt><tt class="py-op">.</tt><tt id="link-16" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.split" class="py-name" href="#" onclick="return doclink('link-16', 'split', 'link-6');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">"="</tt><tt class="py-op">)</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt class="py-name">setattr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt><tt class="py-name">key</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name"><a title="Bio.Seq.Seq.lower
Bio.Seq.UnknownSeq.lower
Bio.SeqRecord.SeqRecord.lower" class="py-name" href="#" onclick="return doclink('link-17', 'lower', 'link-8');">lower</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">val</tt><tt class="py-op">)</tt> </tt>
</div><a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> </tt>
<a name="STSLine.__repr__"></a><div id="STSLine.__repr__-def"><a name="L196"></a><tt class="py-lineno">196</tt> <a class="py-toggle" href="#" id="STSLine.__repr__-toggle" onclick="return toggle('STSLine.__repr__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene.STSLine-class.html#__repr__">__repr__</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="STSLine.__repr__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="STSLine.__repr__-expanded"><a name="L197"></a><tt class="py-lineno">197</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">text</tt> </tt>
</div></div><a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> </tt>
<a name="Record"></a><div id="Record-def"><a name="L200"></a><tt class="py-lineno">200</tt> <a class="py-toggle" href="#" id="Record-toggle" onclick="return toggle('Record');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.UniGene.Record-class.html">Record</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Record-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Record-expanded"><a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-docstring">"""Store a Unigene record</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"><tt class="py-docstring"> Here is what is stored:</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"><tt class="py-docstring"> self.ID = '' # ID line</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"><tt class="py-docstring"> self.species = '' # Hs, Bt, etc.</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"><tt class="py-docstring"> self.title = '' # TITLE line</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"><tt class="py-docstring"> self.symbol = '' # GENE line</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"><tt class="py-docstring"> self.cytoband = '' # CYTOBAND line</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"><tt class="py-docstring"> self.express = [] # EXPRESS line, parsed on ';'</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"><tt class="py-docstring"> # Will be an array of strings</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"><tt class="py-docstring"> self.restr_expr = '' # RESTR_EXPR line</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"><tt class="py-docstring"> self.gnm_terminus = '' # GNM_TERMINUS line</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"><tt class="py-docstring"> self.gene_id = '' # GENE_ID line</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"><tt class="py-docstring"> self.locuslink = '' # LOCUSLINK line</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"><tt class="py-docstring"> self.homol = '' # HOMOL line</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"><tt class="py-docstring"> self.chromosome = '' # CHROMOSOME line</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"><tt class="py-docstring"> self.protsim = [] # PROTSIM entries, array of Protsims</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"><tt class="py-docstring"> # Type ProtsimLine</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"><tt class="py-docstring"> self.sequence = [] # SEQUENCE entries, array of Sequence entries</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"><tt class="py-docstring"> # Type SequenceLine</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"><tt class="py-docstring"> self.sts = [] # STS entries, array of STS entries</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"><tt class="py-docstring"> # Type STSLine</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"><tt class="py-docstring"> self.txmap = [] # TXMAP entries, array of TXMap entries</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> </tt>
<a name="Record.__init__"></a><div id="Record.__init__-def"><a name="L227"></a><tt class="py-lineno">227</tt> <a class="py-toggle" href="#" id="Record.__init__-toggle" onclick="return toggle('Record.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene.Record-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="Record.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Record.__init__-expanded"><a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name" targets="Method Bio.UniGene._RecordConsumer.ID()=Bio.UniGene._RecordConsumer-class.html#ID"><a title="Bio.UniGene._RecordConsumer.ID" class="py-name" href="#" onclick="return doclink('link-18', 'ID', 'link-18');">ID</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> <tt class="py-comment"># ID line</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name" targets="Method Bio.Pathway.Network.species()=Bio.Pathway.Network-class.html#species,Method Bio.Pathway.Reaction.species()=Bio.Pathway.Reaction-class.html#species,Method Bio.Pathway.System.species()=Bio.Pathway.System-class.html#species"><a title="Bio.Pathway.Network.species
Bio.Pathway.Reaction.species
Bio.Pathway.System.species" class="py-name" href="#" onclick="return doclink('link-19', 'species', 'link-19');">species</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> <tt class="py-comment"># Hs, Bt, etc.</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name" targets="Method Bio.Blast.NCBIStandalone._AlignmentConsumer.title()=Bio.Blast.NCBIStandalone._AlignmentConsumer-class.html#title,Method Bio.GenBank._FeatureConsumer.title()=Bio.GenBank._FeatureConsumer-class.html#title,Method Bio.GenBank._RecordConsumer.title()=Bio.GenBank._RecordConsumer-class.html#title"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title" class="py-name" href="#" onclick="return doclink('link-20', 'title', 'link-20');">title</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> <tt class="py-comment"># TITLE line</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 id="link-21" class="py-name" targets="Method Bio.Phylo.PhyloXMLIO.Writer.symbol()=Bio.Phylo.PhyloXMLIO.Writer-class.html#symbol"><a title="Bio.Phylo.PhyloXMLIO.Writer.symbol" class="py-name" href="#" onclick="return doclink('link-21', 'symbol', 'link-21');">symbol</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> <tt class="py-comment"># GENE line</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">cytoband</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> <tt class="py-comment"># CYTOBAND line</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">express</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> <tt class="py-comment"># EXPRESS line, parsed on ';'</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">restr_expr</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> <tt class="py-comment"># RESTR_EXPR line</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">gnm_terminus</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> <tt class="py-comment"># GNM_TERMINUS line</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">gene_id</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> <tt class="py-comment"># GENE_ID line</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">locuslink</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> <tt class="py-comment"># LOCUSLINK line</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">homol</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> <tt class="py-comment"># HOMOL line</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">chromosome</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> <tt class="py-comment"># CHROMOSOME line</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">protsim</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> <tt class="py-comment"># PROTSIM entries, array of Protsims</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name" targets="Method Bio.FSSP.FSSPAlignDict.sequence()=Bio.FSSP.FSSPAlignDict-class.html#sequence,Method Bio.GenBank._FeatureConsumer.sequence()=Bio.GenBank._FeatureConsumer-class.html#sequence,Method Bio.GenBank._RecordConsumer.sequence()=Bio.GenBank._RecordConsumer-class.html#sequence,Method Bio.Phylo.PhyloXMLIO.Writer.sequence()=Bio.Phylo.PhyloXMLIO.Writer-class.html#sequence"><a title="Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.Phylo.PhyloXMLIO.Writer.sequence" class="py-name" href="#" onclick="return doclink('link-22', 'sequence', 'link-22');">sequence</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> <tt class="py-comment"># SEQUENCE entries, array of Sequence entries</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sts</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> <tt class="py-comment"># STS entries, array of STS entries</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">txmap</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> <tt class="py-comment"># TXMAP entries, array of TXMap entries</tt> </tt>
</div><a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> </tt>
<a name="Record.__repr__"></a><div id="Record.__repr__-def"><a name="L245"></a><tt class="py-lineno">245</tt> <a class="py-toggle" href="#" id="Record.__repr__-toggle" onclick="return toggle('Record.__repr__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene.Record-class.html#__repr__">__repr__</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="Record.__repr__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Record.__repr__-expanded"><a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"<%s> %s %s\n%s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__class__</tt><tt class="py-op">.</tt><tt class="py-name">__name__</tt><tt class="py-op">,</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 id="link-23" class="py-name"><a title="Bio.UniGene._RecordConsumer.ID" class="py-name" href="#" onclick="return doclink('link-23', 'ID', 'link-18');">ID</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-24" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.symbol" class="py-name" href="#" onclick="return doclink('link-24', 'symbol', 'link-21');">symbol</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-25" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title" class="py-name" href="#" onclick="return doclink('link-25', 'title', 'link-20');">title</a></tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> </tt>
<a name="parse"></a><div id="parse-def"><a name="L249"></a><tt class="py-lineno">249</tt> <a class="py-toggle" href="#" id="parse-toggle" onclick="return toggle('parse');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene-module.html#parse">parse</a><tt class="py-op">(</tt><tt class="py-param">handle</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="parse-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="parse-expanded"><a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-name">True</tt><tt class="py-op">:</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"> <tt class="py-name">record</tt> <tt class="py-op">=</tt> <tt id="link-26" class="py-name" targets="Method Bio.Motif._Motif.Motif._read()=Bio.Motif._Motif.Motif-class.html#_read,Function Bio.SwissProt._read()=Bio.SwissProt-module.html#_read,Function Bio.UniGene._read()=Bio.UniGene-module.html#_read"><a title="Bio.Motif._Motif.Motif._read
Bio.SwissProt._read
Bio.UniGene._read" class="py-name" href="#" onclick="return doclink('link-26', '_read', 'link-26');">_read</a></tt><tt class="py-op">(</tt><tt id="link-27" class="py-name" targets="Variable Bio.UniGene.UniGene.handle=Bio.UniGene.UniGene-module.html#handle"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-27', 'handle', 'link-27');">handle</a></tt><tt class="py-op">)</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">record</tt><tt class="py-op">:</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-name">record</tt> </tt>
</div><a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> </tt>
<a name="read"></a><div id="read-def"><a name="L257"></a><tt class="py-lineno">257</tt> <a class="py-toggle" href="#" id="read-toggle" onclick="return toggle('read');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene-module.html#read">read</a><tt class="py-op">(</tt><tt class="py-param">handle</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="read-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="read-expanded"><a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> <tt class="py-name">record</tt> <tt class="py-op">=</tt> <tt id="link-28" class="py-name"><a title="Bio.Motif._Motif.Motif._read
Bio.SwissProt._read
Bio.UniGene._read" class="py-name" href="#" onclick="return doclink('link-28', '_read', 'link-26');">_read</a></tt><tt class="py-op">(</tt><tt id="link-29" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-29', 'handle', 'link-27');">handle</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-keyword">not</tt> <tt class="py-name">record</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">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"No SwissProt record found"</tt><tt class="py-op">)</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> <tt class="py-comment"># We should have reached the end of the record by now</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> <tt id="link-30" class="py-name" targets="Variable Bio.Affy.CelFile.remainder=Bio.Affy.CelFile-module.html#remainder"><a title="Bio.Affy.CelFile.remainder" class="py-name" href="#" onclick="return doclink('link-30', 'remainder', 'link-30');">remainder</a></tt> <tt class="py-op">=</tt> <tt id="link-31" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-31', 'handle', 'link-27');">handle</a></tt><tt class="py-op">.</tt><tt id="link-32" class="py-name" targets="Function Bio.Affy.CelFile.read()=Bio.Affy.CelFile-module.html#read,Function Bio.AlignIO.read()=Bio.AlignIO-module.html#read,Function Bio.Blast.NCBIXML.read()=Bio.Blast.NCBIXML-module.html#read,Function Bio.Cluster.read()=Bio.Cluster-module.html#read,Function Bio.Compass.read()=Bio.Compass-module.html#read,Function Bio.Emboss.Primer3.read()=Bio.Emboss.Primer3-module.html#read,Function Bio.Emboss.PrimerSearch.read()=Bio.Emboss.PrimerSearch-module.html#read,Method Bio.Entrez.Parser.DataHandler.read()=Bio.Entrez.Parser.DataHandler-class.html#read,Function Bio.Entrez.read()=Bio.Entrez-module.html#read,Function Bio.ExPASy.Enzyme.read()=Bio.ExPASy.Enzyme-module.html#read,Function Bio.ExPASy.Prodoc.read()=Bio.ExPASy.Prodoc-module.html#read,Function Bio.ExPASy.Prosite.read()=Bio.ExPASy.Prosite-module.html#read,Function Bio.ExPASy.ScanProsite.read()=Bio.ExPASy.ScanProsite-module.html#read,Method Bio.File.UndoHandle.read()=Bio.File.UndoHandle-class.html#read,Function Bio.Medline.read()=Bio.Medline-module.html#read,Function Bio.Motif.Parsers.AlignAce.read()=Bio.Motif.Parsers.AlignAce-module.html#read,Function Bio.Motif.Parsers.MAST.read()=Bio.Motif.Parsers.MAST-module.html#read,Function Bio.Motif.Parsers.MEME.read()=Bio.Motif.Parsers.MEME-module.html#read,Function Bio.Motif.read()=Bio.Motif-module.html#read,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.read()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#read,Method Bio.Nexus.Nexus.Nexus.read()=Bio.Nexus.Nexus.Nexus-class.html#read,Function Bio.Phylo.PAML.baseml.read()=Bio.Phylo.PAML.baseml-module.html#read,Function Bio.Phylo.PAML.codeml.read()=Bio.Phylo.PAML.codeml-module.html#read,Function Bio.Phylo.PAML.yn00.read()=Bio.Phylo.PAML.yn00-module.html#read,Method Bio.Phylo.PhyloXMLIO.Parser.read()=Bio.Phylo.PhyloXMLIO.Parser-class.html#read,Function Bio.Phylo.PhyloXMLIO.read()=Bio.Phylo.PhyloXMLIO-module.html#read,Function Bio.Phylo._io.read()=Bio.Phylo._io-module.html#read,Function Bio.PopGen.GenePop.FileParser.read()=Bio.PopGen.GenePop.FileParser-module.html#read,Function Bio.PopGen.GenePop.LargeFileParser.read()=Bio.PopGen.GenePop.LargeFileParser-module.html#read,Function Bio.PopGen.GenePop.read()=Bio.PopGen.GenePop-module.html#read,Method Bio.SeqIO.SffIO._AddTellHandle.read()=Bio.SeqIO.SffIO._AddTellHandle-class.html#read,Function Bio.SeqIO.read()=Bio.SeqIO-module.html#read,Function Bio.Sequencing.Ace.read()=Bio.Sequencing.Ace-module.html#read,Function Bio.Sequencing.Phd.read()=Bio.Sequencing.Phd-module.html#read,Function Bio.SwissProt.read()=Bio.SwissProt-module.html#read,Function Bio.UniGene.read()=Bio.UniGene-module.html#read"><a title="Bio.Affy.CelFile.read
