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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.GenBank-module.html">Package GenBank</a> ::
Module Record
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<h1 class="epydoc">Source Code for <a href="Bio.GenBank.Record-module.html">Module Bio.GenBank.Record</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-docstring">"""Hold GenBank data in a straightforward format.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-docstring">classes:</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-docstring">o Record - All of the information in a GenBank record.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-docstring">o Reference - hold reference data for a record.</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">o Feature - Hold the information in a Feature Table.</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring">o Qualifier - Qualifiers on a Feature.</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-comment"># local stuff</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">import</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Package Bio.GenBank=Bio.GenBank-module.html"><a title="Bio.GenBank" class="py-name" href="#" onclick="return doclink('link-1', 'GenBank', 'link-1');">GenBank</a></tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"> </tt>
<a name="_wrapped_genbank"></a><div id="_wrapped_genbank-def"><a name="L12"></a><tt class="py-lineno"> 12</tt> <a class="py-toggle" href="#" id="_wrapped_genbank-toggle" onclick="return toggle('_wrapped_genbank');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GenBank.Record-module.html#_wrapped_genbank">_wrapped_genbank</a><tt class="py-op">(</tt><tt class="py-param">information</tt><tt class="py-op">,</tt> <tt class="py-param">indent</tt><tt class="py-op">,</tt> <tt class="py-param">wrap_space</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-param">split_char</tt> <tt class="py-op">=</tt> <tt class="py-string">" "</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_wrapped_genbank-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_wrapped_genbank-expanded"><a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"> <tt class="py-docstring">"""Write a line of GenBank info that can wrap over multiple lines.</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"> This takes a line of information which can potentially wrap over</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring"> multiple lines, and breaks it up with carriage returns and</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-docstring"> indentation so it fits properly into a GenBank record.</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-docstring"> o information - The string holding the information we want</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-docstring"> wrapped in GenBank method.</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring"> o indent - The indentation on the lines we are writing.</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring"> o wrap_space - Whether or not to wrap only on spaces in the</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring"> information.</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-docstring"> o split_char - A specific character to split the lines on. By default</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring"> spaces are used.</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> <tt class="py-name">info_length</tt> <tt class="py-op">=</tt> <tt id="link-2" class="py-name" targets="Module Bio.Blast.Record=Bio.Blast.Record-module.html,Module Bio.CDD.Record=Bio.CDD.Record-module.html,Class Bio.CDD.Record.Record=Bio.CDD.Record.Record-class.html,Class Bio.Cluster.Record=Bio.Cluster.Record-class.html,Class Bio.Compass.Record=Bio.Compass.Record-class.html,Module Bio.ECell.Record=Bio.ECell.Record-module.html,Class Bio.ECell.Record.Record=Bio.ECell.Record.Record-class.html,Class Bio.Fasta.Record=Bio.Fasta.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.Gobase.Record=Bio.Gobase.Record-class.html,Module Bio.IntelliGenetics.Record=Bio.IntelliGenetics.Record-module.html,Class Bio.IntelliGenetics.Record.Record=Bio.IntelliGenetics.Record.Record-class.html,Class Bio.InterPro.Record=Bio.InterPro.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.LocusLink.Record=Bio.LocusLink.Record-class.html,Class Bio.LocusLink.web_parse.Record=Bio.LocusLink.web_parse.Record-class.html,Class Bio.Medline.Record=Bio.Medline.Record-class.html,Module Bio.MetaTool.Record=Bio.MetaTool.Record-module.html,Class Bio.MetaTool.Record.Record=Bio.MetaTool.Record.Record-class.html,Module Bio.NBRF.Record=Bio.NBRF.Record-module.html,Class Bio.NBRF.Record.Record=Bio.NBRF.Record.Record-class.html,Class Bio.Ndb.Record=Bio.Ndb.Record-class.html,Class Bio.PopGen.FDist.Record=Bio.PopGen.FDist.Record-class.html,Class Bio.PopGen.GenePop.Record=Bio.PopGen.GenePop.Record-class.html,Class Bio.Prosite.Prodoc.Record=Bio.Prosite.Prodoc.Record-class.html,Class Bio.Prosite.Record=Bio.Prosite.Record-class.html,Class Bio.Rebase.Record=Bio.Rebase.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,Module Bio.Saf.Record=Bio.Saf.Record-module.html,Class Bio.Saf.Record.Record=Bio.Saf.Record.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.SProt.Record=Bio.SwissProt.SProt.Record-class.html"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-2', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-3" class="py-name" targets="Variable Bio.GenBank.Record.Record.GB_LINE_LENGTH=Bio.GenBank.Record.Record-class.html#GB_LINE_LENGTH"><a title="Bio.GenBank.Record.Record.GB_LINE_LENGTH" class="py-name" href="#" onclick="return doclink('link-3', 'GB_LINE_LENGTH', 'link-3');">GB_LINE_LENGTH</a></tt> <tt class="py-op">-</tt> <tt class="py-name">indent</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">wrap_space</tt><tt class="py-op">:</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> <tt class="py-name">info_parts</tt> <tt class="py-op">=</tt> <tt class="py-name">information</tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Method Bio.Nexus.Trees.Tree.split()=Bio.Nexus.Trees.Tree-class.html#split,Method Bio.Restriction.Restriction.RestrictionBatch.split()=Bio.Restriction.Restriction.RestrictionBatch-class.html#split"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-4', 'split', 'link-4');">split</a></tt><tt class="py-op">(</tt><tt class="py-name">split_char</tt><tt class="py-op">)</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt class="py-name">cur_pos</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt class="py-name">info_parts</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-name">cur_pos</tt> <tt class="py-op"><</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">information</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> <tt class="py-name">info_parts</tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-class.html#append,Method Bio.EUtils.POM.ElementNode.append()=Bio.EUtils.POM.ElementNode-class.html#append,Method Bio.EUtils.sourcegen.SourceFile.append()=Bio.EUtils.sourcegen.SourceFile-class.html#append,Method Bio.SCOP.Raf.SeqMap.append()=Bio.SCOP.Raf.SeqMap-class.html#append,Method Bio.Seq.MutableSeq.append()=Bio.Seq.MutableSeq-class.html#append,Method Bio.Wise.psw.Alignment.append()=Bio.Wise.psw.Alignment-class.html#append,Method Bio.Wise.psw.AlignmentColumn.append()=Bio.Wise.psw.AlignmentColumn-class.html#append,Method Martel.msre_parse.SubPattern.append()=Martel.msre_parse.SubPattern-class.html#append"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-5', 'append', 'link-5');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">information</tt><tt class="py-op">[</tt><tt class="py-name">cur_pos</tt><tt class="py-op">:</tt> <tt class="py-name">cur_pos</tt> <tt class="py-op">+</tt> <tt class="py-name">info_length</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-name">cur_pos</tt> <tt class="py-op">+=</tt> <tt class="py-name">info_length</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt class="py-comment"># first get the information string split up by line</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">output_parts</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> <tt class="py-name">cur_part</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">info_part</tt> <tt class="py-keyword">in</tt> <tt class="py-name">info_parts</tt><tt class="py-op">:</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">cur_part</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt> <tt class="py-op">+</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">info_part</tt><tt class="py-op">)</tt> <tt class="py-op">></tt> <tt class="py-name">info_length</tt><tt class="py-op">:</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">cur_part</tt><tt class="py-op">:</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">split_char</tt> <tt class="py-op">!=</tt> <tt class="py-string">" "</tt><tt class="py-op">:</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt class="py-name">cur_part</tt> <tt class="py-op">+=</tt> <tt class="py-name">split_char</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt class="py-name">output_parts</tt><tt class="py-op">.</tt><tt id="link-6" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-6', 'append', 'link-5');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">cur_part</tt><tt class="py-op">)</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> <tt class="py-name">cur_part</tt> <tt class="py-op">=</tt> <tt class="py-name">info_part</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">cur_part</tt> <tt class="py-op">==</tt> <tt class="py-string">""</tt><tt class="py-op">:</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-name">cur_part</tt> <tt class="py-op">=</tt> <tt class="py-name">info_part</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-name">cur_part</tt> <tt class="py-op">+=</tt> <tt class="py-name">split_char</tt> <tt class="py-op">+</tt> <tt class="py-name">info_part</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-comment"># add the last bit of information to the output</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">cur_part</tt><tt class="py-op">:</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-name">output_parts</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-7', 'append', 'link-5');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">cur_part</tt><tt class="py-op">)</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-comment"># now format the information string for return</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">output_info</tt> <tt class="py-op">=</tt> <tt class="py-name">output_parts</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-string">"\n"</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">output_part</tt> <tt class="py-keyword">in</tt> <tt class="py-name">output_parts</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-name">output_info</tt> <tt class="py-op">+=</tt> <tt class="py-string">" "</tt> <tt class="py-op">*</tt> <tt class="py-name">indent</tt> <tt class="py-op">+</tt> <tt class="py-name">output_part</tt> <tt class="py-op">+</tt> <tt class="py-string">"\n"</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">output_info</tt> </tt>
</div><a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> </tt>