Bio.AlignIO.read
Bio.Blast.NCBIXML.read
Bio.Cluster.read
Bio.Compass.read
Bio.Emboss.Primer3.read
Bio.Emboss.PrimerSearch.read
Bio.Entrez.Parser.DataHandler.read
Bio.Entrez.read
Bio.ExPASy.Enzyme.read
Bio.ExPASy.Prodoc.read
Bio.ExPASy.Prosite.read
Bio.ExPASy.ScanProsite.read
Bio.File.UndoHandle.read
Bio.Medline.read
Bio.Motif.Parsers.AlignAce.read
Bio.Motif.Parsers.MAST.read
Bio.Motif.Parsers.MEME.read
Bio.Motif.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Phylo.PAML.baseml.read
Bio.Phylo.PAML.codeml.read
Bio.Phylo.PAML.yn00.read
Bio.Phylo.PhyloXMLIO.Parser.read
Bio.Phylo.PhyloXMLIO.read
Bio.Phylo._io.read
Bio.PopGen.GenePop.FileParser.read
Bio.PopGen.GenePop.LargeFileParser.read
Bio.PopGen.GenePop.read
Bio.SeqIO.SffIO._AddTellHandle.read
Bio.SeqIO.read
Bio.Sequencing.Ace.read
Bio.Sequencing.Phd.read
Bio.SwissProt.read
Bio.UniGene.read" class="py-name" href="#" onclick="return doclink('link-32', 'read', 'link-32');">read</a></tt><tt class="py-op">(</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 id="link-33" class="py-name"><a title="Bio.Affy.CelFile.remainder" class="py-name" href="#" onclick="return doclink('link-33', 'remainder', 'link-30');">remainder</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-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"More than one SwissProt record found"</tt><tt class="py-op">)</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">record</tt> </tt>
</div><a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"><tt class="py-comment"># Everything below is private</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"> </tt>
<a name="_read"></a><div id="_read-def"><a name="L271"></a><tt class="py-lineno">271</tt> <a class="py-toggle" href="#" id="_read-toggle" onclick="return toggle('_read');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene-module.html#_read">_read</a><tt class="py-op">(</tt><tt class="py-param">handle</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_read-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_read-expanded"><a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> <tt id="link-34" class="py-name" targets="Variable Bio.UniGene.UG_INDENT=Bio.UniGene-module.html#UG_INDENT"><a title="Bio.UniGene.UG_INDENT" class="py-name" href="#" onclick="return doclink('link-34', 'UG_INDENT', 'link-34');">UG_INDENT</a></tt> <tt class="py-op">=</tt> <tt class="py-number">12</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> <tt class="py-name">record</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt id="link-35" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-35', 'handle', 'link-27');">handle</a></tt><tt class="py-op">:</tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"> <tt class="py-name">tag</tt><tt class="py-op">,</tt> <tt id="link-36" class="py-name" targets="Method Bio.Phylo.PhyloXMLIO.Writer.value()=Bio.Phylo.PhyloXMLIO.Writer-class.html#value"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-36', 'value', 'link-36');">value</a></tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt id="link-37" class="py-name"><a title="Bio.UniGene.UG_INDENT" class="py-name" href="#" onclick="return doclink('link-37', 'UG_INDENT', 'link-34');">UG_INDENT</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-38" class="py-name" targets="Method Bio.Seq.Seq.rstrip()=Bio.Seq.Seq-class.html#rstrip"><a title="Bio.Seq.Seq.rstrip" class="py-name" href="#" onclick="return doclink('link-38', 'rstrip', 'link-38');">rstrip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt id="link-39" class="py-name"><a title="Bio.UniGene.UG_INDENT" class="py-name" href="#" onclick="return doclink('link-39', 'UG_INDENT', 'link-34');">UG_INDENT</a></tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-40" class="py-name"><a title="Bio.Seq.Seq.rstrip" class="py-name" href="#" onclick="return doclink('link-40', 'rstrip', 'link-38');">rstrip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-41" class="py-name"><a title="Bio.Seq.Seq.rstrip" class="py-name" href="#" onclick="return doclink('link-41', 'rstrip', 'link-38');">rstrip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">tag</tt><tt class="py-op">==</tt><tt class="py-string">"ID"</tt><tt class="py-op">:</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> <tt class="py-name">record</tt> <tt class="py-op">=</tt> <tt id="link-42" class="py-name" targets="Class Bio.Affy.CelFile.Record=Bio.Affy.CelFile.Record-class.html,Module Bio.Blast.Record=Bio.Blast.Record-module.html,Class Bio.Cluster.Record=Bio.Cluster.Record-class.html,Class Bio.Compass.Record=Bio.Compass.Record-class.html,Class Bio.Emboss.Primer3.Record=Bio.Emboss.Primer3.Record-class.html,Class Bio.ExPASy.Enzyme.Record=Bio.ExPASy.Enzyme.Record-class.html,Class Bio.ExPASy.Prodoc.Record=Bio.ExPASy.Prodoc.Record-class.html,Class Bio.ExPASy.Prosite.Record=Bio.ExPASy.Prosite.Record-class.html,Class Bio.ExPASy.ScanProsite.Record=Bio.ExPASy.ScanProsite.Record-class.html,Module Bio.GenBank.Record=Bio.GenBank.Record-module.html,Class Bio.GenBank.Record.Record=Bio.GenBank.Record.Record-class.html,Module Bio.Geo.Record=Bio.Geo.Record-module.html,Class Bio.Geo.Record.Record=Bio.Geo.Record.Record-class.html,Class Bio.KEGG.Compound.Record=Bio.KEGG.Compound.Record-class.html,Class Bio.KEGG.Enzyme.Record=Bio.KEGG.Enzyme.Record-class.html,Class Bio.Medline.Record=Bio.Medline.Record-class.html,Class Bio.Motif.Parsers.AlignAce.Record=Bio.Motif.Parsers.AlignAce.Record-class.html,Class Bio.Motif.Parsers.MAST.Record=Bio.Motif.Parsers.MAST.Record-class.html,Class Bio.PopGen.FDist.Record=Bio.PopGen.FDist.Record-class.html,Class Bio.PopGen.GenePop.LargeFileParser.Record=Bio.PopGen.GenePop.LargeFileParser.Record-class.html,Class Bio.PopGen.GenePop.Record=Bio.PopGen.GenePop.Record-class.html,Class Bio.SCOP.Cla.Record=Bio.SCOP.Cla.Record-class.html,Class Bio.SCOP.Des.Record=Bio.SCOP.Des.Record-class.html,Class Bio.SCOP.Dom.Record=Bio.SCOP.Dom.Record-class.html,Class Bio.SCOP.Hie.Record=Bio.SCOP.Hie.Record-class.html,Class Bio.Sequencing.Phd.Record=Bio.Sequencing.Phd.Record-class.html,Class Bio.SwissProt.KeyWList.Record=Bio.SwissProt.KeyWList.Record-class.html,Class Bio.SwissProt.Record=Bio.SwissProt.Record-class.html,Class Bio.UniGene.Record=Bio.UniGene.Record-class.html"><a title="Bio.Affy.CelFile.Record
Bio.Blast.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.Emboss.Primer3.Record
Bio.ExPASy.Enzyme.Record
Bio.ExPASy.Prodoc.Record
Bio.ExPASy.Prosite.Record
Bio.ExPASy.ScanProsite.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.Medline.Record
Bio.Motif.Parsers.AlignAce.Record
Bio.Motif.Parsers.MAST.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.LargeFileParser.Record
Bio.PopGen.GenePop.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.Record
Bio.UniGene.Record" class="py-name" href="#" onclick="return doclink('link-42', 'Record', 'link-42');">Record</a></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">record</tt><tt class="py-op">.</tt><tt id="link-43" class="py-name"><a title="Bio.UniGene._RecordConsumer.ID" class="py-name" href="#" onclick="return doclink('link-43', 'ID', 'link-18');">ID</a></tt> <tt class="py-op">=</tt> <tt id="link-44" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-44', 'value', 'link-36');">value</a></tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-45" class="py-name"><a title="Bio.Pathway.Network.species
Bio.Pathway.Reaction.species
Bio.Pathway.System.species" class="py-name" href="#" onclick="return doclink('link-45', 'species', 'link-19');">species</a></tt> <tt class="py-op">=</tt> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-46" class="py-name"><a title="Bio.UniGene._RecordConsumer.ID" class="py-name" href="#" onclick="return doclink('link-46', 'ID', 'link-18');">ID</a></tt><tt class="py-op">.</tt><tt id="link-47" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.split" class="py-name" href="#" onclick="return doclink('link-47', 'split', 'link-6');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">'.'</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</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">elif</tt> <tt class="py-name">tag</tt><tt class="py-op">==</tt><tt class="py-string">"TITLE"</tt><tt class="py-op">:</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-48" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title" class="py-name" href="#" onclick="return doclink('link-48', 'title', 'link-20');">title</a></tt> <tt class="py-op">=</tt> <tt id="link-49" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-49', 'value', 'link-36');">value</a></tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">tag</tt><tt class="py-op">==</tt><tt class="py-string">"GENE"</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">record</tt><tt class="py-op">.</tt><tt id="link-50" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.symbol" class="py-name" href="#" onclick="return doclink('link-50', 'symbol', 'link-21');">symbol</a></tt> <tt class="py-op">=</tt> <tt id="link-51" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-51', 'value', 'link-36');">value</a></tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">tag</tt><tt class="py-op">==</tt><tt class="py-string">"GENE_ID"</tt><tt class="py-op">:</tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt class="py-name">gene_id</tt> <tt class="py-op">=</tt> <tt id="link-52" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-52', 'value', 'link-36');">value</a></tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">tag</tt><tt class="py-op">==</tt><tt class="py-string">"LOCUSLINK"</tt><tt class="py-op">:</tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt class="py-name">locuslink</tt> <tt class="py-op">=</tt> <tt id="link-53" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-53', 'value', 'link-36');">value</a></tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">tag</tt><tt class="py-op">==</tt><tt class="py-string">"HOMOL"</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 id="link-54" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-54', 'value', 'link-36');">value</a></tt><tt class="py-op">==</tt><tt class="py-string">"YES"</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">record</tt><tt class="py-op">.</tt><tt class="py-name">homol</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-55" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-55', 'value', 'link-36');">value</a></tt><tt class="py-op">==</tt><tt class="py-string">"NO"</tt><tt class="py-op">:</tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt class="py-name">homol</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"> <tt class="py-keyword">else</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">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"Cannot parse HOMOL line %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">line</tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">tag</tt><tt class="py-op">==</tt><tt class="py-string">"EXPRESS"</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">record</tt><tt class="py-op">.</tt><tt class="py-name">express</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">word</tt><tt class="py-op">.</tt><tt id="link-56" class="py-name" targets="Method Bio.File.SGMLStripper.strip()=Bio.File.SGMLStripper-class.html#strip,Method Bio.Seq.Seq.strip()=Bio.Seq.Seq-class.html#strip"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-56', 'strip', 'link-56');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">word</tt> <tt class="py-keyword">in</tt> <tt id="link-57" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-57', 'value', 'link-36');">value</a></tt><tt class="py-op">.</tt><tt id="link-58" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.split" class="py-name" href="#" onclick="return doclink('link-58', 'split', 'link-6');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">"|"</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">tag</tt><tt class="py-op">==</tt><tt class="py-string">"RESTR_EXPR"</tt><tt class="py-op">:</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt class="py-name">restr_expr</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">word</tt><tt class="py-op">.</tt><tt id="link-59" class="py-name"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-59', 'strip', 'link-56');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">word</tt> <tt class="py-keyword">in</tt> <tt id="link-60" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-60', 'value', 'link-36');">value</a></tt><tt class="py-op">.</tt><tt id="link-61" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.split" class="py-name" href="#" onclick="return doclink('link-61', 'split', 'link-6');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">"|"</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">tag</tt><tt class="py-op">==</tt><tt class="py-string">"CHROMOSOME"</tt><tt class="py-op">:</tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt class="py-name">chromosome</tt> <tt class="py-op">=</tt> <tt id="link-62" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-62', 'value', 'link-36');">value</a></tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">tag</tt><tt class="py-op">==</tt><tt class="py-string">"CYTOBAND"</tt><tt class="py-op">:</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt class="py-name">cytoband</tt> <tt class="py-op">=</tt> <tt id="link-63" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-63', 'value', 'link-36');">value</a></tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">tag</tt><tt class="py-op">==</tt><tt class="py-string">"PROTSIM"</tt><tt class="py-op">:</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"> <tt class="py-name">protsim</tt> <tt class="py-op">=</tt> <tt id="link-64" class="py-name" targets="Class Bio.UniGene.ProtsimLine=Bio.UniGene.ProtsimLine-class.html"><a title="Bio.UniGene.ProtsimLine" class="py-name" href="#" onclick="return doclink('link-64', 'ProtsimLine', 'link-64');">ProtsimLine</a></tt><tt class="py-op">(</tt><tt id="link-65" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-65', 'value', 'link-36');">value</a></tt><tt class="py-op">)</tt> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt class="py-name">protsim</tt><tt class="py-op">.