<a name="_indent_genbank"></a><div id="_indent_genbank-def"><a name="L70"></a><tt class="py-lineno"> 70</tt> <a class="py-toggle" href="#" id="_indent_genbank-toggle" onclick="return toggle('_indent_genbank');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GenBank.Record-module.html#_indent_genbank">_indent_genbank</a><tt class="py-op">(</tt><tt class="py-param">information</tt><tt class="py-op">,</tt> <tt class="py-param">indent</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_indent_genbank-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_indent_genbank-expanded"><a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-docstring">"""Write out information with the specified indent.</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"><tt class="py-docstring"> Unlike _wrapped_genbank, this function makes no attempt to wrap</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"><tt class="py-docstring"> lines -- it assumes that the information already has newlines in the</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"><tt class="py-docstring"> appropriate places, and will add the specified indent to the start of</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"><tt class="py-docstring"> each line.</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-comment"># split the info into lines based on line breaks</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">info_parts</tt> <tt class="py-op">=</tt> <tt class="py-name">information</tt><tt class="py-op">.</tt><tt id="link-8" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-8', 'split', 'link-4');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">"\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-comment"># the first line will have no indent</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">output_info</tt> <tt class="py-op">=</tt> <tt class="py-name">info_parts</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-string">"\n"</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">info_part</tt> <tt class="py-keyword">in</tt> <tt class="py-name">info_parts</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-name">output_info</tt> <tt class="py-op">+=</tt> <tt class="py-string">" "</tt> <tt class="py-op">*</tt> <tt class="py-name">indent</tt> <tt class="py-op">+</tt> <tt class="py-name">info_part</tt> <tt class="py-op">+</tt> <tt class="py-string">"\n"</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">output_info</tt> </tt>
</div><a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> </tt>
<a name="Record"></a><div id="Record-def"><a name="L88"></a><tt class="py-lineno"> 88</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.GenBank.Record.Record-class.html">Record</a><tt class="py-op">:</tt> </tt>
</div><div id="Record-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Record-expanded"><a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-docstring">"""Hold GenBank information in a format similar to the original record.</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"><tt class="py-docstring"> The Record class is meant to make data easy to get to when you are</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"><tt class="py-docstring"> just interested in looking at GenBank data.</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"><tt class="py-docstring"> Attributes:</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"><tt class="py-docstring"> o locus - The name specified after the LOCUS keyword in the GenBank</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"><tt class="py-docstring"> record. This may be the accession number, or a clone id or something else.</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"><tt class="py-docstring"> o size - The size of the record.</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"><tt class="py-docstring"> o residue_type - The type of residues making up the sequence in this</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"><tt class="py-docstring"> record. Normally something like RNA, DNA or PROTEIN, but may be as</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"><tt class="py-docstring"> esoteric as 'ss-RNA circular'.</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"><tt class="py-docstring"> o data_file_division - The division this record is stored under in</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"><tt class="py-docstring"> GenBank (ie. PLN -> plants; PRI -> humans, primates; BCT -> bacteria...)</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"><tt class="py-docstring"> o date - The date of submission of the record, in a form like '28-JUL-1998'</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"><tt class="py-docstring"> o accession - list of all accession numbers for the sequence.</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"><tt class="py-docstring"> o nid - Nucleotide identifier number.</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"><tt class="py-docstring"> o pid - Proteint identifier number</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"><tt class="py-docstring"> o version - The accession number + version (ie. AB01234.2)</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"><tt class="py-docstring"> o db_source - Information about the database the record came from</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"><tt class="py-docstring"> o gi - The NCBI gi identifier for the record.</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"><tt class="py-docstring"> o keywords - A list of keywords related to the record.</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"><tt class="py-docstring"> o segment - If the record is one of a series, this is info about which</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"><tt class="py-docstring"> segment this record is (something like '1 of 6').</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"><tt class="py-docstring"> o source - The source of material where the sequence came from.</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"><tt class="py-docstring"> o organism - The genus and species of the organism (ie. 'Homo sapiens')</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"><tt class="py-docstring"> o taxonomy - A listing of the taxonomic classification of the organism,</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"><tt class="py-docstring"> starting general and getting more specific.</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"><tt class="py-docstring"> o references - A list of Reference objects.</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"><tt class="py-docstring"> o comment - Text with any kind of comment about the record.</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"><tt class="py-docstring"> o features - A listing of Features making up the feature table.</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"><tt class="py-docstring"> o base_counts - A string with the counts of bases for the sequence.</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"><tt class="py-docstring"> o origin - A string specifying info about the origin of the sequence.</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"><tt class="py-docstring"> o sequence - A string with the sequence itself.</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"><tt class="py-docstring"> o contig - A string of location information for a CONTIG in a RefSeq</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"><tt class="py-docstring"> file.</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt class="py-comment"># constants for outputting GenBank information</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-9" class="py-name"><a title="Bio.GenBank.Record.Record.GB_LINE_LENGTH" class="py-name" href="#" onclick="return doclink('link-9', 'GB_LINE_LENGTH', 'link-3');">GB_LINE_LENGTH</a></tt> <tt class="py-op">=</tt> <tt class="py-number">79</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt id="link-10" class="py-name" targets="Variable Bio.GenBank.Record.Record.GB_BASE_INDENT=Bio.GenBank.Record.Record-class.html#GB_BASE_INDENT"><a title="Bio.GenBank.Record.Record.GB_BASE_INDENT" class="py-name" href="#" onclick="return doclink('link-10', 'GB_BASE_INDENT', 'link-10');">GB_BASE_INDENT</a></tt> <tt class="py-op">=</tt> <tt class="py-number">12</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt id="link-11" class="py-name" targets="Variable Bio.GenBank.Record.Record.GB_FEATURE_INDENT=Bio.GenBank.Record.Record-class.html#GB_FEATURE_INDENT"><a title="Bio.GenBank.Record.Record.GB_FEATURE_INDENT" class="py-name" href="#" onclick="return doclink('link-11', 'GB_FEATURE_INDENT', 'link-11');">GB_FEATURE_INDENT</a></tt> <tt class="py-op">=</tt> <tt class="py-number">21</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt id="link-12" class="py-name" targets="Variable Bio.GenBank.Record.Record.GB_INTERNAL_INDENT=Bio.GenBank.Record.Record-class.html#GB_INTERNAL_INDENT"><a title="Bio.GenBank.Record.Record.GB_INTERNAL_INDENT" class="py-name" href="#" onclick="return doclink('link-12', 'GB_INTERNAL_INDENT', 'link-12');">GB_INTERNAL_INDENT</a></tt> <tt class="py-op">=</tt> <tt class="py-number">2</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt id="link-13" class="py-name" targets="Variable Bio.GenBank.Record.Record.GB_OTHER_INTERNAL_INDENT=Bio.GenBank.Record.Record-class.html#GB_OTHER_INTERNAL_INDENT"><a title="Bio.GenBank.Record.Record.GB_OTHER_INTERNAL_INDENT" class="py-name" href="#" onclick="return doclink('link-13', 'GB_OTHER_INTERNAL_INDENT', 'link-13');">GB_OTHER_INTERNAL_INDENT</a></tt> <tt class="py-op">=</tt> <tt class="py-number">3</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt id="link-14" class="py-name" targets="Variable Bio.GenBank.Record.Record.GB_FEATURE_INTERNAL_INDENT=Bio.GenBank.Record.Record-class.html#GB_FEATURE_INTERNAL_INDENT"><a title="Bio.GenBank.Record.Record.GB_FEATURE_INTERNAL_INDENT" class="py-name" href="#" onclick="return doclink('link-14', 'GB_FEATURE_INTERNAL_INDENT', 'link-14');">GB_FEATURE_INTERNAL_INDENT</a></tt> <tt class="py-op">=</tt> <tt class="py-number">5</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt id="link-15" class="py-name" targets="Variable Bio.GenBank.Record.Record.GB_SEQUENCE_INDENT=Bio.GenBank.Record.Record-class.html#GB_SEQUENCE_INDENT"><a title="Bio.GenBank.Record.Record.GB_SEQUENCE_INDENT" class="py-name" href="#" onclick="return doclink('link-15', 'GB_SEQUENCE_INDENT', 'link-15');">GB_SEQUENCE_INDENT</a></tt> <tt class="py-op">=</tt> <tt class="py-number">9</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt id="link-16" class="py-name" targets="Variable Bio.GenBank.Record.Record.BASE_FORMAT=Bio.GenBank.Record.Record-class.html#BASE_FORMAT"><a title="Bio.GenBank.Record.Record.BASE_FORMAT" class="py-name" href="#" onclick="return doclink('link-16', 'BASE_FORMAT', 'link-16');">BASE_FORMAT</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"%-"</tt> <tt class="py-op">+</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-17" class="py-name"><a title="Bio.GenBank.Record.Record.GB_BASE_INDENT" class="py-name" href="#" onclick="return doclink('link-17', 'GB_BASE_INDENT', 'link-10');">GB_BASE_INDENT</a></tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">"s"</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt id="link-18" class="py-name" targets="Variable Bio.GenBank.Record.Record.INTERNAL_FORMAT=Bio.GenBank.Record.Record-class.html#INTERNAL_FORMAT"><a title="Bio.GenBank.Record.Record.INTERNAL_FORMAT" class="py-name" href="#" onclick="return doclink('link-18', 'INTERNAL_FORMAT', 'link-18');">INTERNAL_FORMAT</a></tt> <tt class="py-op">=</tt> <tt class="py-string">" "</tt> <tt class="py-op">*</tt> <tt id="link-19" class="py-name"><a title="Bio.GenBank.Record.Record.GB_INTERNAL_INDENT" class="py-name" href="#" onclick="return