</tt><tt id="link-66" class="py-name" targets="Method Bio.Align.MultipleSeqAlignment.append()=Bio.Align.MultipleSeqAlignment-class.html#append,Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-class.html#append,Method Bio.SCOP.Raf.SeqMap.append()=Bio.SCOP.Raf.SeqMap-class.html#append,Method Bio.Seq.MutableSeq.append()=Bio.Seq.MutableSeq-class.html#append,Method Bio.Wise.psw.Alignment.append()=Bio.Wise.psw.Alignment-class.html#append,Method Bio.Wise.psw.AlignmentColumn.append()=Bio.Wise.psw.AlignmentColumn-class.html#append"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-66', 'append', 'link-66');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">protsim</tt><tt class="py-op">)</tt> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">tag</tt><tt class="py-op">==</tt><tt class="py-string">"SCOUNT"</tt><tt class="py-op">:</tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"> <tt class="py-name">scount</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-67" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-67', 'value', 'link-36');">value</a></tt><tt class="py-op">)</tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">tag</tt><tt class="py-op">==</tt><tt class="py-string">"SEQUENCE"</tt><tt class="py-op">:</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"> <tt id="link-68" class="py-name"><a title="Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.Phylo.PhyloXMLIO.Writer.sequence" class="py-name" href="#" onclick="return doclink('link-68', 'sequence', 'link-22');">sequence</a></tt> <tt class="py-op">=</tt> <tt id="link-69" class="py-name" targets="Class Bio.UniGene.SequenceLine=Bio.UniGene.SequenceLine-class.html"><a title="Bio.UniGene.SequenceLine" class="py-name" href="#" onclick="return doclink('link-69', 'SequenceLine', 'link-69');">SequenceLine</a></tt><tt class="py-op">(</tt><tt id="link-70" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-70', 'value', 'link-36');">value</a></tt><tt class="py-op">)</tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-71" class="py-name"><a title="Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.Phylo.PhyloXMLIO.Writer.sequence" class="py-name" href="#" onclick="return doclink('link-71', 'sequence', 'link-22');">sequence</a></tt><tt class="py-op">.</tt><tt id="link-72" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-72', 'append', 'link-66');">append</a></tt><tt class="py-op">(</tt><tt id="link-73" class="py-name"><a title="Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.Phylo.PhyloXMLIO.Writer.sequence" class="py-name" href="#" onclick="return doclink('link-73', 'sequence', 'link-22');">sequence</a></tt><tt class="py-op">)</tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">tag</tt><tt class="py-op">==</tt><tt class="py-string">"STS"</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">sts</tt> <tt class="py-op">=</tt> <tt id="link-74" class="py-name" targets="Class Bio.UniGene.STSLine=Bio.UniGene.STSLine-class.html"><a title="Bio.UniGene.STSLine" class="py-name" href="#" onclick="return doclink('link-74', 'STSLine', 'link-74');">STSLine</a></tt><tt class="py-op">(</tt><tt id="link-75" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-75', 'value', 'link-36');">value</a></tt><tt class="py-op">)</tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt class="py-name">sts</tt><tt class="py-op">.</tt><tt id="link-76" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-76', 'append', 'link-66');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">sts</tt><tt class="py-op">)</tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">tag</tt><tt class="py-op">==</tt><tt class="py-string">'//'</tt><tt class="py-op">:</tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</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">record</tt><tt class="py-op">.</tt><tt id="link-77" class="py-name"><a title="Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.Phylo.PhyloXMLIO.Writer.sequence" class="py-name" href="#" onclick="return doclink('link-77', 'sequence', 'link-22');">sequence</a></tt><tt class="py-op">)</tt><tt class="py-op">!=</tt><tt class="py-name">scount</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">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"The number of sequences specified in the record (%d) does not agree with the number of sequences found (%d)"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">scount</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-78" class="py-name"><a title="Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.Phylo.PhyloXMLIO.Writer.sequence" class="py-name" href="#" onclick="return doclink('link-78', 'sequence', 'link-22');">sequence</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">record</tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L320"></a><tt class="py-lineno">320</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"Unknown tag %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">tag</tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">record</tt><tt class="py-op">:</tt> </tt>
<a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Unexpected end of stream."</tt><tt class="py-op">)</tt> </tt>
</div><a name="L323"></a><tt class="py-lineno">323</tt> <tt class="py-line"> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"> </tt>
<a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"><tt class="py-comment"># Everything below is deprecated</tt> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"> </tt>
<a name="L328"></a><tt class="py-lineno">328</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-79" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-79', 'Bio', 'link-79');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-80" class="py-name" targets="Module Bio.ParserSupport=Bio.ParserSupport-module.html"><a title="Bio.ParserSupport" class="py-name" href="#" onclick="return doclink('link-80', 'ParserSupport', 'link-80');">ParserSupport</a></tt> <tt class="py-keyword">import</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">import</tt> <tt class="py-name">re</tt> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-81" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-81', 'Bio', 'link-79');">Bio</a></tt> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"><tt class="py-comment"># CONSTANTS</tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt> <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"><tt id="link-82" class="py-name"><a title="Bio.UniGene.UG_INDENT" class="py-name" href="#" onclick="return doclink('link-82', 'UG_INDENT', 'link-34');">UG_INDENT</a></tt><tt class="py-op">=</tt><tt class="py-number">12</tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"> </tt>
<a name="UnigeneSequenceRecord"></a><div id="UnigeneSequenceRecord-def"><a name="L337"></a><tt class="py-lineno">337</tt> <a class="py-toggle" href="#" id="UnigeneSequenceRecord-toggle" onclick="return toggle('UnigeneSequenceRecord');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.UniGene.UnigeneSequenceRecord-class.html">UnigeneSequenceRecord</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="UnigeneSequenceRecord-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="UnigeneSequenceRecord-expanded"><a name="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"> <tt class="py-docstring">"""Store the information for one SEQUENCE line from a Unigene file</tt> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt> <tt class="py-line"><tt class="py-docstring"> (DEPRECATED).</tt> </tt>
<a name="L340"></a><tt class="py-lineno">340</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt> <tt class="py-line"><tt class="py-docstring"> Initialize with the text part of the SEQUENCE line, or nothing.</tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt> <tt class="py-line"><tt class="py-docstring"> Attributes and descriptions (access as LOWER CASE)</tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt> <tt class="py-line"><tt class="py-docstring"> ACC= GenBank/EMBL/DDBJ accession number of sequence</tt> </tt>
<a name="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"><tt class="py-docstring"> NID= Unique nucleotide sequence identifier (gi)</tt> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt> <tt class="py-line"><tt class="py-docstring"> PID= Unique protein sequence identifier (used for non-ESTs)</tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt> <tt class="py-line"><tt class="py-docstring"> CLONE= Clone identifier (used for ESTs only)</tt> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"><tt class="py-docstring"> END= End (5'/3') of clone insert read (used for ESTs only) </tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt> <tt class="py-line"><tt class="py-docstring"> LID= Library ID; see Hs.lib.info for library name and tissue</tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt> <tt class="py-line"><tt class="py-docstring"> MGC= 5' CDS-completeness indicator; if present, </tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt> <tt class="py-line"><tt class="py-docstring"> the clone associated with this sequence </tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt> <tt class="py-line"><tt class="py-docstring"> is believed CDS-complete. A value greater than 511</tt> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt> <tt class="py-line"><tt class="py-docstring"> is the gi of the CDS-complete mRNA matched by the EST,</tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt> <tt class="py-line"><tt class="py-docstring"> otherwise the value is an indicator of the reliability</tt> </tt>
<a name="L355"></a><tt class="py-lineno">355</tt> <tt class="py-line"><tt class="py-docstring"> of the test indicating CDS comleteness;</tt> </tt>
<a name="L356"></a><tt class="py-lineno">356</tt> <tt class="py-line"><tt class="py-docstring"> higher values indicate more reliable CDS-completeness predictions. </tt> </tt>
<a name="L357"></a><tt class="py-lineno">357</tt> <tt class="py-line"><tt class="py-docstring"> SEQTYPE= Description of the nucleotide sequence. Possible values are</tt> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt> <tt class="py-line"><tt class="py-docstring"> mRNA, EST and HTC.</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt> <tt class="py-line"><tt class="py-docstring"> TRACE= The Trace ID of the EST sequence, as provided by NCBI Trace Archive</tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt> <tt class="py-line"><tt class="py-docstring"> PERIPHERAL= Indicator that the sequence is a suboptimal </tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt> <tt class="py-line"><tt class="py-docstring"> representative of the gene represented by this cluster.</tt> </tt>
<a name="L362"></a><tt class="py-lineno">362</tt> <tt class="py-line"><tt class="py-docstring"> Peripheral sequences are those that are in a cluster</tt> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt> <tt class="py-line"><tt class="py-docstring"> which represents a spliced gene without sharing a</tt> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt> <tt class="py-line"><tt class="py-docstring"> splice junction with any other sequence. In many</tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt> <tt class="py-line"><tt class="py-docstring"> cases, they are unspliced transcripts originating</tt> </tt>
<a name="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"><tt class="py-docstring"> from the gene.</tt> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt> <tt class="py-line"><tt class="py-docstring"> This class is DEPRECATED; please use the read() function in this module</tt> </tt>
<a name="L369"></a><tt class="py-lineno">369</tt> <tt class="py-line"><tt class="py-docstring"> instead.</tt> </tt>
<a name="L370"></a><tt class="py-lineno">370</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L371"></a><tt class="py-lineno">371</tt> <tt class="py-line"> </tt>
<a name="UnigeneSequenceRecord.__init__"></a><div id="UnigeneSequenceRecord.__init__-def"><a name="L372"></a><tt class="py-lineno">372</tt> <a class="py-toggle" href="#" id="UnigeneSequenceRecord.__init__-toggle" onclick="return toggle('UnigeneSequenceRecord.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene.UnigeneSequenceRecord-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">text</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="UnigeneSequenceRecord.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="UnigeneSequenceRecord.__init__-expanded"><a name="L373"></a><tt class="py-lineno">373</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">warnings</tt> </tt>
<a name="L374"></a><tt class="py-lineno">374</tt> <tt class="py-line"> <tt class="py-name">warnings</tt><tt class="py-op">.</tt><tt class="py-name">warn</tt><tt class="py-op">(</tt><tt class="py-string">"Bio.UniGene.UnigeneSequenceRecord is deprecated; please use the read() function in this module instead"</tt><tt class="py-op">,</tt> <tt id="link-83" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-83', 'Bio', 'link-79');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-84" class="py-name" targets="Class Bio.BiopythonDeprecationWarning=Bio.BiopythonDeprecationWarning-class.html"><a title="Bio.BiopythonDeprecationWarning" class="py-name" href="#" onclick="return doclink('link-84', 'BiopythonDeprecationWarning', 'link-84');">BiopythonDeprecationWarning</a></tt><tt class="py-op">)</tt> </tt>
<a name="L375"></a><tt class="py-lineno">375</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-85" class="py-name"><a title="Bio.FSSP.fssp_rec.align.acc" class="py-name" href="#" onclick="return doclink('link-85', 'acc', 'link-0');">acc</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L376"></a><tt class="py-lineno">376</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-86" class="py-name"><a title="Bio.GenBank._FeatureConsumer.nid
Bio.GenBank._RecordConsumer.nid" class="py-name" href="#" onclick="return doclink('link-86', 'nid', 'link-1');">nid</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L377"></a><tt class="py-lineno">377</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lid</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L378"></a><tt class="py-lineno">378</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-87" class="py-name"><a title="Bio.GenBank._FeatureConsumer.pid
Bio.GenBank._RecordConsumer.pid" class="py-name" href="#" onclick="return doclink('link-87', 'pid', 'link-2');">pid</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L379"></a><tt class="py-lineno">379</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">clone</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L380"></a><tt class="py-lineno">380</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">image</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L381"></a><tt class="py-lineno">381</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">is_image</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L382"></a><tt class="py-lineno">382</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-88" class="py-name"><a title="Bio.SeqFeature.FeatureLocation.end" class="py-name" href="#" onclick="return doclink('link-88', 'end', 'link-3');">end</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L383"></a><tt class="py-lineno">383</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mgc</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">seqtype</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L385"></a><tt class="py-lineno">385</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Trace</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L386"></a><tt class="py-lineno">386</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">peripheral</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L387"></a><tt class="py-lineno">387</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">text</tt><tt class="py-op">==</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L388"></a><tt class="py-lineno">388</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">text</tt><tt class="py-op">=</tt><tt class="py-name">text</tt> </tt>