doclink('link-19', 'GB_INTERNAL_INDENT', 'link-12');">GB_INTERNAL_INDENT</a></tt> <tt class="py-op">+</tt> <tt class="py-string">"%-"</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-20" class="py-name"><a title="Bio.GenBank.Record.Record.GB_BASE_INDENT" class="py-name" href="#" onclick="return doclink('link-20', 'GB_BASE_INDENT', 'link-10');">GB_BASE_INDENT</a></tt> <tt class="py-op">-</tt> <tt id="link-21" class="py-name"><a title="Bio.GenBank.Record.Record.GB_INTERNAL_INDENT" class="py-name" href="#" onclick="return doclink('link-21', 'GB_INTERNAL_INDENT', 'link-12');">GB_INTERNAL_INDENT</a></tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">"s"</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt id="link-22" class="py-name" targets="Variable Bio.GenBank.Record.Record.OTHER_INTERNAL_FORMAT=Bio.GenBank.Record.Record-class.html#OTHER_INTERNAL_FORMAT"><a title="Bio.GenBank.Record.Record.OTHER_INTERNAL_FORMAT" class="py-name" href="#" onclick="return doclink('link-22', 'OTHER_INTERNAL_FORMAT', 'link-22');">OTHER_INTERNAL_FORMAT</a></tt> <tt class="py-op">=</tt> <tt class="py-string">" "</tt> <tt class="py-op">*</tt> <tt id="link-23" class="py-name"><a title="Bio.GenBank.Record.Record.GB_OTHER_INTERNAL_INDENT" class="py-name" href="#" onclick="return doclink('link-23', 'GB_OTHER_INTERNAL_INDENT', 'link-13');">GB_OTHER_INTERNAL_INDENT</a></tt> <tt class="py-op">+</tt> <tt class="py-string">"%-"</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-24" class="py-name"><a title="Bio.GenBank.Record.Record.GB_BASE_INDENT" class="py-name" href="#" onclick="return doclink('link-24', 'GB_BASE_INDENT', 'link-10');">GB_BASE_INDENT</a></tt> <tt class="py-op">-</tt> <tt id="link-25" class="py-name"><a title="Bio.GenBank.Record.Record.GB_OTHER_INTERNAL_INDENT" class="py-name" href="#" onclick="return doclink('link-25', 'GB_OTHER_INTERNAL_INDENT', 'link-13');">GB_OTHER_INTERNAL_INDENT</a></tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-string">"s"</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt id="link-26" class="py-name" targets="Variable Bio.GenBank.Record.Record.BASE_FEATURE_FORMAT=Bio.GenBank.Record.Record-class.html#BASE_FEATURE_FORMAT"><a title="Bio.GenBank.Record.Record.BASE_FEATURE_FORMAT" class="py-name" href="#" onclick="return doclink('link-26', 'BASE_FEATURE_FORMAT', 'link-26');">BASE_FEATURE_FORMAT</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"%-"</tt> <tt class="py-op">+</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-27" class="py-name"><a title="Bio.GenBank.Record.Record.GB_FEATURE_INDENT" class="py-name" href="#" onclick="return doclink('link-27', 'GB_FEATURE_INDENT', 'link-11');">GB_FEATURE_INDENT</a></tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">"s"</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt id="link-28" class="py-name" targets="Variable Bio.GenBank.Record.Record.INTERNAL_FEATURE_FORMAT=Bio.GenBank.Record.Record-class.html#INTERNAL_FEATURE_FORMAT"><a title="Bio.GenBank.Record.Record.INTERNAL_FEATURE_FORMAT" class="py-name" href="#" onclick="return doclink('link-28', 'INTERNAL_FEATURE_FORMAT', 'link-28');">INTERNAL_FEATURE_FORMAT</a></tt> <tt class="py-op">=</tt> <tt class="py-string">" "</tt> <tt class="py-op">*</tt> <tt id="link-29" class="py-name"><a title="Bio.GenBank.Record.Record.GB_FEATURE_INTERNAL_INDENT" class="py-name" href="#" onclick="return doclink('link-29', 'GB_FEATURE_INTERNAL_INDENT', 'link-14');">GB_FEATURE_INTERNAL_INDENT</a></tt> <tt class="py-op">+</tt> <tt class="py-string">"%-"</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-30" class="py-name"><a title="Bio.GenBank.Record.Record.GB_FEATURE_INDENT" class="py-name" href="#" onclick="return doclink('link-30', 'GB_FEATURE_INDENT', 'link-11');">GB_FEATURE_INDENT</a></tt> <tt class="py-op">-</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt id="link-31" class="py-name"><a title="Bio.GenBank.Record.Record.GB_FEATURE_INTERNAL_INDENT" class="py-name" href="#" onclick="return doclink('link-31', 'GB_FEATURE_INTERNAL_INDENT', 'link-14');">GB_FEATURE_INTERNAL_INDENT</a></tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">"s"</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt id="link-32" class="py-name" targets="Variable Bio.GenBank.Record.Record.SEQUENCE_FORMAT=Bio.GenBank.Record.Record-class.html#SEQUENCE_FORMAT"><a title="Bio.GenBank.Record.Record.SEQUENCE_FORMAT" class="py-name" href="#" onclick="return doclink('link-32', 'SEQUENCE_FORMAT', 'link-32');">SEQUENCE_FORMAT</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"%"</tt> <tt class="py-op">+</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-33" class="py-name"><a title="Bio.GenBank.Record.Record.GB_SEQUENCE_INDENT" class="py-name" href="#" onclick="return doclink('link-33', 'GB_SEQUENCE_INDENT', 'link-15');">GB_SEQUENCE_INDENT</a></tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">"s"</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> </tt>
<a name="Record.__init__"></a><div id="Record.__init__-def"><a name="L148"></a><tt class="py-lineno">148</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.GenBank.Record.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="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-34" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.locus()=Bio.GenBank._FeatureConsumer-class.html#locus,Method Bio.GenBank._RecordConsumer.locus()=Bio.GenBank._RecordConsumer-class.html#locus,Variable Bio.expressions.genbank.locus=Bio.expressions.genbank-module.html#locus"><a title="Bio.GenBank._FeatureConsumer.locus
Bio.GenBank._RecordConsumer.locus
Bio.expressions.genbank.locus" class="py-name" href="#" onclick="return doclink('link-34', 'locus', 'link-34');">locus</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-35" class="py-name" targets="Method Bio.Affy.CelFile.CelRecord.size()=Bio.Affy.CelFile.CelRecord-class.html#size,Variable Bio.Alphabet.Alphabet.size=Bio.Alphabet.Alphabet-class.html#size,Variable Bio.Alphabet.Reduced.HPModel.size=Bio.Alphabet.Reduced.HPModel-class.html#size,Variable Bio.Alphabet.Reduced.Murphy10.size=Bio.Alphabet.Reduced.Murphy10-class.html#size,Variable Bio.Alphabet.Reduced.Murphy15.size=Bio.Alphabet.Reduced.Murphy15-class.html#size,Variable Bio.Alphabet.Reduced.Murphy4.size=Bio.Alphabet.Reduced.Murphy4-class.html#size,Variable Bio.Alphabet.Reduced.Murphy8.size=Bio.Alphabet.Reduced.Murphy8-class.html#size,Variable Bio.Alphabet.Reduced.PC5.size=Bio.Alphabet.Reduced.PC5-class.html#size,Variable Bio.Alphabet.SingleLetterAlphabet.size=Bio.Alphabet.SingleLetterAlphabet-class.html#size,Variable Bio.Alphabet.ThreeLetterProtein.size=Bio.Alphabet.ThreeLetterProtein-class.html#size,Method Bio.GenBank._FeatureConsumer.size()=Bio.GenBank._FeatureConsumer-class.html#size,Method Bio.GenBank._RecordConsumer.size()=Bio.GenBank._RecordConsumer-class.html#size,Variable Bio.expressions.genbank.size=Bio.expressions.genbank-module.html#size"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-35', 'size', 'link-35');">size</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-36" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.residue_type()=Bio.GenBank._FeatureConsumer-class.html#residue_type,Method Bio.GenBank._RecordConsumer.residue_type()=Bio.GenBank._RecordConsumer-class.html#residue_type,Variable Bio.expressions.genbank.residue_type=Bio.expressions.genbank-module.html#residue_type"><a title="Bio.GenBank._FeatureConsumer.residue_type
Bio.GenBank._RecordConsumer.residue_type
Bio.expressions.genbank.residue_type" class="py-name" href="#" onclick="return doclink('link-36', 'residue_type', 'link-36');">residue_type</a></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 id="link-37" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.data_file_division()=Bio.GenBank._FeatureConsumer-class.html#data_file_division,Method Bio.GenBank._RecordConsumer.data_file_division()=Bio.GenBank._RecordConsumer-class.html#data_file_division,Variable Bio.expressions.genbank.data_file_division=Bio.expressions.genbank-module.html#data_file_division"><a title="Bio.GenBank._FeatureConsumer.data_file_division
Bio.GenBank._RecordConsumer.data_file_division
Bio.expressions.genbank.data_file_division" class="py-name" href="#" onclick="return doclink('link-37', 'data_file_division', 'link-37');">data_file_division</a></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 id="link-38" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.date()=Bio.GenBank._FeatureConsumer-class.html#date,Method Bio.GenBank._RecordConsumer.date()=Bio.GenBank._RecordConsumer-class.html#date,Method Bio.Prosite._RecordConsumer.date()=Bio.Prosite._RecordConsumer-class.html#date,Method Bio.SwissProt.SProt._RecordConsumer.date()=Bio.SwissProt.SProt._RecordConsumer-class.html#date,Method Bio.SwissProt.SProt._SequenceConsumer.date()=Bio.SwissProt.SProt._SequenceConsumer-class.html#date,Variable Bio.expressions.embl.embl65.date=Bio.expressions.embl.embl65-module.html#date,Variable Bio.expressions.genbank.date=Bio.expressions.genbank-module.html#date"><a title="Bio.GenBank._FeatureConsumer.date
Bio.GenBank._RecordConsumer.date
Bio.Prosite._RecordConsumer.date
Bio.SwissProt.SProt._RecordConsumer.date
Bio.SwissProt.SProt._SequenceConsumer.date
Bio.expressions.embl.embl65.date
Bio.expressions.genbank.date" class="py-name" href="#" onclick="return doclink('link-38', 'date', 'link-38');">date</a></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 id="link-39" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.definition()=Bio.GenBank._FeatureConsumer-class.html#definition,Method Bio.GenBank._RecordConsumer.definition()=Bio.GenBank._RecordConsumer-class.html#definition"><a title="Bio.GenBank._FeatureConsumer.definition
Bio.GenBank._RecordConsumer.definition" class="py-name" href="#" onclick="return doclink('link-39', 'definition', 'link-39');">definition</a></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 id="link-40" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.accession()=Bio.GenBank._FeatureConsumer-class.html#accession,Method Bio.GenBank._RecordConsumer.accession()=Bio.GenBank._RecordConsumer-class.html#accession,Method Bio.Prosite.Prodoc._RecordConsumer.accession()=Bio.Prosite.Prodoc._RecordConsumer-class.html#accession,Method Bio.Prosite._RecordConsumer.accession()=Bio.Prosite._RecordConsumer-class.html#accession,Method Bio.SwissProt.SProt._RecordConsumer.accession()=Bio.SwissProt.SProt._RecordConsumer-class.html#accession,Method Bio.SwissProt.SProt._SequenceConsumer.accession()=Bio.SwissProt.SProt._SequenceConsumer-class.html#accession,Variable Bio.expressions.embl.embl65.accession=Bio.expressions.embl.embl65-module.html#accession,Variable Bio.expressions.genbank.accession=Bio.expressions.genbank-module.html#accession"><a title="Bio.GenBank._FeatureConsumer.accession
Bio.GenBank._RecordConsumer.accession
Bio.Prosite.Prodoc._RecordConsumer.accession
Bio.Prosite._RecordConsumer.accession
Bio.SwissProt.SProt._RecordConsumer.accession
Bio.SwissProt.SProt._SequenceConsumer.accession
Bio.expressions.embl.embl65.accession
Bio.expressions.genbank.accession" class="py-name" href="#" onclick="return doclink('link-40', 'accession', 'link-40');">accession</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-41" 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,Variable Bio.expressions.genbank.nid=Bio.expressions.genbank-module.html#nid"><a title="Bio.GenBank._FeatureConsumer.nid
Bio.GenBank._RecordConsumer.nid