<a name="L389"></a><tt class="py-lineno">389</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-89" class="py-name"><a title="Bio.UniGene.ProtsimLine._init_from_text
Bio.UniGene.STSLine._init_from_text
Bio.UniGene.SequenceLine._init_from_text
Bio.UniGene.UnigeneProtsimRecord._init_from_text
Bio.UniGene.UnigeneSTSRecord._init_from_text
Bio.UniGene.UnigeneSequenceRecord._init_from_text" class="py-name" href="#" onclick="return doclink('link-89', '_init_from_text', 'link-5');">_init_from_text</a></tt><tt class="py-op">(</tt><tt class="py-name">text</tt><tt class="py-op">)</tt> </tt>
</div><a name="L390"></a><tt class="py-lineno">390</tt> <tt class="py-line"> </tt>
<a name="UnigeneSequenceRecord._init_from_text"></a><div id="UnigeneSequenceRecord._init_from_text-def"><a name="L391"></a><tt class="py-lineno">391</tt> <a class="py-toggle" href="#" id="UnigeneSequenceRecord._init_from_text-toggle" onclick="return toggle('UnigeneSequenceRecord._init_from_text');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene.UnigeneSequenceRecord-class.html#_init_from_text">_init_from_text</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">text</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="UnigeneSequenceRecord._init_from_text-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="UnigeneSequenceRecord._init_from_text-expanded"><a name="L392"></a><tt class="py-lineno">392</tt> <tt class="py-line"> <tt class="py-name">parts</tt> <tt class="py-op">=</tt> <tt class="py-name">text</tt><tt class="py-op">.</tt><tt id="link-90" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.split" class="py-name" href="#" onclick="return doclink('link-90', 'split', 'link-6');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">'; '</tt><tt class="py-op">)</tt><tt class="py-op">;</tt> </tt>
<a name="L393"></a><tt class="py-lineno">393</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">part</tt> <tt class="py-keyword">in</tt> <tt class="py-name">parts</tt><tt class="py-op">:</tt> </tt>
<a name="L394"></a><tt class="py-lineno">394</tt> <tt class="py-line"> <tt class="py-name">key</tt><tt class="py-op">,</tt><tt class="py-name">val</tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-91" class="py-name" targets="Method Bio.Parsers.spark.GenericASTMatcher.match()=Bio.Parsers.spark.GenericASTMatcher-class.html#match,Function Bio.triefind.match()=Bio.triefind-module.html#match"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.triefind.match" class="py-name" href="#" onclick="return doclink('link-91', 'match', 'link-91');">match</a></tt><tt class="py-op">(</tt><tt class="py-string">'(\w+)=(\S+)'</tt><tt class="py-op">,</tt><tt class="py-name">part</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">groups</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-keyword">if</tt> <tt class="py-name">key</tt><tt class="py-op">==</tt><tt class="py-string">'CLONE'</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">if</tt> <tt class="py-name">val</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">5</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-string">'IMAGE'</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">self</tt><tt class="py-op">.</tt><tt class="py-name">is_image</tt><tt class="py-op">=</tt><tt class="py-name">True</tt> </tt>
<a name="L398"></a><tt class="py-lineno">398</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">image</tt> <tt class="py-op">=</tt> <tt class="py-name">val</tt><tt class="py-op">[</tt><tt class="py-number">6</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">setattr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt><tt class="py-name">key</tt><tt class="py-op">.</tt><tt id="link-92" class="py-name"><a title="Bio.Seq.Seq.lower
Bio.Seq.UnknownSeq.lower
Bio.SeqRecord.SeqRecord.lower" class="py-name" href="#" onclick="return doclink('link-92', 'lower', 'link-8');">lower</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">val</tt><tt class="py-op">)</tt> </tt>
</div><a name="L400"></a><tt class="py-lineno">400</tt> <tt class="py-line"> </tt>
<a name="UnigeneSequenceRecord.__repr__"></a><div id="UnigeneSequenceRecord.__repr__-def"><a name="L401"></a><tt class="py-lineno">401</tt> <a class="py-toggle" href="#" id="UnigeneSequenceRecord.__repr__-toggle" onclick="return toggle('UnigeneSequenceRecord.__repr__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene.UnigeneSequenceRecord-class.html#__repr__">__repr__</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="UnigeneSequenceRecord.__repr__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="UnigeneSequenceRecord.__repr__-expanded"><a name="L402"></a><tt class="py-lineno">402</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">text</tt> </tt>
</div></div><a name="L403"></a><tt class="py-lineno">403</tt> <tt class="py-line"> </tt>
<a name="L404"></a><tt class="py-lineno">404</tt> <tt class="py-line"> </tt>
<a name="UnigeneProtsimRecord"></a><div id="UnigeneProtsimRecord-def"><a name="L405"></a><tt class="py-lineno">405</tt> <a class="py-toggle" href="#" id="UnigeneProtsimRecord-toggle" onclick="return toggle('UnigeneProtsimRecord');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.UniGene.UnigeneProtsimRecord-class.html">UnigeneProtsimRecord</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="UnigeneProtsimRecord-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="UnigeneProtsimRecord-expanded"><a name="L406"></a><tt class="py-lineno">406</tt> <tt class="py-line"> <tt class="py-docstring">"""Store the information for one PROTSIM line from a Unigene file</tt> </tt>
<a name="L407"></a><tt class="py-lineno">407</tt> <tt class="py-line"><tt class="py-docstring"> (DEPRECATED).</tt> </tt>
<a name="L408"></a><tt class="py-lineno">408</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L409"></a><tt class="py-lineno">409</tt> <tt class="py-line"><tt class="py-docstring"> Initialize with the text part of the PROTSIM line, or nothing.</tt> </tt>
<a name="L410"></a><tt class="py-lineno">410</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L411"></a><tt class="py-lineno">411</tt> <tt class="py-line"><tt class="py-docstring"> Attributes and descriptions (access as LOWER CASE)</tt> </tt>
<a name="L412"></a><tt class="py-lineno">412</tt> <tt class="py-line"><tt class="py-docstring"> ORG= Organism</tt> </tt>
<a name="L413"></a><tt class="py-lineno">413</tt> <tt class="py-line"><tt class="py-docstring"> PROTGI= Sequence GI of protein</tt> </tt>
<a name="L414"></a><tt class="py-lineno">414</tt> <tt class="py-line"><tt class="py-docstring"> PROTID= Sequence ID of protein</tt> </tt>
<a name="L415"></a><tt class="py-lineno">415</tt> <tt class="py-line"><tt class="py-docstring"> PCT= Percent alignment</tt> </tt>
<a name="L416"></a><tt class="py-lineno">416</tt> <tt class="py-line"><tt class="py-docstring"> ALN= length of aligned region (aa)</tt> </tt>
<a name="L417"></a><tt class="py-lineno">417</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L418"></a><tt class="py-lineno">418</tt> <tt class="py-line"><tt class="py-docstring"> This class is DEPRECATED; please use the read() function in this module</tt> </tt>
<a name="L419"></a><tt class="py-lineno">419</tt> <tt class="py-line"><tt class="py-docstring"> instead.</tt> </tt>
<a name="L420"></a><tt class="py-lineno">420</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L421"></a><tt class="py-lineno">421</tt> <tt class="py-line"> </tt>
<a name="UnigeneProtsimRecord.__init__"></a><div id="UnigeneProtsimRecord.__init__-def"><a name="L422"></a><tt class="py-lineno">422</tt> <a class="py-toggle" href="#" id="UnigeneProtsimRecord.__init__-toggle" onclick="return toggle('UnigeneProtsimRecord.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene.UnigeneProtsimRecord-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">text</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="UnigeneProtsimRecord.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="UnigeneProtsimRecord.__init__-expanded"><a name="L423"></a><tt class="py-lineno">423</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">warnings</tt> </tt>
<a name="L424"></a><tt class="py-lineno">424</tt> <tt class="py-line"> <tt class="py-name">warnings</tt><tt class="py-op">.</tt><tt class="py-name">warn</tt><tt class="py-op">(</tt><tt class="py-string">"Bio.UniGene.UnigeneProtsimRecord is deprecated; please use the read() function in this module instead"</tt><tt class="py-op">,</tt> <tt id="link-93" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-93', 'Bio', 'link-79');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-94" class="py-name"><a title="Bio.BiopythonDeprecationWarning" class="py-name" href="#" onclick="return doclink('link-94', 'BiopythonDeprecationWarning', 'link-84');">BiopythonDeprecationWarning</a></tt><tt class="py-op">)</tt> </tt>
<a name="L425"></a><tt class="py-lineno">425</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">org</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L426"></a><tt class="py-lineno">426</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">protgi</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L427"></a><tt class="py-lineno">427</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">protid</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L428"></a><tt class="py-lineno">428</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pct</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L429"></a><tt class="py-lineno">429</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">aln</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L430"></a><tt class="py-lineno">430</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">text</tt><tt class="py-op">==</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L431"></a><tt class="py-lineno">431</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">text</tt><tt class="py-op">=</tt><tt class="py-name">text</tt> </tt>
<a name="L432"></a><tt class="py-lineno">432</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-95" class="py-name"><a title="Bio.UniGene.ProtsimLine._init_from_text
Bio.UniGene.STSLine._init_from_text
Bio.UniGene.SequenceLine._init_from_text
Bio.UniGene.UnigeneProtsimRecord._init_from_text
Bio.UniGene.UnigeneSTSRecord._init_from_text
Bio.UniGene.UnigeneSequenceRecord._init_from_text" class="py-name" href="#" onclick="return doclink('link-95', '_init_from_text', 'link-5');">_init_from_text</a></tt><tt class="py-op">(</tt><tt class="py-name">text</tt><tt class="py-op">)</tt> </tt>
</div><a name="L433"></a><tt class="py-lineno">433</tt> <tt class="py-line"> </tt>
<a name="UnigeneProtsimRecord._init_from_text"></a><div id="UnigeneProtsimRecord._init_from_text-def"><a name="L434"></a><tt class="py-lineno">434</tt> <a class="py-toggle" href="#" id="UnigeneProtsimRecord._init_from_text-toggle" onclick="return toggle('UnigeneProtsimRecord._init_from_text');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene.UnigeneProtsimRecord-class.html#_init_from_text">_init_from_text</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">text</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="UnigeneProtsimRecord._init_from_text-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="UnigeneProtsimRecord._init_from_text-expanded"><a name="L435"></a><tt class="py-lineno">435</tt> <tt class="py-line"> <tt class="py-name">parts</tt> <tt class="py-op">=</tt> <tt class="py-name">text</tt><tt class="py-op">.</tt><tt id="link-96" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.split" class="py-name" href="#" onclick="return doclink('link-96', 'split', 'link-6');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">'; '</tt><tt class="py-op">)</tt><tt class="py-op">;</tt> </tt>
<a name="L436"></a><tt class="py-lineno">436</tt> <tt class="py-line"> </tt>
<a name="L437"></a><tt class="py-lineno">437</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">part</tt> <tt class="py-keyword">in</tt> <tt class="py-name">parts</tt><tt class="py-op">:</tt> </tt>
<a name="L438"></a><tt class="py-lineno">438</tt> <tt class="py-line"> <tt class="py-name">key</tt><tt class="py-op">,</tt><tt class="py-name">val</tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-97" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.triefind.match" class="py-name" href="#" onclick="return doclink('link-97', 'match', 'link-91');">match</a></tt><tt class="py-op">(</tt><tt class="py-string">'(\w+)=(\S+)'</tt><tt class="py-op">,</tt><tt class="py-name">part</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">groups</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">setattr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt><tt class="py-name">key</tt><tt class="py-op">.</tt><tt id="link-98" class="py-name"><a title="Bio.Seq.Seq.lower
Bio.Seq.UnknownSeq.lower
Bio.SeqRecord.SeqRecord.lower" class="py-name" href="#" onclick="return doclink('link-98', 'lower', 'link-8');">lower</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">val</tt><tt class="py-op">)</tt> </tt>
</div><a name="L440"></a><tt class="py-lineno">440</tt> <tt class="py-line"> </tt>
<a name="UnigeneProtsimRecord.__repr__"></a><div id="UnigeneProtsimRecord.__repr__-def"><a name="L441"></a><tt class="py-lineno">441</tt> <a class="py-toggle" href="#" id="UnigeneProtsimRecord.__repr__-toggle" onclick="return toggle('UnigeneProtsimRecord.__repr__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene.UnigeneProtsimRecord-class.html#__repr__">__repr__</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="UnigeneProtsimRecord.__repr__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="UnigeneProtsimRecord.__repr__-expanded"><a name="L442"></a><tt class="py-lineno">442</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">text</tt> </tt>
</div></div><a name="L443"></a><tt class="py-lineno">443</tt> <tt class="py-line"> </tt>
<a name="L444"></a><tt class="py-lineno">444</tt> <tt class="py-line"> </tt>
<a name="UnigeneSTSRecord"></a><div id="UnigeneSTSRecord-def"><a name="L445"></a><tt class="py-lineno">445</tt> <a class="py-toggle" href="#" id="UnigeneSTSRecord-toggle" onclick="return toggle('UnigeneSTSRecord');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.UniGene.UnigeneSTSRecord-class.html">UnigeneSTSRecord</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="UnigeneSTSRecord-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="UnigeneSTSRecord-expanded"><a name="L446"></a><tt class="py-lineno">446</tt> <tt class="py-line"> <tt class="py-docstring">"""Store the information for one STS line from a Unigene file</tt> </tt>
<a name="L447"></a><tt class="py-lineno">447</tt> <tt class="py-line"><tt class="py-docstring"> (DEPRECATED).</tt> </tt>
<a name="L448"></a><tt class="py-lineno">448</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L449"></a><tt class="py-lineno">449</tt> <tt class="py-line"><tt class="py-docstring"> Initialize with the text part of the STS line, or nothing.</tt> </tt>
<a name="L450"></a><tt class="py-lineno">450</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L451"></a><tt class="py-lineno">451</tt> <tt class="py-line"><tt class="py-docstring"> Attributes and descriptions (access as LOWER CASE)</tt> </tt>
<a name="L452"></a><tt class="py-lineno">452</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L453"></a><tt class="py-lineno">453</tt> <tt class="py-line"><tt class="py-docstring"> NAME= Name of STS</tt> </tt>
<a name="L454"></a><tt class="py-lineno">454</tt> <tt class="py-line"><tt class="py-docstring"> ACC= GenBank/EMBL/DDBJ accession number of STS [optional field]</tt> </tt>
<a name="L455"></a><tt class="py-lineno">455</tt> <tt class="py-line"><tt class="py-docstring"> DSEG= GDB Dsegment number [optional field]</tt> </tt>
<a name="L456"></a><tt class="py-lineno">456</tt> <tt class="py-line"><tt class="py-docstring"> UNISTS= identifier in NCBI's UNISTS database</tt> </tt>
<a name="L457"></a><tt class="py-lineno">457</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L458"></a><tt class="py-lineno">458</tt> <tt class="py-line"><tt class="py-docstring"> This class is DEPRECATED; please use the read() function in this module</tt> </tt>
<a name="L459"></a><tt class="py-lineno">459</tt> <tt class="py-line"><tt class="py-docstring"> instead.</tt> </tt>
<a name="L460"></a><tt class="py-lineno">460</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L461"></a><tt class="py-lineno">461</tt> <tt class="py-line"> </tt>
<a name="UnigeneSTSRecord.__init__"></a><div id="UnigeneSTSRecord.__init__-def"><a name="L462"></a><tt class="py-lineno">462</tt> <a class="py-toggle" href="#" id="UnigeneSTSRecord.__init__-toggle" onclick="return toggle('UnigeneSTSRecord.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene.UnigeneSTSRecord-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">text</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="UnigeneSTSRecord.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="UnigeneSTSRecord.__init__-expanded"><a name="L463"></a><tt class="py-lineno">463</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">warnings</tt> </tt>
<a name="L464"></a><tt class="py-lineno">464</tt> <tt class="py-line"> <tt class="py-name">warnings</tt><tt class="py-op">.</tt><tt class="py-name">warn</tt><tt class="py-op">(</tt><tt class="py-string">"Bio.UniGene.UnigeneSTSRecord is deprecated; please use the read() function in this module instead"</tt><tt class="py-op">,</tt> <tt id="link-99" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-99', 'Bio', 'link-79');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-100" class="py-name"><a title="Bio.BiopythonDeprecationWarning" class="py-name" href="#" onclick="return doclink('link-100', 'BiopythonDeprecationWarning', 'link-84');">BiopythonDeprecationWarning</a></tt><tt class="py-op">)</tt> </tt>
<a name="L465"></a><tt class="py-lineno">465</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-101" class="py-name" targets="Method Bio.Phylo.PhyloXMLIO.Writer.name()=Bio.Phylo.PhyloXMLIO.Writer-class.html#name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-101', 'name', 'link-101');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<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-102" class="py-name"><a title="Bio.FSSP.fssp_rec.align.acc" class="py-name" href="#" onclick="return doclink('link-102', 'acc', 'link-0');">acc</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L467"></a><tt class="py-lineno">467</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dseg</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L468"></a><tt class="py-lineno">468</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">unists</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L469"></a><tt class="py-lineno">469</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">text</tt><tt class="py-op">==</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L470"></a><tt class="py-lineno">470</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">text</tt><tt class="py-op">=</tt><tt class="py-name">text</tt> </tt>
<a name="L471"></a><tt class="py-lineno">471</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-103" class="py-name"><a title="Bio.UniGene.ProtsimLine._init_from_text
Bio.UniGene.STSLine._init_from_text
Bio.UniGene.SequenceLine._init_from_text
Bio.UniGene.UnigeneProtsimRecord._init_from_text
Bio.UniGene.UnigeneSTSRecord._init_from_text
Bio.UniGene.UnigeneSequenceRecord._init_from_text" class="py-name" href="#" onclick="return doclink('link-103', '_init_from_text', 'link-5');">_init_from_text</a></tt><tt class="py-op">(</tt><tt class="py-name">text</tt><tt class="py-op">)</tt> </tt>
</div><a name="L472"></a><tt class="py-lineno">472</tt> <tt class="py-line"> </tt>
<a name="UnigeneSTSRecord._init_from_text"></a><div id="UnigeneSTSRecord._init_from_text-def"><a name="L473"></a><tt class="py-lineno">473</tt> <a class="py-toggle" href="#" id="UnigeneSTSRecord._init_from_text-toggle" onclick="return toggle('UnigeneSTSRecord._init_from_text');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene.UnigeneSTSRecord-class.html#_init_from_text">_init_from_text</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">text</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="UnigeneSTSRecord._init_from_text-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="UnigeneSTSRecord._init_from_text-expanded"><a name="L474"></a><tt class="py-lineno">474</tt> <tt class="py-line"> <tt class="py-name">parts</tt> <tt class="py-op">=</tt> <tt class="py-name">text</tt><tt class="py-op">.</tt><tt id="link-104" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.split" class="py-name" href="#" onclick="return doclink('link-104', 'split', 'link-6');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">' '</tt><tt class="py-op">)</tt><tt class="py-op">;</tt> </tt>
<a name="L475"></a><tt class="py-lineno">475</tt> <tt class="py-line"> </tt>
<a name="L476"></a><tt class="py-lineno">476</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">part</tt> <tt class="py-keyword">in</tt> <tt class="py-name">parts</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">key</tt><tt class="py-op">,</tt><tt class="py-name">val</tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-105" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.triefind.match" class="py-name" href="#" onclick="return doclink('link-105', 'match', 'link-91');">match</a></tt><tt class="py-op">(</tt><tt class="py-string">'(\w+)=(\S+)'</tt><tt class="py-op">,</tt><tt class="py-name">part</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">groups</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L478"></a><tt class="py-lineno">478</tt> <tt class="py-line"> <tt class="py-name">setattr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt><tt class="py-name">key</tt><tt class="py-op">.</tt><tt id="link-106" class="py-name"><a title="Bio.Seq.Seq.lower
Bio.Seq.UnknownSeq.lower
Bio.SeqRecord.SeqRecord.lower" class="py-name" href="#" onclick="return doclink('link-106', 'lower', 'link-8');">lower</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">val</tt><tt class="py-op">)</tt> </tt>
</div><a name="L479"></a><tt class="py-lineno">479</tt> <tt class="py-line"> </tt>
<a name="UnigeneSTSRecord.__repr__"></a><div id="UnigeneSTSRecord.__repr__-def"><a name="L480"></a><tt class="py-lineno">480</tt> <a class="py-toggle" href="#" id="UnigeneSTSRecord.__repr__-toggle" onclick="return toggle('UnigeneSTSRecord.__repr__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene.UnigeneSTSRecord-class.html#__repr__">__repr__</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="UnigeneSTSRecord.__repr__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="UnigeneSTSRecord.__repr__-expanded"><a name="L481"></a><tt class="py-lineno">481</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">text</tt> </tt>
</div></div><a name="L482"></a><tt class="py-lineno">482</tt> <tt class="py-line"> </tt>
<a name="L483"></a><tt class="py-lineno">483</tt> <tt class="py-line"> </tt>
<a name="UnigeneRecord"></a><div id="UnigeneRecord-def"><a name="L484"></a><tt class="py-lineno">484</tt> <a class="py-toggle" href="#" id="UnigeneRecord-toggle" onclick="return toggle('UnigeneRecord');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.UniGene.UnigeneRecord-class.html">UnigeneRecord</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="UnigeneRecord-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="UnigeneRecord-expanded"><a name="L485"></a><tt class="py-lineno">485</tt> <tt class="py-line"> <tt class="py-docstring">"""Store a Unigene record (DEPRECATED).</tt> </tt>
<a name="L486"></a><tt class="py-lineno">486</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L487"></a><tt class="py-lineno">487</tt> <tt class="py-line"><tt class="py-docstring"> Here is what is stored:</tt> </tt>
<a name="L488"></a><tt class="py-lineno">488</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L489"></a><tt class="py-lineno">489</tt> <tt class="py-line"><tt class="py-docstring"> self.ID = '' # ID line</tt> </tt>
<a name="L490"></a><tt class="py-lineno">490</tt> <tt class="py-line"><tt class="py-docstring"> self.species = '' # Hs, Bt, etc.</tt> </tt>
<a name="L491"></a><tt class="py-lineno">491</tt> <tt class="py-line"><tt class="py-docstring"> self.title = '' # TITLE line</tt> </tt>
<a name="L492"></a><tt class="py-lineno">492</tt> <tt class="py-line"><tt class="py-docstring"> self.symbol = '' # GENE line</tt> </tt>
<a name="L493"></a><tt class="py-lineno">493</tt> <tt class="py-line"><tt class="py-docstring"> self.cytoband = '' # CYTOBAND line</tt> </tt>
<a name="L494"></a><tt class="py-lineno">494</tt> <tt class="py-line"><tt class="py-docstring"> self.express = [] # EXPRESS line, parsed on ';'</tt> </tt>
<a name="L495"></a><tt class="py-lineno">495</tt> <tt class="py-line"><tt class="py-docstring"> # Will be an array of strings</tt> </tt>
<a name="L496"></a><tt class="py-lineno">496</tt> <tt class="py-line"><tt class="py-docstring"> self.restr_expr = '' # RESTR_EXPR line</tt> </tt>
<a name="L497"></a><tt class="py-lineno">497</tt> <tt class="py-line"><tt class="py-docstring"> self.gnm_terminus = '' # GNM_TERMINUS line</tt> </tt>
<a name="L498"></a><tt class="py-lineno">498</tt> <tt class="py-line"><tt class="py-docstring"> self.gene_id = '' # GENE_ID line</tt> </tt>
<a name="L499"></a><tt class="py-lineno">499</tt> <tt class="py-line"><tt class="py-docstring"> self.chromosome = '' # CHROMOSOME</tt> </tt>
<a name="L500"></a><tt class="py-lineno">500</tt> <tt class="py-line"><tt class="py-docstring"> self.protsim = [] # PROTSIM entries, array of Protsims</tt> </tt>
<a name="L501"></a><tt class="py-lineno">501</tt> <tt class="py-line"><tt class="py-docstring"> # Type UnigeneProtsimRecord</tt> </tt>
<a name="L502"></a><tt class="py-lineno">502</tt> <tt class="py-line"><tt class="py-docstring"> self.sequence = [] # SEQUENCE entries, array of Sequence entries</tt> </tt>
<a name="L503"></a><tt class="py-lineno">503</tt> <tt class="py-line"><tt class="py-docstring"> # Type UnigeneSequenceRecord</tt> </tt>
<a name="L504"></a><tt class="py-lineno">504</tt> <tt class="py-line"><tt class="py-docstring"> self.sts = [] # STS entries, array of STS entries</tt> </tt>
<a name="L505"></a><tt class="py-lineno">505</tt> <tt class="py-line"><tt class="py-docstring"> # Type UnigeneSTSRecord</tt> </tt>
<a name="L506"></a><tt class="py-lineno">506</tt> <tt class="py-line"><tt class="py-docstring"> self.txmap = [] # TXMAP entries, array of TXMap entries</tt> </tt>
<a name="L507"></a><tt class="py-lineno">507</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L508"></a><tt class="py-lineno">508</tt> <tt class="py-line"><tt class="py-docstring"> This class is DEPRECATED; please use the read() function in this module</tt> </tt>
<a name="L509"></a><tt class="py-lineno">509</tt> <tt class="py-line"><tt class="py-docstring"> instead.</tt> </tt>
<a name="L510"></a><tt class="py-lineno">510</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L511"></a><tt class="py-lineno">511</tt> <tt class="py-line"> </tt>
<a name="UnigeneRecord.__init__"></a><div id="UnigeneRecord.__init__-def"><a name="L512"></a><tt class="py-lineno">512</tt> <a class="py-toggle" href="#" id="UnigeneRecord.__init__-toggle" onclick="return toggle('UnigeneRecord.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene.UnigeneRecord-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="UnigeneRecord.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="UnigeneRecord.__init__-expanded"><a name="L513"></a><tt class="py-lineno">513</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">warnings</tt> </tt>
<a name="L514"></a><tt class="py-lineno">514</tt> <tt class="py-line"> <tt class="py-name">warnings</tt><tt class="py-op">.</tt><tt class="py-name">warn</tt><tt class="py-op">(</tt><tt class="py-string">"Bio.UniGene.UnigeneRecord is deprecated; please use the read() function in this module instead"</tt><tt class="py-op">,</tt> <tt id="link-107" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-107', 'Bio', 'link-79');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-108" class="py-name"><a title="Bio.BiopythonDeprecationWarning" class="py-name" href="#" onclick="return doclink('link-108', 'BiopythonDeprecationWarning', 'link-84');">BiopythonDeprecationWarning</a></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">self</tt><tt class="py-op">.</tt><tt id="link-109" class="py-name"><a title="Bio.UniGene._RecordConsumer.ID" class="py-name" href="#" onclick="return doclink('link-109', 'ID', 'link-18');">ID</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> <tt class="py-comment"># ID line</tt> </tt>
<a name="L516"></a><tt class="py-lineno">516</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-110" class="py-name"><a title="Bio.Pathway.Network.species
Bio.Pathway.Reaction.species
Bio.Pathway.System.species" class="py-name" href="#" onclick="return doclink('link-110', 'species', 'link-19');">species</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> <tt class="py-comment"># Hs, Bt, etc.</tt> </tt>
<a name="L517"></a><tt class="py-lineno">517</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-111" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title" class="py-name" href="#" onclick="return doclink('link-111', 'title', 'link-20');">title</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> <tt class="py-comment"># TITLE line</tt> </tt>
<a name="L518"></a><tt class="py-lineno">518</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-112" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.symbol" class="py-name" href="#" onclick="return doclink('link-112', 'symbol', 'link-21');">symbol</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> <tt class="py-comment"># GENE line</tt> </tt>
<a name="L519"></a><tt class="py-lineno">519</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">cytoband</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> <tt class="py-comment"># CYTOBAND line</tt> </tt>
<a name="L520"></a><tt class="py-lineno">520</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">express</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> <tt class="py-comment"># EXPRESS line, parsed on ';'</tt> </tt>
<a name="L521"></a><tt class="py-lineno">521</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">restr_expr</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> <tt class="py-comment"># RESTR_EXPR line</tt> </tt>
<a name="L522"></a><tt class="py-lineno">522</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">gnm_terminus</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> <tt class="py-comment"># GNM_TERMINUS line</tt> </tt>
<a name="L523"></a><tt class="py-lineno">523</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">gene_id</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> <tt class="py-comment"># GENE_ID line</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 class="py-name">chromosome</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> <tt class="py-comment"># CHROMOSOME</tt> </tt>
<a name="L525"></a><tt class="py-lineno">525</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">protsim</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> <tt class="py-comment"># PROTSIM entries, array of Protsims</tt> </tt>