Bio.expressions.genbank.nid" class="py-name" href="#" onclick="return doclink('link-41', 'nid', 'link-41');">nid</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</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 id="link-42" 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,Variable Bio.expressions.genbank.pid=Bio.expressions.genbank-module.html#pid"><a title="Bio.GenBank._FeatureConsumer.pid
Bio.GenBank._RecordConsumer.pid
Bio.expressions.genbank.pid" class="py-name" href="#" onclick="return doclink('link-42', 'pid', 'link-42');">pid</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</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-43" class="py-name" targets="Method Bio.AlignAce.Parser.AlignAceConsumer.version()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#version,Method Bio.Blast.NCBIStandalone._HeaderConsumer.version()=Bio.Blast.NCBIStandalone._HeaderConsumer-class.html#version,Method Bio.GenBank._FeatureConsumer.version()=Bio.GenBank._FeatureConsumer-class.html#version,Method Bio.GenBank._RecordConsumer.version()=Bio.GenBank._RecordConsumer-class.html#version,Variable Bio.MetaTool.metatool_format.version=Bio.MetaTool.metatool_format-module.html#version,Variable Bio.expressions.genbank.version=Bio.expressions.genbank-module.html#version"><a title="Bio.AlignAce.Parser.AlignAceConsumer.version
Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version
Bio.MetaTool.metatool_format.version
Bio.expressions.genbank.version" class="py-name" href="#" onclick="return doclink('link-43', 'version', 'link-43');">version</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-44" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.db_source()=Bio.GenBank._FeatureConsumer-class.html#db_source,Method Bio.GenBank._RecordConsumer.db_source()=Bio.GenBank._RecordConsumer-class.html#db_source"><a title="Bio.GenBank._FeatureConsumer.db_source
Bio.GenBank._RecordConsumer.db_source" class="py-name" href="#" onclick="return doclink('link-44', 'db_source', 'link-44');">db_source</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-45" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.gi()=Bio.GenBank._FeatureConsumer-class.html#gi,Method Bio.GenBank._RecordConsumer.gi()=Bio.GenBank._RecordConsumer-class.html#gi,Variable Bio.expressions.genbank.gi=Bio.expressions.genbank-module.html#gi"><a title="Bio.GenBank._FeatureConsumer.gi
Bio.GenBank._RecordConsumer.gi
Bio.expressions.genbank.gi" class="py-name" href="#" onclick="return doclink('link-45', 'gi', 'link-45');">gi</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-46" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.keywords()=Bio.GenBank._FeatureConsumer-class.html#keywords,Method Bio.GenBank._RecordConsumer.keywords()=Bio.GenBank._RecordConsumer-class.html#keywords"><a title="Bio.GenBank._FeatureConsumer.keywords
Bio.GenBank._RecordConsumer.keywords" class="py-name" href="#" onclick="return doclink('link-46', 'keywords', 'link-46');">keywords</a></tt> <tt class="py-op">=</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 class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-47" class="py-name" targets="Method Bio.GFF.Connection.segment()=Bio.GFF.Connection-class.html#segment,Method Bio.GenBank._FeatureConsumer.segment()=Bio.GenBank._FeatureConsumer-class.html#segment,Method Bio.GenBank._RecordConsumer.segment()=Bio.GenBank._RecordConsumer-class.html#segment,Variable Bio.expressions.blocks.segment=Bio.expressions.blocks-module.html#segment,Variable Bio.expressions.genbank.segment=Bio.expressions.genbank-module.html#segment"><a title="Bio.GFF.Connection.segment
Bio.GenBank._FeatureConsumer.segment
Bio.GenBank._RecordConsumer.segment
Bio.expressions.blocks.segment
Bio.expressions.genbank.segment" class="py-name" href="#" onclick="return doclink('link-47', 'segment', 'link-47');">segment</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-48" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.source()=Bio.GenBank._FeatureConsumer-class.html#source,Method Bio.GenBank._RecordConsumer.source()=Bio.GenBank._RecordConsumer-class.html#source,Method Bio.Medline._RecordConsumer.source()=Bio.Medline._RecordConsumer-class.html#source,Method Bio.Pathway.Network.source()=Bio.Pathway.Network-class.html#source,Method Bio.Rebase._RecordConsumer.source()=Bio.Rebase._RecordConsumer-class.html#source"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-48', 'source', 'link-48');">source</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-49" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.organism()=Bio.GenBank._FeatureConsumer-class.html#organism,Method Bio.GenBank._RecordConsumer.organism()=Bio.GenBank._RecordConsumer-class.html#organism,Variable Bio.expressions.embl.embl65.organism=Bio.expressions.embl.embl65-module.html#organism,Variable Bio.expressions.genbank.organism=Bio.expressions.genbank-module.html#organism"><a title="Bio.GenBank._FeatureConsumer.organism
Bio.GenBank._RecordConsumer.organism
Bio.expressions.embl.embl65.organism
Bio.expressions.genbank.organism" class="py-name" href="#" onclick="return doclink('link-49', 'organism', 'link-49');">organism</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-50" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.taxonomy()=Bio.GenBank._FeatureConsumer-class.html#taxonomy,Method Bio.GenBank._RecordConsumer.taxonomy()=Bio.GenBank._RecordConsumer-class.html#taxonomy,Variable Bio.expressions.genbank.taxonomy=Bio.expressions.genbank-module.html#taxonomy"><a title="Bio.GenBank._FeatureConsumer.taxonomy
Bio.GenBank._RecordConsumer.taxonomy
Bio.expressions.genbank.taxonomy" class="py-name" href="#" onclick="return doclink('link-50', 'taxonomy', 'link-50');">taxonomy</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">references</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-51" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.comment()=Bio.EUtils.POM.ElementNode-class.html#comment,Method Bio.Enzyme._RecordConsumer.comment()=Bio.Enzyme._RecordConsumer-class.html#comment,Method Bio.GenBank._FeatureConsumer.comment()=Bio.GenBank._FeatureConsumer-class.html#comment,Method Bio.GenBank._RecordConsumer.comment()=Bio.GenBank._RecordConsumer-class.html#comment,Method Bio.IntelliGenetics._RecordConsumer.comment()=Bio.IntelliGenetics._RecordConsumer-class.html#comment,Method Bio.NBRF._RecordConsumer.comment()=Bio.NBRF._RecordConsumer-class.html#comment,Method Bio.PopGen.GenePop._RecordConsumer.comment()=Bio.PopGen.GenePop._RecordConsumer-class.html#comment,Method Bio.Prosite._RecordConsumer.comment()=Bio.Prosite._RecordConsumer-class.html#comment,Method Bio.SwissProt.SProt._RecordConsumer.comment()=Bio.SwissProt.SProt._RecordConsumer-class.html#comment,Method Bio.SwissProt.SProt._SequenceConsumer.comment()=Bio.SwissProt.SProt._SequenceConsumer-class.html#comment,Variable Bio.expressions.swissprot.sprot38.comment=Bio.expressions.swissprot.sprot38-module.html#comment,Variable Martel.test.test_swissprot38.comment=Martel.test.test_swissprot38-module.html#comment,Variable Martel.test.testformats.swissprot38.comment=Martel.test.testformats.swissprot38-module.html#comment"><a title="Bio.EUtils.POM.ElementNode.comment
Bio.Enzyme._RecordConsumer.comment
Bio.GenBank._FeatureConsumer.comment
Bio.GenBank._RecordConsumer.comment
Bio.IntelliGenetics._RecordConsumer.comment
Bio.NBRF._RecordConsumer.comment
Bio.PopGen.GenePop._RecordConsumer.comment
Bio.Prosite._RecordConsumer.comment
Bio.SwissProt.SProt._RecordConsumer.comment
Bio.SwissProt.SProt._SequenceConsumer.comment
Bio.expressions.swissprot.sprot38.comment
Martel.test.test_swissprot38.comment
Martel.test.testformats.swissprot38.comment" class="py-name" href="#" onclick="return doclink('link-51', 'comment', 'link-51');">comment</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-52" class="py-name" targets="Method Bio.GFF.Segment.features()=Bio.GFF.Segment-class.html#features,Variable BioSQL.BioSeq.DBSeqRecord.features=BioSQL.BioSeq.DBSeqRecord-class.html#features,Method Martel.Expression.Expression.features()=Martel.Expression.Expression-class.html#features,Method Martel.Expression.ExpressionList.features()=Martel.Expression.ExpressionList-class.html#features,Method Martel.Expression.FastFeature.features()=Martel.Expression.FastFeature-class.html#features,Method Martel.Expression.Group.features()=Martel.Expression.Group-class.html#features,Method Martel.Expression.HeaderFooter.features()=Martel.Expression.HeaderFooter-class.html#features,Method Martel.Expression.MaxRepeat.features()=Martel.Expression.MaxRepeat-class.html#features,Method Martel.Expression.ParseRecords.features()=Martel.Expression.ParseRecords-class.html#features,Method Martel.Expression.PassThrough.features()=Martel.Expression.PassThrough-class.html#features"><a title="Bio.GFF.Segment.features
BioSQL.BioSeq.DBSeqRecord.features
Martel.Expression.Expression.features
Martel.Expression.ExpressionList.features
Martel.Expression.FastFeature.features
Martel.Expression.Group.features
Martel.Expression.HeaderFooter.features
Martel.Expression.MaxRepeat.features
Martel.Expression.ParseRecords.features
Martel.Expression.PassThrough.features" class="py-name" href="#" onclick="return doclink('link-52', 'features', 'link-52');">features</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">base_counts</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">origin</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-53" class="py-name" targets="Method Bio.AlignAce.Parser.AlignAceConsumer.sequence()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#sequence,Variable Bio.Emboss.primer3_format.sequence=Bio.Emboss.primer3_format-module.html#sequence,Method Bio.FSSP.FSSPAlignDict.sequence()=Bio.FSSP.FSSPAlignDict-class.html#sequence,Method Bio.GenBank._FeatureConsumer.sequence()=Bio.GenBank._FeatureConsumer-class.html#sequence,Method Bio.GenBank._RecordConsumer.sequence()=Bio.GenBank._RecordConsumer-class.html#sequence,Method Bio.IntelliGenetics._RecordConsumer.sequence()=Bio.IntelliGenetics._RecordConsumer-class.html#sequence,Method Bio.Rebase._RecordConsumer.sequence()=Bio.Rebase._RecordConsumer-class.html#sequence,Function Bio.Std.sequence()=Bio.Std-module.html#sequence,Module Bio.builders.SeqRecord.sequence=Bio.builders.SeqRecord.sequence-module.html,Variable Bio.expressions.fasta.sequence=Bio.expressions.fasta-module.html#sequence,Variable Bio.expressions.genbank.sequence=Bio.expressions.genbank-module.html#sequence,Variable Bio.expressions.swissprot.sprot38.sequence=Bio.expressions.swissprot.sprot38-module.html#sequence,Module Bio.formatdefs.sequence=Bio.formatdefs.sequence-module.html,Variable Bio.formatdefs.sequence.sequence=Bio.formatdefs.sequence-module.html#sequence,Variable Martel.test.test_swissprot38.sequence=Martel.test.test_swissprot38-module.html#sequence,Variable Martel.test.testformats.swissprot38.sequence=Martel.test.testformats.swissprot38-module.html#sequence"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-53', 'sequence', 'link-53');">sequence</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">contig</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-54" class="py-name" targets="Method Bio.GenBank._RecordConsumer.primary()=Bio.GenBank._RecordConsumer-class.html#primary,Variable Bio.expressions.genbank.primary=Bio.expressions.genbank-module.html#primary"><a title="Bio.GenBank._RecordConsumer.primary
Bio.expressions.genbank.primary" class="py-name" href="#" onclick="return doclink('link-54', 'primary', 'link-54');">primary</a></tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
</div><a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> </tt>