<a name="L526"></a><tt class="py-lineno">526</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-113" class="py-name"><a title="Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.Phylo.PhyloXMLIO.Writer.sequence" class="py-name" href="#" onclick="return doclink('link-113', 'sequence', 'link-22');">sequence</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> <tt class="py-comment"># SEQUENCE entries, array of Sequence entries</tt> </tt>
<a name="L527"></a><tt class="py-lineno">527</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sts</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> <tt class="py-comment"># STS entries, array of STS entries</tt> </tt>
<a name="L528"></a><tt class="py-lineno">528</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">txmap</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> <tt class="py-comment"># TXMAP entries, array of TXMap entries</tt> </tt>
</div><a name="L529"></a><tt class="py-lineno">529</tt> <tt class="py-line"> </tt>
<a name="UnigeneRecord.__repr__"></a><div id="UnigeneRecord.__repr__-def"><a name="L530"></a><tt class="py-lineno">530</tt> <a class="py-toggle" href="#" id="UnigeneRecord.__repr__-toggle" onclick="return toggle('UnigeneRecord.__repr__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene.UnigeneRecord-class.html#__repr__">__repr__</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="UnigeneRecord.__repr__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="UnigeneRecord.__repr__-expanded"><a name="L531"></a><tt class="py-lineno">531</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"<%s> %s %s\n%s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__class__</tt><tt class="py-op">.</tt><tt class="py-name">__name__</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-114" class="py-name"><a title="Bio.UniGene._RecordConsumer.ID" class="py-name" href="#" onclick="return doclink('link-114', 'ID', 'link-18');">ID</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-115" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.symbol" class="py-name" href="#" onclick="return doclink('link-115', 'symbol', 'link-21');">symbol</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-116" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title" class="py-name" href="#" onclick="return doclink('link-116', 'title', 'link-20');">title</a></tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L533"></a><tt class="py-lineno">533</tt> <tt class="py-line"> </tt>
<a name="L534"></a><tt class="py-lineno">534</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer"></a><div id="_RecordConsumer-def"><a name="L535"></a><tt class="py-lineno">535</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.UniGene._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="L536"></a><tt class="py-lineno">536</tt> <tt class="py-line"> <tt class="py-docstring">"""This class is DEPRECATED; please use the read() function in this module</tt> </tt>
<a name="L537"></a><tt class="py-lineno">537</tt> <tt class="py-line"><tt class="py-docstring"> instead."""</tt> </tt>
<a name="L538"></a><tt class="py-lineno">538</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.__init__"></a><div id="_RecordConsumer.__init__-def"><a name="L539"></a><tt class="py-lineno">539</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.UniGene._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="L540"></a><tt class="py-lineno">540</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">warnings</tt> </tt>
<a name="L541"></a><tt class="py-lineno">541</tt> <tt class="py-line"> <tt class="py-name">warnings</tt><tt class="py-op">.</tt><tt class="py-name">warn</tt><tt class="py-op">(</tt><tt class="py-string">"Bio.UniGene._RecordConsumer is deprecated; please use the read() function in this module instead"</tt><tt class="py-op">,</tt> <tt id="link-117" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-117', 'Bio', 'link-79');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-118" class="py-name"><a title="Bio.BiopythonDeprecationWarning" class="py-name" href="#" onclick="return doclink('link-118', 'BiopythonDeprecationWarning', 'link-84');">BiopythonDeprecationWarning</a></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 class="py-name">unigene_record</tt> <tt class="py-op">=</tt> <tt id="link-119" class="py-name" targets="Class Bio.UniGene.UnigeneRecord=Bio.UniGene.UnigeneRecord-class.html"><a title="Bio.UniGene.UnigeneRecord" class="py-name" href="#" onclick="return doclink('link-119', 'UnigeneRecord', 'link-119');">UnigeneRecord</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="_RecordConsumer.ID"></a><div id="_RecordConsumer.ID-def"><a name="L543"></a><tt class="py-lineno">543</tt> <a class="py-toggle" href="#" id="_RecordConsumer.ID-toggle" onclick="return toggle('_RecordConsumer.ID');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene._RecordConsumer-class.html#ID">ID</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.ID-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.ID-expanded"><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 class="py-name">unigene_record</tt><tt class="py-op">.</tt><tt id="link-120" class="py-name"><a title="Bio.UniGene._RecordConsumer.ID" class="py-name" href="#" onclick="return doclink('link-120', 'ID', 'link-18');">ID</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-121" class="py-name" targets="Method Bio.UniGene._RecordConsumer._get_single_entry()=Bio.UniGene._RecordConsumer-class.html#_get_single_entry"><a title="Bio.UniGene._RecordConsumer._get_single_entry" class="py-name" href="#" onclick="return doclink('link-121', '_get_single_entry', 'link-121');">_get_single_entry</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L545"></a><tt class="py-lineno">545</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">unigene_record</tt><tt class="py-op">.</tt><tt id="link-122" class="py-name"><a title="Bio.Pathway.Network.species
Bio.Pathway.Reaction.species
Bio.Pathway.System.species" class="py-name" href="#" onclick="return doclink('link-122', 'species', 'link-19');">species</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">unigene_record</tt><tt class="py-op">.</tt><tt id="link-123" class="py-name"><a title="Bio.UniGene._RecordConsumer.ID" class="py-name" href="#" onclick="return doclink('link-123', 'ID', 'link-18');">ID</a></tt><tt class="py-op">.</tt><tt id="link-124" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.split" class="py-name" href="#" onclick="return doclink('link-124', 'split', 'link-6');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">'.'</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
</div><a name="_RecordConsumer.TITLE"></a><div id="_RecordConsumer.TITLE-def"><a name="L546"></a><tt class="py-lineno">546</tt> <a class="py-toggle" href="#" id="_RecordConsumer.TITLE-toggle" onclick="return toggle('_RecordConsumer.TITLE');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene._RecordConsumer-class.html#TITLE">TITLE</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.TITLE-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.TITLE-expanded"><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 class="py-name">unigene_record</tt><tt class="py-op">.</tt><tt id="link-125" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title" class="py-name" href="#" onclick="return doclink('link-125', 'title', 'link-20');">title</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-126" class="py-name"><a title="Bio.UniGene._RecordConsumer._get_single_entry" class="py-name" href="#" onclick="return doclink('link-126', '_get_single_entry', 'link-121');">_get_single_entry</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
</div><a name="_RecordConsumer.GENE"></a><div id="_RecordConsumer.GENE-def"><a name="L548"></a><tt class="py-lineno">548</tt> <a class="py-toggle" href="#" id="_RecordConsumer.GENE-toggle" onclick="return toggle('_RecordConsumer.GENE');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene._RecordConsumer-class.html#GENE">GENE</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.GENE-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.GENE-expanded"><a name="L549"></a><tt class="py-lineno">549</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">unigene_record</tt><tt class="py-op">.</tt><tt id="link-127" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.symbol" class="py-name" href="#" onclick="return doclink('link-127', 'symbol', 'link-21');">symbol</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-128" class="py-name"><a title="Bio.UniGene._RecordConsumer._get_single_entry" class="py-name" href="#" onclick="return doclink('link-128', '_get_single_entry', 'link-121');">_get_single_entry</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
</div><a name="_RecordConsumer.EXPRESS"></a><div id="_RecordConsumer.EXPRESS-def"><a name="L550"></a><tt class="py-lineno">550</tt> <a class="py-toggle" href="#" id="_RecordConsumer.EXPRESS-toggle" onclick="return toggle('_RecordConsumer.EXPRESS');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene._RecordConsumer-class.html#EXPRESS">EXPRESS</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.EXPRESS-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.EXPRESS-expanded"><a name="L551"></a><tt class="py-lineno">551</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">unigene_record</tt><tt class="py-op">.</tt><tt class="py-name">express</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-129" class="py-name" targets="Method Bio.UniGene._RecordConsumer._get_array_entry()=Bio.UniGene._RecordConsumer-class.html#_get_array_entry"><a title="Bio.UniGene._RecordConsumer._get_array_entry" class="py-name" href="#" onclick="return doclink('link-129', '_get_array_entry', 'link-129');">_get_array_entry</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">,</tt><tt class="py-name">split_on</tt><tt class="py-op">=</tt><tt class="py-string">'; '</tt><tt class="py-op">)</tt> </tt>
</div><a name="_RecordConsumer.RESTR_EXPR"></a><div id="_RecordConsumer.RESTR_EXPR-def"><a name="L552"></a><tt class="py-lineno">552</tt> <a class="py-toggle" href="#" id="_RecordConsumer.RESTR_EXPR-toggle" onclick="return toggle('_RecordConsumer.RESTR_EXPR');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene._RecordConsumer-class.html#RESTR_EXPR">RESTR_EXPR</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.RESTR_EXPR-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.RESTR_EXPR-expanded"><a name="L553"></a><tt class="py-lineno">553</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">unigene_record</tt><tt class="py-op">.</tt><tt class="py-name">restr_expr</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-130" class="py-name"><a title="Bio.UniGene._RecordConsumer._get_single_entry" class="py-name" href="#" onclick="return doclink('link-130', '_get_single_entry', 'link-121');">_get_single_entry</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
</div><a name="_RecordConsumer.GENE_ID"></a><div id="_RecordConsumer.GENE_ID-def"><a name="L554"></a><tt class="py-lineno">554</tt> <a class="py-toggle" href="#" id="_RecordConsumer.GENE_ID-toggle" onclick="return toggle('_RecordConsumer.GENE_ID');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene._RecordConsumer-class.html#GENE_ID">GENE_ID</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.GENE_ID-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.GENE_ID-expanded"><a name="L555"></a><tt class="py-lineno">555</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">unigene_record</tt><tt class="py-op">.</tt><tt class="py-name">gene_id</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-131" class="py-name"><a title="Bio.UniGene._RecordConsumer._get_single_entry" class="py-name" href="#" onclick="return doclink('link-131', '_get_single_entry', 'link-121');">_get_single_entry</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
</div><a name="_RecordConsumer.CHROMOSOME"></a><div id="_RecordConsumer.CHROMOSOME-def"><a name="L556"></a><tt class="py-lineno">556</tt> <a class="py-toggle" href="#" id="_RecordConsumer.CHROMOSOME-toggle" onclick="return toggle('_RecordConsumer.CHROMOSOME');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene._RecordConsumer-class.html#CHROMOSOME">CHROMOSOME</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.CHROMOSOME-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.CHROMOSOME-expanded"><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 class="py-name">unigene_record</tt><tt class="py-op">.</tt><tt class="py-name">chromosome</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-132" class="py-name"><a title="Bio.UniGene._RecordConsumer._get_single_entry" class="py-name" href="#" onclick="return doclink('link-132', '_get_single_entry', 'link-121');">_get_single_entry</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
</div><a name="_RecordConsumer.GENE_ID"></a><div id="_RecordConsumer.GENE_ID-def"><a name="L558"></a><tt class="py-lineno">558</tt> <a class="py-toggle" href="#" id="_RecordConsumer.GENE_ID-toggle" onclick="return toggle('_RecordConsumer.GENE_ID');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene._RecordConsumer-class.html#GENE_ID">GENE_ID</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.GENE_ID-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.GENE_ID-expanded"><a name="L559"></a><tt class="py-lineno">559</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">unigene_record</tt><tt class="py-op">.</tt><tt class="py-name">gene_id</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-133" class="py-name"><a title="Bio.UniGene._RecordConsumer._get_single_entry" class="py-name" href="#" onclick="return doclink('link-133', '_get_single_entry', 'link-121');">_get_single_entry</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
</div><a name="_RecordConsumer.SEQUENCE"></a><div id="_RecordConsumer.SEQUENCE-def"><a name="L560"></a><tt class="py-lineno">560</tt> <a class="py-toggle" href="#" id="_RecordConsumer.SEQUENCE-toggle" onclick="return toggle('_RecordConsumer.SEQUENCE');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene._RecordConsumer-class.html#SEQUENCE">SEQUENCE</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.SEQUENCE-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.SEQUENCE-expanded"><a name="L561"></a><tt class="py-lineno">561</tt> <tt class="py-line"> <tt class="py-name">ug_seqrecord</tt> <tt class="py-op">=</tt> <tt id="link-134" class="py-name" targets="Class Bio.UniGene.UnigeneSequenceRecord=Bio.UniGene.UnigeneSequenceRecord-class.html"><a title="Bio.UniGene.UnigeneSequenceRecord" class="py-name" href="#" onclick="return doclink('link-134', 'UnigeneSequenceRecord', 'link-134');">UnigeneSequenceRecord</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-135" class="py-name"><a title="Bio.UniGene._RecordConsumer._get_single_entry" class="py-name" href="#" onclick="return doclink('link-135', '_get_single_entry', 'link-121');">_get_single_entry</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="L562"></a><tt class="py-lineno">562</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">unigene_record</tt><tt class="py-op">.</tt><tt id="link-136" class="py-name"><a title="Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.Phylo.PhyloXMLIO.Writer.sequence" class="py-name" href="#" onclick="return doclink('link-136', 'sequence', 'link-22');">sequence</a></tt><tt class="py-op">.</tt><tt id="link-137" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-137', 'append', 'link-66');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">ug_seqrecord</tt><tt class="py-op">)</tt> </tt>