<a name="Record.__str__"></a><div id="Record.__str__-def"><a name="L175"></a><tt class="py-lineno">175</tt> <a class="py-toggle" href="#" id="Record.__str__-toggle" onclick="return toggle('Record.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GenBank.Record.Record-class.html#__str__">__str__</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.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Record.__str__-expanded"><a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt class="py-docstring">"""Provide a GenBank formatted output option for a Record.</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"> The objective of this is to provide an easy way to read in a GenBank</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"><tt class="py-docstring"> record, modify it somehow, and then output it in 'GenBank format.'</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"><tt class="py-docstring"> We are striving to make this work so that a parsed Record that is</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"><tt class="py-docstring"> output using this function will look exactly like the original</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"><tt class="py-docstring"> record.</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"><tt class="py-docstring"> Much of the output is based on format description info at:</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"><tt class="py-docstring"> ftp://ncbi.nlm.nih.gov/genbank/gbrel.txt</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-55" class="py-name" targets="Method Bio.GenBank.Record.Record._locus_line()=Bio.GenBank.Record.Record-class.html#_locus_line"><a title="Bio.GenBank.Record.Record._locus_line" class="py-name" href="#" onclick="return doclink('link-55', '_locus_line', 'link-55');">_locus_line</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-56" class="py-name" targets="Method Bio.GenBank.Record.Record._definition_line()=Bio.GenBank.Record.Record-class.html#_definition_line"><a title="Bio.GenBank.Record.Record._definition_line" class="py-name" href="#" onclick="return doclink('link-56', '_definition_line', 'link-56');">_definition_line</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-57" class="py-name" targets="Method Bio.GenBank.Record.Record._accession_line()=Bio.GenBank.Record.Record-class.html#_accession_line"><a title="Bio.GenBank.Record.Record._accession_line" class="py-name" href="#" onclick="return doclink('link-57', '_accession_line', 'link-57');">_accession_line</a></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 class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-58" class="py-name" targets="Method Bio.GenBank.Record.Record._version_line()=Bio.GenBank.Record.Record-class.html#_version_line"><a title="Bio.GenBank.Record.Record._version_line" class="py-name" href="#" onclick="return doclink('link-58', '_version_line', 'link-58');">_version_line</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-59" class="py-name" targets="Method Bio.GenBank.Record.Record._nid_line()=Bio.GenBank.Record.Record-class.html#_nid_line"><a title="Bio.GenBank.Record.Record._nid_line" class="py-name" href="#" onclick="return doclink('link-59', '_nid_line', 'link-59');">_nid_line</a></tt><tt class="py-op">(</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">output</tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-60" class="py-name" targets="Method Bio.GenBank.Record.Record._pid_line()=Bio.GenBank.Record.Record-class.html#_pid_line"><a title="Bio.GenBank.Record.Record._pid_line" class="py-name" href="#" onclick="return doclink('link-60', '_pid_line', 'link-60');">_pid_line</a></tt><tt class="py-op">(</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">output</tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-61" class="py-name" targets="Method Bio.GenBank.Record.Record._keywords_line()=Bio.GenBank.Record.Record-class.html#_keywords_line"><a title="Bio.GenBank.Record.Record._keywords_line" class="py-name" href="#" onclick="return doclink('link-61', '_keywords_line', 'link-61');">_keywords_line</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-62" class="py-name" targets="Method Bio.GenBank.Record.Record._db_source_line()=Bio.GenBank.Record.Record-class.html#_db_source_line"><a title="Bio.GenBank.Record.Record._db_source_line" class="py-name" href="#" onclick="return doclink('link-62', '_db_source_line', 'link-62');">_db_source_line</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-63" class="py-name" targets="Method Bio.GenBank.Record.Record._segment_line()=Bio.GenBank.Record.Record-class.html#_segment_line"><a title="Bio.GenBank.Record.Record._segment_line" class="py-name" href="#" onclick="return doclink('link-63', '_segment_line', 'link-63');">_segment_line</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-64" class="py-name" targets="Method Bio.GenBank.Record.Record._source_line()=Bio.GenBank.Record.Record-class.html#_source_line"><a title="Bio.GenBank.Record.Record._source_line" class="py-name" href="#" onclick="return doclink('link-64', '_source_line', 'link-64');">_source_line</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-65" class="py-name" targets="Method Bio.GenBank.Record.Record._organism_line()=Bio.GenBank.Record.Record-class.html#_organism_line"><a title="Bio.GenBank.Record.Record._organism_line" class="py-name" href="#" onclick="return doclink('link-65', '_organism_line', 'link-65');">_organism_line</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-66" class="py-name" targets="Method Bio.Blast.NCBIStandalone._HeaderConsumer.reference()=Bio.Blast.NCBIStandalone._HeaderConsumer-class.html#reference,Method Bio.Prosite.Prodoc._RecordConsumer.reference()=Bio.Prosite.Prodoc._RecordConsumer-class.html#reference,Variable Bio.expressions.embl.embl65.reference=Bio.expressions.embl.embl65-module.html#reference,Variable Bio.expressions.genbank.reference=Bio.expressions.genbank-module.html#reference,Variable Bio.expressions.swissprot.sprot38.reference=Bio.expressions.swissprot.sprot38-module.html#reference,Variable Martel.test.test_swissprot38.reference=Martel.test.test_swissprot38-module.html#reference,Variable Martel.test.testformats.swissprot38.reference=Martel.test.testformats.swissprot38-module.html#reference"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.reference
Bio.Prosite.Prodoc._RecordConsumer.reference
Bio.expressions.embl.embl65.reference
Bio.expressions.genbank.reference
Bio.expressions.swissprot.sprot38.reference
Martel.test.test_swissprot38.reference
Martel.test.testformats.swissprot38.reference" class="py-name" href="#" onclick="return doclink('link-66', 'reference', 'link-66');">reference</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">references</tt><tt class="py-op">:</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-67" class="py-name"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.reference
Bio.Prosite.Prodoc._RecordConsumer.reference
Bio.expressions.embl.embl65.reference
Bio.expressions.genbank.reference
Bio.expressions.swissprot.sprot38.reference
Martel.test.test_swissprot38.reference
Martel.test.testformats.swissprot38.reference" class="py-name" href="#" onclick="return doclink('link-67', 'reference', 'link-66');">reference</a></tt><tt class="py-op">)</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-68" class="py-name" targets="Method Bio.GenBank.Record.Record._comment_line()=Bio.GenBank.Record.Record-class.html#_comment_line"><a title="Bio.GenBank.Record.Record._comment_line" class="py-name" href="#" onclick="return doclink('link-68', '_comment_line', 'link-68');">_comment_line</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-69" class="py-name" targets="Method Bio.GenBank.Record.Record._features_line()=Bio.GenBank.Record.Record-class.html#_features_line"><a title="Bio.GenBank.Record.Record._features_line" class="py-name" href="#" onclick="return doclink('link-69', '_features_line', 'link-69');">_features_line</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-70" class="py-name" targets="Function Bio.Std.feature()=Bio.Std-module.html#feature,Variable Bio.expressions.embl.embl65.feature=Bio.expressions.embl.embl65-module.html#feature,Variable Bio.expressions.genbank.feature=Bio.expressions.genbank-module.html#feature"><a title="Bio.Std.feature
Bio.expressions.embl.embl65.feature
Bio.expressions.genbank.feature" class="py-name" href="#" onclick="return doclink('link-70', 'feature', 'link-70');">feature</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-71" class="py-name"><a title="Bio.GFF.Segment.features
BioSQL.BioSeq.DBSeqRecord.features
Martel.Expression.Expression.features
Martel.Expression.ExpressionList.features
Martel.Expression.FastFeature.features
Martel.Expression.Group.features
Martel.Expression.HeaderFooter.features
Martel.Expression.MaxRepeat.features
Martel.Expression.ParseRecords.features
Martel.Expression.PassThrough.features" class="py-name" href="#" onclick="return doclink('link-71', 'features', 'link-52');">features</a></tt><tt class="py-op">:</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-72" class="py-name"><a title="Bio.Std.feature
Bio.expressions.embl.embl65.feature
Bio.expressions.genbank.feature" class="py-name" href="#" onclick="return doclink('link-72', 'feature', 'link-70');">feature</a></tt><tt class="py-op">)</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-73" class="py-name" targets="Method Bio.GenBank.Record.Record._base_count_line()=Bio.GenBank.Record.Record-class.html#_base_count_line"><a title="Bio.GenBank.Record.Record._base_count_line" class="py-name" href="#" onclick="return doclink('link-73', '_base_count_line', 'link-73');">_base_count_line</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-74" class="py-name" targets="Method Bio.GenBank.Record.Record._origin_line()=Bio.GenBank.Record.Record-class.html#_origin_line"><a title="Bio.GenBank.Record.Record._origin_line" class="py-name" href="#" onclick="return doclink('link-74', '_origin_line', 'link-74');">_origin_line</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-75" class="py-name" targets="Method Bio.GenBank.Record.Record._sequence_line()=Bio.GenBank.Record.Record-class.html#_sequence_line"><a title="Bio.GenBank.Record.Record._sequence_line" class="py-name" href="#" onclick="return doclink('link-75', '_sequence_line', 'link-75');">_sequence_line</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-76" class="py-name" targets="Method Bio.GenBank.Record.Record._contig_line()=Bio.GenBank.Record.Record-class.html#_contig_line"><a title="Bio.GenBank.Record.Record._contig_line" class="py-name" href="#" onclick="return doclink('link-76', '_contig_line', 'link-76');">_contig_line</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-string">"//"</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">output</tt> </tt>
</div><a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> </tt>
<a name="Record._locus_line"></a><div id="Record._locus_line-def"><a name="L212"></a><tt class="py-lineno">212</tt> <a class="py-toggle" href="#" id="Record._locus_line-toggle" onclick="return toggle('Record._locus_line');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GenBank.Record.Record-class.html#_locus_line">_locus_line</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._locus_line-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Record._locus_line-expanded"><a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-docstring">"""Provide the output string for the LOCUS line.</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-string">"LOCUS"</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-string">" "</tt> <tt class="py-op">*</tt> <tt class="py-number">7</tt> <tt class="py-comment"># 6-12 spaces</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-string">"%-9s"</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-77" class="py-name"><a title="Bio.GenBank._FeatureConsumer.locus
Bio.GenBank._RecordConsumer.locus
Bio.expressions.genbank.locus" class="py-name" href="#" onclick="return doclink('link-77', 'locus', 'link-34');">locus</a></tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-string">" "</tt> <tt class="py-comment"># 22 space</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-string">"%7s"</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-78" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-78', 'size', 'link-35');">size</a></tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-79" class="py-name"><a title="Bio.GenBank._FeatureConsumer.residue_type
Bio.GenBank._RecordConsumer.residue_type
Bio.expressions.genbank.residue_type" class="py-name" href="#" onclick="return doclink('link-79', 'residue_type', 'link-36');">residue_type</a></tt><tt class="py-op">.</tt><tt id="link-80" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.find()=Bio.EUtils.POM.ElementNode-class.html#find,Method Bio.NeuralNetwork.Gene.Motif.MotifFinder.find()=Bio.NeuralNetwork.Gene.Motif.MotifFinder-class.html#find,Method Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find()=Bio.NeuralNetwork.Gene.Schema.SchemaFinder-class.html#find,Method Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find()=Bio.NeuralNetwork.Gene.Signature.SignatureFinder-class.html#find,Method Bio.biblio.Biblio.find()=Bio.biblio.Biblio-class.html#find,Function Bio.triefind.find()=Bio.triefind-module.html#find"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-80', 'find', 'link-80');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">"PROTEIN"</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="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-string">" aa"</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-string">" bp "</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> <tt class="py-comment"># treat circular types differently, since they'll have long residue</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># types</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-81" class="py-name"><a title="Bio.GenBank._FeatureConsumer.residue_type
Bio.GenBank._RecordConsumer.residue_type
Bio.expressions.genbank.residue_type" class="py-name" href="#" onclick="return doclink('link-81', 'residue_type', 'link-36');">residue_type</a></tt><tt class="py-op">.</tt><tt id="link-82" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-82', 'find', 'link-80');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">"circular"</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="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-string">"%17s"</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-83" class="py-name"><a title="Bio.GenBank._FeatureConsumer.residue_type
Bio.GenBank._RecordConsumer.residue_type
Bio.expressions.genbank.residue_type" class="py-name" href="#" onclick="return doclink('link-83', 'residue_type', 'link-36');">residue_type</a></tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> <tt class="py-comment"># second case: ss-DNA types of records</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">elif</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-84" class="py-name"><a title="Bio.GenBank._FeatureConsumer.residue_type
Bio.GenBank._RecordConsumer.residue_type
Bio.expressions.genbank.residue_type" class="py-name" href="#" onclick="return doclink('link-84', 'residue_type', 'link-36');">residue_type</a></tt><tt class="py-op">.</tt><tt id="link-85" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-85', 'find', 'link-80');">find</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="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-string">"%7s"</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-86" class="py-name"><a title="Bio.GenBank._FeatureConsumer.residue_type
Bio.GenBank._RecordConsumer.residue_type
Bio.expressions.genbank.residue_type" class="py-name" href="#" onclick="return doclink('link-86', 'residue_type', 'link-36');">residue_type</a></tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-string">" "</tt> <tt class="py-op">*</tt> <tt class="py-number">10</tt> <tt class="py-comment"># spaces for circular</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-string">" "</tt> <tt class="py-op">*</tt> <tt class="py-number">3</tt> <tt class="py-comment"># spaces for stuff like ss-</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-string">"%-4s"</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-87" class="py-name"><a title="Bio.GenBank._FeatureConsumer.residue_type
Bio.GenBank._RecordConsumer.residue_type
Bio.expressions.genbank.residue_type" class="py-name" href="#" onclick="return doclink('link-87', 'residue_type', 'link-36');">residue_type</a></tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-string">" "</tt> <tt class="py-op">*</tt> <tt class="py-number">10</tt> <tt class="py-comment"># spaces for circular</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-string">" "</tt> <tt class="py-op">*</tt> <tt class="py-number">2</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-string">"%3s"</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-88" class="py-name"><a title="Bio.GenBank._FeatureConsumer.data_file_division
Bio.GenBank._RecordConsumer.data_file_division
Bio.expressions.genbank.data_file_division" class="py-name" href="#" onclick="return doclink('link-88', 'data_file_division', 'link-37');">data_file_division</a></tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-string">" "</tt> <tt class="py-op">*</tt> <tt class="py-number">7</tt> <tt class="py-comment"># spaces for 56-63</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-string">"%11s"</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-89" class="py-name"><a title="Bio.GenBank._FeatureConsumer.date
Bio.GenBank._RecordConsumer.date
Bio.Prosite._RecordConsumer.date
Bio.SwissProt.SProt._RecordConsumer.date
Bio.SwissProt.SProt._SequenceConsumer.date
Bio.expressions.embl.embl65.date
Bio.expressions.genbank.date" class="py-name" href="#" onclick="return doclink('link-89', 'date', 'link-38');">date</a></tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-string">"\n"</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">output</tt> </tt>
</div><a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> </tt>
<a name="Record._definition_line"></a><div id="Record._definition_line-def"><a name="L245"></a><tt class="py-lineno">245</tt> <a class="py-toggle" href="#" id="Record._definition_line-toggle" onclick="return toggle('Record._definition_line');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GenBank.Record.Record-class.html#_definition_line">_definition_line</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._definition_line-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Record._definition_line-expanded"><a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> <tt class="py-docstring">"""Provide output for the DEFINITION line.</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt id="link-90" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-90', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-91" class="py-name"><a title="Bio.GenBank.Record.Record.BASE_FORMAT" class="py-name" href="#" onclick="return doclink('link-91', 'BASE_FORMAT', 'link-16');">BASE_FORMAT</a></tt> <tt class="py-op">%</tt> <tt class="py-string">"DEFINITION"</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt id="link-92" class="py-name" targets="Function Bio.GenBank.Record._wrapped_genbank()=Bio.GenBank.Record-module.html#_wrapped_genbank"><a title="Bio.GenBank.Record._wrapped_genbank" class="py-name" href="#" onclick="return doclink('link-92', '_wrapped_genbank', 'link-92');">_wrapped_genbank</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-93" class="py-name"><a title="Bio.GenBank._FeatureConsumer.definition
Bio.GenBank._RecordConsumer.definition" class="py-name" href="#" onclick="return doclink('link-93', 'definition', 'link-39');">definition</a></tt><tt class="py-op">,</tt> <tt id="link-94" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-94', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-95" class="py-name"><a title="Bio.GenBank.Record.Record.GB_BASE_INDENT" class="py-name" href="#" onclick="return doclink('link-95', 'GB_BASE_INDENT', 'link-10');">GB_BASE_INDENT</a></tt><tt class="py-op">)</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">output</tt> </tt>
</div><a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"> </tt>
<a name="Record._accession_line"></a><div id="Record._accession_line-def"><a name="L252"></a><tt class="py-lineno">252</tt> <a class="py-toggle" href="#" id="Record._accession_line-toggle" onclick="return toggle('Record._accession_line');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GenBank.Record.Record-class.html#_accession_line">_accession_line</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._accession_line-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Record._accession_line-expanded"><a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> <tt class="py-docstring">"""Output for the ACCESSION line.</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt id="link-96" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-96', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-97" class="py-name"><a title="Bio.GenBank.Record.Record.BASE_FORMAT" class="py-name" href="#" onclick="return doclink('link-97', 'BASE_FORMAT', 'link-16');">BASE_FORMAT</a></tt> <tt class="py-op">%</tt> <tt class="py-string">"ACCESSION"</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"> <tt class="py-name">acc_info</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-98" class="py-name"><a title="Bio.GenBank._FeatureConsumer.accession
Bio.GenBank._RecordConsumer.accession
Bio.Prosite.Prodoc._RecordConsumer.accession
Bio.Prosite._RecordConsumer.accession
Bio.SwissProt.SProt._RecordConsumer.accession
Bio.SwissProt.SProt._SequenceConsumer.accession
Bio.expressions.embl.embl65.accession
Bio.expressions.genbank.accession" class="py-name" href="#" onclick="return doclink('link-98', 'accession', 'link-40');">accession</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-99" class="py-name"><a title="Bio.GenBank._FeatureConsumer.accession
Bio.GenBank._RecordConsumer.accession
Bio.Prosite.Prodoc._RecordConsumer.accession
Bio.Prosite._RecordConsumer.accession
Bio.SwissProt.SProt._RecordConsumer.accession
Bio.SwissProt.SProt._SequenceConsumer.accession
Bio.expressions.embl.embl65.accession
Bio.expressions.genbank.accession" class="py-name" href="#" onclick="return doclink('link-99', 'accession', 'link-40');">accession</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-name">acc_info</tt> <tt class="py-op">+=</tt> <tt class="py-string">"%s "</tt> <tt class="py-op">%</tt> <tt id="link-100" class="py-name"><a title="Bio.GenBank._FeatureConsumer.accession
Bio.GenBank._RecordConsumer.accession
Bio.Prosite.Prodoc._RecordConsumer.accession
Bio.Prosite._RecordConsumer.accession
Bio.SwissProt.SProt._RecordConsumer.accession
Bio.SwissProt.SProt._SequenceConsumer.accession
Bio.expressions.embl.embl65.accession