</div><a name="_RecordConsumer.PROTSIM"></a><div id="_RecordConsumer.PROTSIM-def"><a name="L563"></a><tt class="py-lineno">563</tt> <a class="py-toggle" href="#" id="_RecordConsumer.PROTSIM-toggle" onclick="return toggle('_RecordConsumer.PROTSIM');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene._RecordConsumer-class.html#PROTSIM">PROTSIM</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.PROTSIM-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.PROTSIM-expanded"><a name="L564"></a><tt class="py-lineno">564</tt> <tt class="py-line"> <tt class="py-name">ug_protsimrecord</tt> <tt class="py-op">=</tt> <tt id="link-138" class="py-name" targets="Class Bio.UniGene.UnigeneProtsimRecord=Bio.UniGene.UnigeneProtsimRecord-class.html"><a title="Bio.UniGene.UnigeneProtsimRecord" class="py-name" href="#" onclick="return doclink('link-138', 'UnigeneProtsimRecord', 'link-138');">UnigeneProtsimRecord</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-139" class="py-name"><a title="Bio.UniGene._RecordConsumer._get_single_entry" class="py-name" href="#" onclick="return doclink('link-139', '_get_single_entry', 'link-121');">_get_single_entry</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="L565"></a><tt class="py-lineno">565</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">unigene_record</tt><tt class="py-op">.</tt><tt class="py-name">protsim</tt><tt class="py-op">.</tt><tt id="link-140" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-140', 'append', 'link-66');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">ug_protsimrecord</tt><tt class="py-op">)</tt> </tt>
</div><a name="_RecordConsumer.STS"></a><div id="_RecordConsumer.STS-def"><a name="L566"></a><tt class="py-lineno">566</tt> <a class="py-toggle" href="#" id="_RecordConsumer.STS-toggle" onclick="return toggle('_RecordConsumer.STS');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene._RecordConsumer-class.html#STS">STS</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.STS-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.STS-expanded"><a name="L567"></a><tt class="py-lineno">567</tt> <tt class="py-line"> <tt class="py-name">ug_stsrecord</tt> <tt class="py-op">=</tt> <tt id="link-141" class="py-name" targets="Class Bio.UniGene.UnigeneSTSRecord=Bio.UniGene.UnigeneSTSRecord-class.html"><a title="Bio.UniGene.UnigeneSTSRecord" class="py-name" href="#" onclick="return doclink('link-141', 'UnigeneSTSRecord', 'link-141');">UnigeneSTSRecord</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-142" class="py-name"><a title="Bio.UniGene._RecordConsumer._get_single_entry" class="py-name" href="#" onclick="return doclink('link-142', '_get_single_entry', 'link-121');">_get_single_entry</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="L568"></a><tt class="py-lineno">568</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">unigene_record</tt><tt class="py-op">.</tt><tt class="py-name">sts</tt><tt class="py-op">.</tt><tt id="link-143" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-143', 'append', 'link-66');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">ug_stsrecord</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="L570"></a><tt class="py-lineno">570</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer._get_single_entry"></a><div id="_RecordConsumer._get_single_entry-def"><a name="L571"></a><tt class="py-lineno">571</tt> <a class="py-toggle" href="#" id="_RecordConsumer._get_single_entry-toggle" onclick="return toggle('_RecordConsumer._get_single_entry');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene._RecordConsumer-class.html#_get_single_entry">_get_single_entry</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._get_single_entry-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer._get_single_entry-expanded"><a name="L572"></a><tt class="py-lineno">572</tt> <tt class="py-line"> <tt class="py-docstring">"""Consume a single-value line</tt> </tt>
<a name="L573"></a><tt class="py-lineno">573</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L574"></a><tt class="py-lineno">574</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt id="link-144" class="py-name"><a title="Bio.UniGene.UG_INDENT" class="py-name" href="#" onclick="return doclink('link-144', 'UG_INDENT', 'link-34');">UG_INDENT</a></tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
</div><a name="L575"></a><tt class="py-lineno">575</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer._get_array_entry"></a><div id="_RecordConsumer._get_array_entry-def"><a name="L576"></a><tt class="py-lineno">576</tt> <a class="py-toggle" href="#" id="_RecordConsumer._get_array_entry-toggle" onclick="return toggle('_RecordConsumer._get_array_entry');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene._RecordConsumer-class.html#_get_array_entry">_get_array_entry</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-param">split_on</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer._get_array_entry-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer._get_array_entry-expanded"><a name="L577"></a><tt class="py-lineno">577</tt> <tt class="py-line"> <tt class="py-docstring">"""Consume a multi-value line by splitting on split_on</tt> </tt>
<a name="L578"></a><tt class="py-lineno">578</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L579"></a><tt class="py-lineno">579</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt id="link-145" class="py-name"><a title="Bio.UniGene.UG_INDENT" class="py-name" href="#" onclick="return doclink('link-145', 'UG_INDENT', 'link-34');">UG_INDENT</a></tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-146" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.split" class="py-name" href="#" onclick="return doclink('link-146', 'split', 'link-6');">split</a></tt><tt class="py-op">(</tt><tt class="py-name">split_on</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L580"></a><tt class="py-lineno">580</tt> <tt class="py-line"> </tt>
<a name="L581"></a><tt class="py-lineno">581</tt> <tt class="py-line"> </tt>
<a name="_Scanner"></a><div id="_Scanner-def"><a name="L582"></a><tt class="py-lineno">582</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.UniGene._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="L583"></a><tt class="py-lineno">583</tt> <tt class="py-line"> <tt class="py-docstring">"""Scans a Unigene Flat File Format file (DEPRECATED).</tt> </tt>
<a name="L584"></a><tt class="py-lineno">584</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L585"></a><tt class="py-lineno">585</tt> <tt class="py-line"><tt class="py-docstring"> This class is DEPRECATED; please use the read() function in this module</tt> </tt>
<a name="L586"></a><tt class="py-lineno">586</tt> <tt class="py-line"><tt class="py-docstring"> instead.</tt> </tt>
<a name="L587"></a><tt class="py-lineno">587</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L588"></a><tt class="py-lineno">588</tt> <tt class="py-line"> </tt>
<a name="_Scanner.__init__"></a><div id="_Scanner.__init__-def"><a name="L589"></a><tt class="py-lineno">589</tt> <a class="py-toggle" href="#" id="_Scanner.__init__-toggle" onclick="return toggle('_Scanner.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.UniGene._Scanner-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="_Scanner.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Scanner.__init__-expanded"><a name="L590"></a><tt class="py-lineno">590</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">warnings</tt> </tt>
<a name="L591"></a><tt class="py-lineno">591</tt> <tt class="py-line"> <tt class="py-name">warnings</tt><tt class="py-op">.</tt><tt class="py-name">warn</tt><tt class="py-op">(</tt><tt class="py-string">"Bio.UniGene._Scanner is deprecated; please use the read() function in this module instead"</tt><tt class="py-op">,</tt> <tt id="link-147" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-147', 'Bio', 'link-79');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-148" class="py-name"><a title="Bio.BiopythonDeprecationWarning" class="py-name" href="#" onclick="return doclink('link-148', 'BiopythonDeprecationWarning', 'link-84');">BiopythonDeprecationWarning</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L592"></a><tt class="py-lineno">592</tt> <tt class="py-line"> </tt>
<a name="_Scanner.feed"></a><div id="_Scanner.feed-def"><a name="L593"></a><tt class="py-lineno">593</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.UniGene._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="L594"></a><tt class="py-lineno">594</tt> <tt class="py-line"> <tt class="py-docstring">"""feed(self, handle, consumer)</tt> </tt>
<a name="L595"></a><tt class="py-lineno">595</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L596"></a><tt class="py-lineno">596</tt> <tt class="py-line"><tt class="py-docstring"> Feed events from parsing a Unigene file to a consumer.</tt> </tt>
<a name="L597"></a><tt class="py-lineno">597</tt> <tt class="py-line"><tt class="py-docstring"> handle is a file-like object, and consumer is a consumer object</tt> </tt>
<a name="L598"></a><tt class="py-lineno">598</tt> <tt class="py-line"><tt class="py-docstring"> that will receive events as the file is scanned</tt> </tt>
<a name="L599"></a><tt class="py-lineno">599</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L600"></a><tt class="py-lineno">600</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L601"></a><tt class="py-lineno">601</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt class="py-name">start_record</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L602"></a><tt class="py-lineno">602</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt id="link-149" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-149', 'handle', 'link-27');">handle</a></tt><tt class="py-op">:</tt> </tt>
<a name="L603"></a><tt class="py-lineno">603</tt> <tt class="py-line"> <tt class="py-name">tag</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-150" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.split" class="py-name" href="#" onclick="return doclink('link-150', 'split', 'link-6');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">' '</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L604"></a><tt class="py-lineno">604</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-151" class="py-name"><a title="Bio.Seq.Seq.rstrip" class="py-name" href="#" onclick="return doclink('link-151', 'rstrip', 'link-38');">rstrip</a></tt><tt class="py-op">(</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">if</tt> <tt class="py-name">line</tt><tt class="py-op">==</tt><tt class="py-string">'//'</tt><tt class="py-op">:</tt> </tt>
<a name="L606"></a><tt class="py-lineno">606</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt class="py-name">end_record</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L607"></a><tt class="py-lineno">607</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L608"></a><tt class="py-lineno">608</tt> <tt class="py-line"> <tt class="py-keyword">try</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">f</tt> <tt class="py-op">=</tt> <tt class="py-name">getattr</tt><tt class="py-op">(</tt><tt class="py-name">consumer</tt><tt class="py-op">,</tt> <tt class="py-name">tag</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">except</tt> <tt class="py-name">AttributeError</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-string">'no method called'</tt><tt class="py-op">,</tt> <tt class="py-name">tag</tt> </tt>
<a name="L612"></a><tt class="py-lineno">612</tt> <tt class="py-line"> <tt class="py-keyword">else</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">if</tt> <tt class="py-name">callable</tt><tt class="py-op">(</tt><tt class="py-name">f</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L614"></a><tt class="py-lineno">614</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L615"></a><tt class="py-lineno">615</tt> <tt class="py-line"> </tt>
<a name="L616"></a><tt class="py-lineno">616</tt> <tt class="py-line"> </tt>
<a name="RecordParser"></a><div id="RecordParser-def"><a name="L617"></a><tt class="py-lineno">617</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.UniGene.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="L618"></a><tt class="py-lineno">618</tt> <tt class="py-line"> <tt class="py-docstring">"""This class is DEPRECATED; please use the read() function in this module</tt> </tt>
<a name="L619"></a><tt class="py-lineno">619</tt> <tt class="py-line"><tt class="py-docstring"> instead."""</tt> </tt>
<a name="L620"></a><tt class="py-lineno">620</tt> <tt class="py-line"> </tt>
<a name="RecordParser.__init__"></a><div id="RecordParser.__init__-def"><a name="L621"></a><tt class="py-lineno">621</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.UniGene.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="L622"></a><tt class="py-lineno">622</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">warnings</tt> </tt>
<a name="L623"></a><tt class="py-lineno">623</tt> <tt class="py-line"> <tt class="py-name">warnings</tt><tt class="py-op">.</tt><tt class="py-name">warn</tt><tt class="py-op">(</tt><tt class="py-string">"Bio.UniGene._RecordParser is deprecated; please use the read() function in this module instead"</tt><tt class="py-op">,</tt> <tt id="link-152" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-152', 'Bio', 'link-79');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-153" class="py-name"><a title="Bio.BiopythonDeprecationWarning" class="py-name" href="#" onclick="return doclink('link-153', 'BiopythonDeprecationWarning', 'link-84');">BiopythonDeprecationWarning</a></tt><tt class="py-op">)</tt> </tt>
<a name="L624"></a><tt class="py-lineno">624</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-154" class="py-name" targets="Class Bio.Blast.NCBIStandalone._Scanner=Bio.Blast.NCBIStandalone._Scanner-class.html,Class Bio.Compass._Scanner=Bio.Compass._Scanner-class.html,Class Bio.UniGene._Scanner=Bio.UniGene._Scanner-class.html"><a title="Bio.Blast.NCBIStandalone._Scanner
Bio.Compass._Scanner
Bio.UniGene._Scanner" class="py-name" href="#" onclick="return doclink('link-154', '_Scanner', 'link-154');">_Scanner</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L625"></a><tt class="py-lineno">625</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-155" class="py-name" targets="Class Bio.GenBank._RecordConsumer=Bio.GenBank._RecordConsumer-class.html,Class Bio.UniGene._RecordConsumer=Bio.UniGene._RecordConsumer-class.html"><a title="Bio.GenBank._RecordConsumer
Bio.UniGene._RecordConsumer" class="py-name" href="#" onclick="return doclink('link-155', '_RecordConsumer', 'link-155');">_RecordConsumer</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L626"></a><tt class="py-lineno">626</tt> <tt class="py-line"> </tt>
<a name="RecordParser.parse"></a><div id="RecordParser.parse-def"><a name="L627"></a><tt class="py-lineno">627</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.UniGene.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="L628"></a><tt class="py-lineno">628</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-156" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-156', 'handle', 'link-27');">handle</a></tt><tt class="py-op">,</tt> <tt id="link-157" class="py-name" targets="Module Bio.File=Bio.File-module.html"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-157', 'File', 'link-157');">File</a></tt><tt class="py-op">.</tt><tt id="link-158" 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-158', 'UndoHandle', 'link-158');">UndoHandle</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L629"></a><tt class="py-lineno">629</tt> <tt class="py-line"> <tt class="py-name">uhandle</tt> <tt class="py-op">=</tt> <tt id="link-159" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-159', 'handle', 'link-27');">handle</a></tt> </tt>