Bio.expressions.genbank.accession" class="py-name" href="#" onclick="return doclink('link-100', 'accession', 'link-40');">accession</a></tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"> <tt class="py-comment"># strip off an extra space at the end</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">acc_info</tt> <tt class="py-op">=</tt> <tt class="py-name">acc_info</tt><tt class="py-op">.</tt><tt class="py-name">rstrip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt id="link-101" class="py-name"><a title="Bio.GenBank.Record._wrapped_genbank" class="py-name" href="#" onclick="return doclink('link-101', '_wrapped_genbank', 'link-92');">_wrapped_genbank</a></tt><tt class="py-op">(</tt><tt class="py-name">acc_info</tt><tt class="py-op">,</tt> <tt id="link-102" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-102', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-103" class="py-name"><a title="Bio.GenBank.Record.Record.GB_BASE_INDENT" class="py-name" href="#" onclick="return doclink('link-103', 'GB_BASE_INDENT', 'link-10');">GB_BASE_INDENT</a></tt><tt class="py-op">)</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">output</tt> </tt>
</div><a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"> </tt>
<a name="Record._version_line"></a><div id="Record._version_line-def"><a name="L266"></a><tt class="py-lineno">266</tt> <a class="py-toggle" href="#" id="Record._version_line-toggle" onclick="return toggle('Record._version_line');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GenBank.Record.Record-class.html#_version_line">_version_line</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._version_line-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Record._version_line-expanded"><a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> <tt class="py-docstring">"""Output for the VERSION line.</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt id="link-104" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-104', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-105" class="py-name"><a title="Bio.GenBank.Record.Record.BASE_FORMAT" class="py-name" href="#" onclick="return doclink('link-105', 'BASE_FORMAT', 'link-16');">BASE_FORMAT</a></tt> <tt class="py-op">%</tt> <tt class="py-string">"VERSION"</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-106" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.version
Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version
Bio.MetaTool.metatool_format.version
Bio.expressions.genbank.version" class="py-name" href="#" onclick="return doclink('link-106', 'version', 'link-43');">version</a></tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-string">" GI:"</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-string">"%s\n"</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-107" class="py-name"><a title="Bio.GenBank._FeatureConsumer.gi
Bio.GenBank._RecordConsumer.gi
Bio.expressions.genbank.gi" class="py-name" href="#" onclick="return doclink('link-107', 'gi', 'link-45');">gi</a></tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">output</tt> </tt>
</div><a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> </tt>
<a name="Record._nid_line"></a><div id="Record._nid_line-def"><a name="L275"></a><tt class="py-lineno">275</tt> <a class="py-toggle" href="#" id="Record._nid_line-toggle" onclick="return toggle('Record._nid_line');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GenBank.Record.Record-class.html#_nid_line">_nid_line</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._nid_line-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Record._nid_line-expanded"><a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"> <tt class="py-docstring">"""Output for the NID line. Use of NID is obsolete in GenBank files.</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-108" class="py-name"><a title="Bio.GenBank._FeatureConsumer.nid
Bio.GenBank._RecordConsumer.nid
Bio.expressions.genbank.nid" class="py-name" href="#" onclick="return doclink('link-108', 'nid', 'link-41');">nid</a></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">output</tt> <tt class="py-op">=</tt> <tt id="link-109" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-109', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-110" class="py-name"><a title="Bio.GenBank.Record.Record.BASE_FORMAT" class="py-name" href="#" onclick="return doclink('link-110', 'BASE_FORMAT', 'link-16');">BASE_FORMAT</a></tt> <tt class="py-op">%</tt> <tt class="py-string">"NID"</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-string">"%s\n"</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-111" class="py-name"><a title="Bio.GenBank._FeatureConsumer.nid
Bio.GenBank._RecordConsumer.nid
Bio.expressions.genbank.nid" class="py-name" href="#" onclick="return doclink('link-111', 'nid', 'link-41');">nid</a></tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"> <tt class="py-keyword">else</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">output</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">output</tt> </tt>
</div><a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> </tt>
<a name="Record._pid_line"></a><div id="Record._pid_line-def"><a name="L285"></a><tt class="py-lineno">285</tt> <a class="py-toggle" href="#" id="Record._pid_line-toggle" onclick="return toggle('Record._pid_line');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GenBank.Record.Record-class.html#_pid_line">_pid_line</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._pid_line-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Record._pid_line-expanded"><a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"> <tt class="py-docstring">"""Output for PID line. Presumedly, PID usage is also obsolete.</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-112" class="py-name"><a title="Bio.GenBank._FeatureConsumer.pid
Bio.GenBank._RecordConsumer.pid
Bio.expressions.genbank.pid" class="py-name" href="#" onclick="return doclink('link-112', 'pid', 'link-42');">pid</a></tt><tt class="py-op">:</tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt id="link-113" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-113', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-114" class="py-name"><a title="Bio.GenBank.Record.Record.BASE_FORMAT" class="py-name" href="#" onclick="return doclink('link-114', 'BASE_FORMAT', 'link-16');">BASE_FORMAT</a></tt> <tt class="py-op">%</tt> <tt class="py-string">"PID"</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-string">"%s\n"</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.GenBank._FeatureConsumer.pid
Bio.GenBank._RecordConsumer.pid
Bio.expressions.genbank.pid" class="py-name" href="#" onclick="return doclink('link-115', 'pid', 'link-42');">pid</a></tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">output</tt> </tt>
</div><a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"> </tt>
<a name="Record._keywords_line"></a><div id="Record._keywords_line-def"><a name="L295"></a><tt class="py-lineno">295</tt> <a class="py-toggle" href="#" id="Record._keywords_line-toggle" onclick="return toggle('Record._keywords_line');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GenBank.Record.Record-class.html#_keywords_line">_keywords_line</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._keywords_line-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Record._keywords_line-expanded"><a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"> <tt class="py-docstring">"""Output for the KEYWORDS line.</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</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">self</tt><tt class="py-op">.</tt><tt id="link-116" class="py-name"><a title="Bio.GenBank._FeatureConsumer.keywords
Bio.GenBank._RecordConsumer.keywords" class="py-name" href="#" onclick="return doclink('link-116', 'keywords', 'link-46');">keywords</a></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="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt id="link-117" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-117', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-118" class="py-name"><a title="Bio.GenBank.Record.Record.BASE_FORMAT" class="py-name" href="#" onclick="return doclink('link-118', 'BASE_FORMAT', 'link-16');">BASE_FORMAT</a></tt> <tt class="py-op">%</tt> <tt class="py-string">"KEYWORDS"</tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"> <tt class="py-name">keyword_info</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-119" class="py-name" targets="Method Bio.SwissProt.KeyWList._ListConsumer.keyword()=Bio.SwissProt.KeyWList._ListConsumer-class.html#keyword,Method Bio.SwissProt.SProt._RecordConsumer.keyword()=Bio.SwissProt.SProt._RecordConsumer-class.html#keyword,Method Bio.SwissProt.SProt._SequenceConsumer.keyword()=Bio.SwissProt.SProt._SequenceConsumer-class.html#keyword"><a title="Bio.SwissProt.KeyWList._ListConsumer.keyword
Bio.SwissProt.SProt._RecordConsumer.keyword
Bio.SwissProt.SProt._SequenceConsumer.keyword" class="py-name" href="#" onclick="return doclink('link-119', 'keyword', 'link-119');">keyword</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-120" class="py-name"><a title="Bio.GenBank._FeatureConsumer.keywords
Bio.GenBank._RecordConsumer.keywords" class="py-name" href="#" onclick="return doclink('link-120', 'keywords', 'link-46');">keywords</a></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">keyword_info</tt> <tt class="py-op">+=</tt> <tt class="py-string">"%s; "</tt> <tt class="py-op">%</tt> <tt id="link-121" class="py-name"><a title="Bio.SwissProt.KeyWList._ListConsumer.keyword
Bio.SwissProt.SProt._RecordConsumer.keyword
Bio.SwissProt.SProt._SequenceConsumer.keyword" class="py-name" href="#" onclick="return doclink('link-121', 'keyword', 'link-119');">keyword</a></tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"> <tt class="py-comment"># replace the ; at the end with a period</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">keyword_info</tt> <tt class="py-op">=</tt> <tt class="py-name">keyword_info</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"> <tt class="py-name">keyword_info</tt> <tt class="py-op">+=</tt> <tt class="py-string">"."</tt> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt id="link-122" class="py-name"><a title="Bio.GenBank.Record._wrapped_genbank" class="py-name" href="#" onclick="return doclink('link-122', '_wrapped_genbank', 'link-92');">_wrapped_genbank</a></tt><tt class="py-op">(</tt><tt class="py-name">keyword_info</tt><tt class="py-op">,</tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"> <tt id="link-123" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-123', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-124" class="py-name"><a title="Bio.GenBank.Record.Record.GB_BASE_INDENT" class="py-name" href="#" onclick="return doclink('link-124', 'GB_BASE_INDENT', 'link-10');">GB_BASE_INDENT</a></tt><tt class="py-op">)</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">output</tt> </tt>
</div><a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"> </tt>
<a name="Record._db_source_line"></a><div id="Record._db_source_line-def"><a name="L313"></a><tt class="py-lineno">313</tt> <a class="py-toggle" href="#" id="Record._db_source_line-toggle" onclick="return toggle('Record._db_source_line');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GenBank.Record.Record-class.html#_db_source_line">_db_source_line</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._db_source_line-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Record._db_source_line-expanded"><a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"> <tt class="py-docstring">"""Output for DBSOURCE line.</tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"><tt class="py-docstring"> """</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">self</tt><tt class="py-op">.</tt><tt id="link-125" class="py-name"><a title="Bio.GenBank._FeatureConsumer.db_source