<a name="L630"></a><tt class="py-lineno">630</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L631"></a><tt class="py-lineno">631</tt> <tt class="py-line"> <tt class="py-name">uhandle</tt> <tt class="py-op">=</tt> <tt id="link-160" class="py-name"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-160', 'File', 'link-157');">File</a></tt><tt class="py-op">.</tt><tt id="link-161" class="py-name"><a title="Bio.File.UndoHandle" class="py-name" href="#" onclick="return doclink('link-161', 'UndoHandle', 'link-158');">UndoHandle</a></tt><tt class="py-op">(</tt><tt id="link-162" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-162', 'handle', 'link-27');">handle</a></tt><tt class="py-op">)</tt> </tt>
<a name="L632"></a><tt class="py-lineno">632</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-163" class="py-name" targets="Method Bio.Affy.CelFile.CelScanner.feed()=Bio.Affy.CelFile.CelScanner-class.html#feed,Method Bio.Blast.NCBIStandalone._Scanner.feed()=Bio.Blast.NCBIStandalone._Scanner-class.html#feed,Method Bio.Compass._Scanner.feed()=Bio.Compass._Scanner-class.html#feed,Method Bio.ExPASy.ScanProsite.Parser.feed()=Bio.ExPASy.ScanProsite.Parser-class.html#feed,Method Bio.GenBank.Scanner.InsdcScanner.feed()=Bio.GenBank.Scanner.InsdcScanner-class.html#feed,Method Bio.UniGene.UniGene.UniGeneParser.feed()=Bio.UniGene.UniGene.UniGeneParser-class.html#feed,Method Bio.UniGene._Scanner.feed()=Bio.UniGene._Scanner-class.html#feed"><a title="Bio.Affy.CelFile.CelScanner.feed
Bio.Blast.NCBIStandalone._Scanner.feed
Bio.Compass._Scanner.feed
Bio.ExPASy.ScanProsite.Parser.feed
Bio.GenBank.Scanner.InsdcScanner.feed
Bio.UniGene.UniGene.UniGeneParser.feed
Bio.UniGene._Scanner.feed" class="py-name" href="#" onclick="return doclink('link-163', 'feed', 'link-163');">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="L633"></a><tt class="py-lineno">633</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 class="py-name">unigene_record</tt> </tt>
</div></div><a name="L634"></a><tt class="py-lineno">634</tt> <tt class="py-line"> </tt>
<a name="Iterator"></a><div id="Iterator-def"><a name="L635"></a><tt class="py-lineno">635</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.UniGene.Iterator-class.html">Iterator</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Iterator-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Iterator-expanded"><a name="L636"></a><tt class="py-lineno">636</tt> <tt class="py-line"> <tt class="py-docstring">"""This class is DEPRECATED; please use the parse() function in this module</tt> </tt>
<a name="L637"></a><tt class="py-lineno">637</tt> <tt class="py-line"><tt class="py-docstring"> instead."""</tt> </tt>
<a name="L638"></a><tt class="py-lineno">638</tt> <tt class="py-line"> </tt>
<a name="Iterator.__init__"></a><div id="Iterator.__init__-def"><a name="L639"></a><tt class="py-lineno">639</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.UniGene.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="L640"></a><tt class="py-lineno">640</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">warnings</tt> </tt>
<a name="L641"></a><tt class="py-lineno">641</tt> <tt class="py-line"> <tt class="py-name">warnings</tt><tt class="py-op">.</tt><tt class="py-name">warn</tt><tt class="py-op">(</tt><tt class="py-string">"Bio.UniGene.Iterator is deprecated; please use the parse() function in this module instead"</tt><tt class="py-op">,</tt> <tt id="link-164" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-164', 'Bio', 'link-79');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-165" class="py-name"><a title="Bio.BiopythonDeprecationWarning" class="py-name" href="#" onclick="return doclink('link-165', 'BiopythonDeprecationWarning', 'link-84');">BiopythonDeprecationWarning</a></tt><tt class="py-op">)</tt> </tt>
<a name="L642"></a><tt class="py-lineno">642</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-166" class="py-name"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-166', 'File', 'link-157');">File</a></tt><tt class="py-op">.</tt><tt id="link-167" class="py-name"><a title="Bio.File.UndoHandle" class="py-name" href="#" onclick="return doclink('link-167', 'UndoHandle', 'link-158');">UndoHandle</a></tt><tt class="py-op">(</tt><tt id="link-168" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-168', 'handle', 'link-27');">handle</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L643"></a><tt class="py-lineno">643</tt> <tt class="py-line"> </tt>
<a name="Iterator.next"></a><div id="Iterator.next-def"><a name="L644"></a><tt class="py-lineno">644</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.UniGene.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="L645"></a><tt class="py-lineno">645</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 id="link-169" class="py-name" targets="Class Bio.Compass.RecordParser=Bio.Compass.RecordParser-class.html,Class Bio.GenBank.RecordParser=Bio.GenBank.RecordParser-class.html,Class Bio.UniGene.RecordParser=Bio.UniGene.RecordParser-class.html"><a title="Bio.Compass.RecordParser
Bio.GenBank.RecordParser
Bio.UniGene.RecordParser" class="py-name" href="#" onclick="return doclink('link-169', 'RecordParser', 'link-169');">RecordParser</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L646"></a><tt class="py-lineno">646</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="L647"></a><tt class="py-lineno">647</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-name">True</tt><tt class="py-op">:</tt> </tt>
<a name="L648"></a><tt class="py-lineno">648</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-170" class="py-name" targets="Method Bio.File.UndoHandle.readline()=Bio.File.UndoHandle-class.html#readline"><a title="Bio.File.UndoHandle.readline" class="py-name" href="#" onclick="return doclink('link-170', 'readline', 'link-170');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L649"></a><tt class="py-lineno">649</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">line</tt><tt class="py-op">:</tt> <tt class="py-keyword">break</tt> </tt>
<a name="L650"></a><tt class="py-lineno">650</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">'//'</tt><tt class="py-op">:</tt> </tt>
<a name="L651"></a><tt class="py-lineno">651</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L652"></a><tt class="py-lineno">652</tt> <tt class="py-line"> <tt class="py-name">lines</tt><tt class="py-op">.</tt><tt id="link-171" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-171', 'append', 'link-66');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L653"></a><tt class="py-lineno">653</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="L654"></a><tt class="py-lineno">654</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L655"></a><tt class="py-lineno">655</tt> <tt class="py-line"> <tt class="py-name">lines</tt><tt class="py-op">.</tt><tt id="link-172" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-172', 'append', 'link-66');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">'//'</tt><tt class="py-op">)</tt> </tt>
<a name="L656"></a><tt class="py-lineno">656</tt> <tt class="py-line"> <tt id="link-173" class="py-name" targets="Variable Bio.Seq.Seq.data=Bio.Seq.Seq-class.html#data,Variable BioSQL.BioSeq.DBSeq.data=BioSQL.BioSeq.DBSeq-class.html#data"><a title="Bio.Seq.Seq.data
BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-173', 'data', 'link-173');">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="L657"></a><tt class="py-lineno">657</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="L658"></a><tt class="py-lineno">658</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-174" class="py-name" targets="Method Bio.Affy.CelFile.CelParser.parse()=Bio.Affy.CelFile.CelParser-class.html#parse,Function Bio.AlignIO.parse()=Bio.AlignIO-module.html#parse,Method Bio.Blast.NCBIStandalone.BlastErrorParser.parse()=Bio.Blast.NCBIStandalone.BlastErrorParser-class.html#parse,Method Bio.Blast.NCBIStandalone.BlastParser.parse()=Bio.Blast.NCBIStandalone.BlastParser-class.html#parse,Method Bio.Blast.NCBIStandalone.PSIBlastParser.parse()=Bio.Blast.NCBIStandalone.PSIBlastParser-class.html#parse,Function Bio.Blast.NCBIXML.parse()=Bio.Blast.NCBIXML-module.html#parse,Method Bio.Compass.RecordParser.parse()=Bio.Compass.RecordParser-class.html#parse,Function Bio.Compass.parse()=Bio.Compass-module.html#parse,Function Bio.Emboss.Primer3.parse()=Bio.Emboss.Primer3-module.html#parse,Method Bio.Entrez.Parser.DataHandler.parse()=Bio.Entrez.Parser.DataHandler-class.html#parse,Function Bio.Entrez.parse()=Bio.Entrez-module.html#parse,Function Bio.ExPASy.Enzyme.parse()=Bio.ExPASy.Enzyme-module.html#parse,Function Bio.ExPASy.Prodoc.parse()=Bio.ExPASy.Prodoc-module.html#parse,Function Bio.ExPASy.Prosite.parse()=Bio.ExPASy.Prosite-module.html#parse,Method Bio.GenBank.FeatureParser.parse()=Bio.GenBank.FeatureParser-class.html#parse,Function Bio.GenBank.LocationParser.parse()=Bio.GenBank.LocationParser-module.html#parse,Method Bio.GenBank.RecordParser.parse()=Bio.GenBank.RecordParser-class.html#parse,Method Bio.GenBank.Scanner.InsdcScanner.parse()=Bio.GenBank.Scanner.InsdcScanner-class.html#parse,Function Bio.Geo.parse()=Bio.Geo-module.html#parse,Function Bio.KEGG.Compound.parse()=Bio.KEGG.Compound-module.html#parse,Function Bio.KEGG.Enzyme.parse()=Bio.KEGG.Enzyme-module.html#parse,Function Bio.KEGG.Map.parse()=Bio.KEGG.Map-module.html#parse,Function Bio.Medline.parse()=Bio.Medline-module.html#parse,Function Bio.Motif.parse()=Bio.Motif-module.html#parse,Method Bio.ParserSupport.AbstractParser.parse()=Bio.ParserSupport.AbstractParser-class.html#parse,Method Bio.Parsers.spark.GenericParser.parse()=Bio.Parsers.spark.GenericParser-class.html#parse,Method Bio.Phylo.NewickIO.Parser.parse()=Bio.Phylo.NewickIO.Parser-class.html#parse,Function Bio.Phylo.NewickIO.parse()=Bio.Phylo.NewickIO-module.html#parse,Function Bio.Phylo.NexusIO.parse()=Bio.Phylo.NexusIO-module.html#parse,Method Bio.Phylo.PhyloXMLIO.Parser.parse()=Bio.Phylo.PhyloXMLIO.Parser-class.html#parse,Function Bio.Phylo.PhyloXMLIO.parse()=Bio.Phylo.PhyloXMLIO-module.html#parse,Function Bio.Phylo._io.parse()=Bio.Phylo._io-module.html#parse,Function Bio.SCOP.Cla.parse()=Bio.SCOP.Cla-module.html#parse,Function Bio.SCOP.Des.parse()=Bio.SCOP.Des-module.html#parse,Function Bio.SCOP.Dom.parse()=Bio.SCOP.Dom-module.html#parse,Function Bio.SCOP.Hie.parse()=Bio.SCOP.Hie-module.html#parse,Function Bio.SCOP.Raf.parse()=Bio.SCOP.Raf-module.html#parse,Method Bio.SeqIO.UniprotIO.Parser.parse()=Bio.SeqIO.UniprotIO.Parser-class.html#parse,Function Bio.SeqIO.parse()=Bio.SeqIO-module.html#parse,Function Bio.Sequencing.Ace.parse()=Bio.Sequencing.Ace-module.html#parse,Function Bio.Sequencing.Phd.parse()=Bio.Sequencing.Phd-module.html#parse,Function Bio.SwissProt.KeyWList.parse()=Bio.SwissProt.KeyWList-module.html#parse,Function Bio.SwissProt.parse()=Bio.SwissProt-module.html#parse,Method Bio.UniGene.RecordParser.parse()=Bio.UniGene.RecordParser-class.html#parse,Method Bio.UniGene.UniGene.UniGeneParser.parse()=Bio.UniGene.UniGene.UniGeneParser-class.html#parse,Function Bio.UniGene.parse()=Bio.UniGene-module.html#parse,Function Bio.Wise.psw.parse()=Bio.Wise.psw-module.html#parse"><a title="Bio.Affy.CelFile.CelParser.parse
Bio.AlignIO.parse
Bio.Blast.NCBIStandalone.BlastErrorParser.parse
Bio.Blast.NCBIStandalone.BlastParser.parse
Bio.Blast.NCBIStandalone.PSIBlastParser.parse
Bio.Blast.NCBIXML.parse
Bio.Compass.RecordParser.parse
Bio.Compass.parse
Bio.Emboss.Primer3.parse
Bio.Entrez.Parser.DataHandler.parse
Bio.Entrez.parse
Bio.ExPASy.Enzyme.parse
Bio.ExPASy.Prodoc.parse
Bio.ExPASy.Prosite.parse
Bio.GenBank.FeatureParser.parse
Bio.GenBank.LocationParser.parse
Bio.GenBank.RecordParser.parse
Bio.GenBank.Scanner.InsdcScanner.parse
Bio.Geo.parse
Bio.KEGG.Compound.parse
Bio.KEGG.Enzyme.parse
Bio.KEGG.Map.parse
Bio.Medline.parse
Bio.Motif.parse
Bio.ParserSupport.AbstractParser.parse
Bio.Parsers.spark.GenericParser.parse
Bio.Phylo.NewickIO.Parser.parse
Bio.Phylo.NewickIO.parse
Bio.Phylo.NexusIO.parse
Bio.Phylo.PhyloXMLIO.Parser.parse
Bio.Phylo.PhyloXMLIO.parse
Bio.Phylo._io.parse
Bio.SCOP.Cla.parse
Bio.SCOP.Des.parse
Bio.SCOP.Dom.parse
Bio.SCOP.Hie.parse
Bio.SCOP.Raf.parse
Bio.SeqIO.UniprotIO.Parser.parse
Bio.SeqIO.parse
Bio.Sequencing.Ace.parse
Bio.Sequencing.Phd.parse
Bio.SwissProt.KeyWList.parse
Bio.SwissProt.parse
Bio.UniGene.RecordParser.parse
Bio.UniGene.UniGene.UniGeneParser.parse
Bio.UniGene.parse
Bio.Wise.psw.parse" class="py-name" href="#" onclick="return doclink('link-174', 'parse', 'link-174');">parse</a></tt><tt class="py-op">(</tt><tt id="link-175" class="py-name"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-175', 'File', 'link-157');">File</a></tt><tt class="py-op">.</tt><tt class="py-name">StringHandle</tt><tt class="py-op">(</tt><tt id="link-176" class="py-name"><a title="Bio.Seq.Seq.data
BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-176', 'data', 'link-173');">data</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L659"></a><tt class="py-lineno">659</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-177" class="py-name"><a title="Bio.Seq.Seq.data
BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-177', 'data', 'link-173');">data</a></tt> </tt>
</div><a name="L660"></a><tt class="py-lineno">660</tt> <tt class="py-line"> </tt>
<a name="Iterator.__iter__"></a><div id="Iterator.__iter__-def"><a name="L661"></a><tt class="py-lineno">661</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.UniGene.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="L662"></a><tt class="py-lineno">662</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-178" class="py-name" targets="Method Bio.AlignIO.ClustalIO.ClustalIterator.next()=Bio.AlignIO.ClustalIO.ClustalIterator-class.html#next,Method Bio.AlignIO.EmbossIO.EmbossIterator.next()=Bio.AlignIO.EmbossIO.EmbossIterator-class.html#next,Method Bio.AlignIO.Interfaces.AlignmentIterator.next()=Bio.AlignIO.Interfaces.AlignmentIterator-class.html#next,Method Bio.AlignIO.PhylipIO.PhylipIterator.next()=Bio.AlignIO.PhylipIO.PhylipIterator-class.html#next,Method Bio.AlignIO.StockholmIO.StockholmIterator.next()=Bio.AlignIO.StockholmIO.StockholmIterator-class.html#next,Method Bio.Blast.NCBIStandalone.Iterator.next()=Bio.Blast.NCBIStandalone.Iterator-class.html#next,Method Bio.Blast.ParseBlastTable.BlastTableReader.next()=Bio.Blast.ParseBlastTable.BlastTableReader-class.html#next,Method Bio.Compass.Iterator.next()=Bio.Compass.Iterator-class.html#next,Method Bio.DocSQL.IterationCursor.next()=Bio.DocSQL.IterationCursor-class.html#next,Method Bio.File.UndoHandle.next()=Bio.File.UndoHandle-class.html#next,Method Bio.GenBank.Iterator.next()=Bio.GenBank.Iterator-class.html#next,Method Bio.Nexus.Nexus.CharBuffer.next()=Bio.Nexus.Nexus.CharBuffer-class.html#next,Method Bio.PopGen.GenePop.Controller._FileIterator.next()=Bio.PopGen.GenePop.Controller._FileIterator-class.html#next,Method Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next()=Bio.SeqIO.Interfaces.InterlacedSequenceIterator-class.html#next,Method Bio.SeqIO.Interfaces.SequenceIterator.next()=Bio.SeqIO.Interfaces.SequenceIterator-class.html#next,Method Bio.UniGene.Iterator.next()=Bio.UniGene.Iterator-class.html#next"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.File.UndoHandle.next
Bio.GenBank.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.PopGen.GenePop.Controller._FileIterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.UniGene.Iterator.next" class="py-name" href="#" onclick="return doclink('link-178', 'next', 'link-178');">next</a></tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L663"></a><tt class="py-lineno">663</tt> <tt class="py-line"> </tt><script type="text/javascript">
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