Bio.GenBank._RecordConsumer.db_source" class="py-name" href="#" onclick="return doclink('link-125', 'db_source', 'link-44');">db_source</a></tt><tt class="py-op">:</tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt id="link-126" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-126', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-127" class="py-name"><a title="Bio.GenBank.Record.Record.BASE_FORMAT" class="py-name" href="#" onclick="return doclink('link-127', 'BASE_FORMAT', 'link-16');">BASE_FORMAT</a></tt> <tt class="py-op">%</tt> <tt class="py-string">"DBSOURCE"</tt> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-string">"%s\n"</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.GenBank._FeatureConsumer.db_source
Bio.GenBank._RecordConsumer.db_source" class="py-name" href="#" onclick="return doclink('link-128', 'db_source', 'link-44');">db_source</a></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-name">output</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">output</tt> </tt>
</div><a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"> </tt>
<a name="Record._segment_line"></a><div id="Record._segment_line-def"><a name="L323"></a><tt class="py-lineno">323</tt> <a class="py-toggle" href="#" id="Record._segment_line-toggle" onclick="return toggle('Record._segment_line');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GenBank.Record.Record-class.html#_segment_line">_segment_line</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._segment_line-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Record._segment_line-expanded"><a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"> <tt class="py-docstring">"""Output for the SEGMENT line.</tt> </tt>
<a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-129" class="py-name"><a title="Bio.GFF.Connection.segment
Bio.GenBank._FeatureConsumer.segment
Bio.GenBank._RecordConsumer.segment
Bio.expressions.blocks.segment
Bio.expressions.genbank.segment" class="py-name" href="#" onclick="return doclink('link-129', 'segment', 'link-47');">segment</a></tt><tt class="py-op">:</tt> </tt>
<a name="L328"></a><tt class="py-lineno">328</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt id="link-130" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-130', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-131" class="py-name"><a title="Bio.GenBank.Record.Record.BASE_FORMAT" class="py-name" href="#" onclick="return doclink('link-131', 'BASE_FORMAT', 'link-16');">BASE_FORMAT</a></tt> <tt class="py-op">%</tt> <tt class="py-string">"SEGMENT"</tt> </tt>
<a name="L329"></a><tt class="py-lineno">329</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt id="link-132" class="py-name"><a title="Bio.GenBank.Record._wrapped_genbank" class="py-name" href="#" onclick="return doclink('link-132', '_wrapped_genbank', 'link-92');">_wrapped_genbank</a></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.GFF.Connection.segment
Bio.GenBank._FeatureConsumer.segment
Bio.GenBank._RecordConsumer.segment
Bio.expressions.blocks.segment
Bio.expressions.genbank.segment" class="py-name" href="#" onclick="return doclink('link-133', 'segment', 'link-47');">segment</a></tt><tt class="py-op">,</tt> <tt id="link-134" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-134', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-135" class="py-name"><a title="Bio.GenBank.Record.Record.GB_BASE_INDENT" class="py-name" href="#" onclick="return doclink('link-135', 'GB_BASE_INDENT', 'link-10');">GB_BASE_INDENT</a></tt><tt class="py-op">)</tt> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">output</tt> </tt>
</div><a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"> </tt>
<a name="Record._source_line"></a><div id="Record._source_line-def"><a name="L332"></a><tt class="py-lineno">332</tt> <a class="py-toggle" href="#" id="Record._source_line-toggle" onclick="return toggle('Record._source_line');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GenBank.Record.Record-class.html#_source_line">_source_line</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._source_line-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Record._source_line-expanded"><a name="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"> <tt class="py-docstring">"""Output for SOURCE line on where the sample came from.</tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt id="link-136" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-136', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-137" class="py-name"><a title="Bio.GenBank.Record.Record.BASE_FORMAT" class="py-name" href="#" onclick="return doclink('link-137', 'BASE_FORMAT', 'link-16');">BASE_FORMAT</a></tt> <tt class="py-op">%</tt> <tt class="py-string">"SOURCE"</tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt id="link-138" class="py-name"><a title="Bio.GenBank.Record._wrapped_genbank" class="py-name" href="#" onclick="return doclink('link-138', '_wrapped_genbank', 'link-92');">_wrapped_genbank</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.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-139', 'source', 'link-48');">source</a></tt><tt class="py-op">,</tt> <tt id="link-140" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-140', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-141" class="py-name"><a title="Bio.GenBank.Record.Record.GB_BASE_INDENT" class="py-name" href="#" onclick="return doclink('link-141', 'GB_BASE_INDENT', 'link-10');">GB_BASE_INDENT</a></tt><tt class="py-op">)</tt> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">output</tt> </tt>
</div><a name="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"> </tt>
<a name="Record._organism_line"></a><div id="Record._organism_line-def"><a name="L339"></a><tt class="py-lineno">339</tt> <a class="py-toggle" href="#" id="Record._organism_line-toggle" onclick="return toggle('Record._organism_line');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GenBank.Record.Record-class.html#_organism_line">_organism_line</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._organism_line-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Record._organism_line-expanded"><a name="L340"></a><tt class="py-lineno">340</tt> <tt class="py-line"> <tt class="py-docstring">"""Output for ORGANISM line with taxonomy info.</tt> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt id="link-142" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-142', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-143" class="py-name"><a title="Bio.GenBank.Record.Record.INTERNAL_FORMAT" class="py-name" href="#" onclick="return doclink('link-143', 'INTERNAL_FORMAT', 'link-18');">INTERNAL_FORMAT</a></tt> <tt class="py-op">%</tt> <tt class="py-string">"ORGANISM"</tt> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-string">"%s\n"</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-144" class="py-name"><a title="Bio.GenBank._FeatureConsumer.organism
Bio.GenBank._RecordConsumer.organism
Bio.expressions.embl.embl65.organism
Bio.expressions.genbank.organism" class="py-name" href="#" onclick="return doclink('link-144', 'organism', 'link-49');">organism</a></tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-string">" "</tt> <tt class="py-op">*</tt> <tt id="link-145" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-145', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-146" class="py-name"><a title="Bio.GenBank.Record.Record.GB_BASE_INDENT" class="py-name" href="#" onclick="return doclink('link-146', 'GB_BASE_INDENT', 'link-10');">GB_BASE_INDENT</a></tt> </tt>
<a name="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"> <tt class="py-name">taxonomy_info</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">tax</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-147" class="py-name"><a title="Bio.GenBank._FeatureConsumer.taxonomy
Bio.GenBank._RecordConsumer.taxonomy
Bio.expressions.genbank.taxonomy" class="py-name" href="#" onclick="return doclink('link-147', 'taxonomy', 'link-50');">taxonomy</a></tt><tt class="py-op">:</tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt> <tt class="py-line"> <tt class="py-name">taxonomy_info</tt> <tt class="py-op">+=</tt> <tt class="py-string">"%s; "</tt> <tt class="py-op">%</tt> <tt class="py-name">tax</tt> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"> <tt class="py-comment"># replace the ; at the end with a period</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">taxonomy_info</tt> <tt class="py-op">=</tt> <tt class="py-name">taxonomy_info</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt> <tt class="py-line"> <tt class="py-name">taxonomy_info</tt> <tt class="py-op">+=</tt> <tt class="py-string">"."</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt id="link-148" class="py-name"><a title="Bio.GenBank.Record._wrapped_genbank" class="py-name" href="#" onclick="return doclink('link-148', '_wrapped_genbank', 'link-92');">_wrapped_genbank</a></tt><tt class="py-op">(</tt><tt class="py-name">taxonomy_info</tt><tt class="py-op">,</tt> <tt id="link-149" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-149', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-150" class="py-name"><a title="Bio.GenBank.Record.Record.GB_BASE_INDENT" class="py-name" href="#" onclick="return doclink('link-150', 'GB_BASE_INDENT', 'link-10');">GB_BASE_INDENT</a></tt><tt class="py-op">)</tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt> <tt class="py-line"> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">output</tt> </tt>
</div><a name="L354"></a><tt class="py-lineno">354</tt> <tt class="py-line"> </tt>
<a name="Record._comment_line"></a><div id="Record._comment_line-def"><a name="L355"></a><tt class="py-lineno">355</tt> <a class="py-toggle" href="#" id="Record._comment_line-toggle" onclick="return toggle('Record._comment_line');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GenBank.Record.Record-class.html#_comment_line">_comment_line</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._comment_line-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Record._comment_line-expanded"><a name="L356"></a><tt class="py-lineno">356</tt> <tt class="py-line"> <tt class="py-docstring">"""Output for the COMMENT lines.</tt> </tt>
<a name="L357"></a><tt class="py-lineno">357</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-151" class="py-name"><a title="Bio.EUtils.POM.ElementNode.comment
Bio.Enzyme._RecordConsumer.comment
Bio.GenBank._FeatureConsumer.comment
Bio.GenBank._RecordConsumer.comment
Bio.IntelliGenetics._RecordConsumer.comment
Bio.NBRF._RecordConsumer.comment
Bio.PopGen.GenePop._RecordConsumer.comment
Bio.Prosite._RecordConsumer.comment
Bio.SwissProt.SProt._RecordConsumer.comment
Bio.SwissProt.SProt._SequenceConsumer.comment
Bio.expressions.swissprot.sprot38.comment
Martel.test.test_swissprot38.comment
Martel.test.testformats.swissprot38.comment" class="py-name" href="#" onclick="return doclink('link-151', 'comment', 'link-51');">comment</a></tt><tt class="py-op">:</tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt id="link-152" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-152', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-153" class="py-name"><a title="Bio.GenBank.Record.Record.BASE_FORMAT" class="py-name" href="#" onclick="return doclink('link-153', 'BASE_FORMAT', 'link-16');">BASE_FORMAT</a></tt> <tt class="py-op">%</tt> <tt class="py-string">"COMMENT"</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt id="link-154" class="py-name" targets="Function Bio.GenBank.Record._indent_genbank()=Bio.GenBank.Record-module.html#_indent_genbank"><a title="Bio.GenBank.Record._indent_genbank" class="py-name" href="#" onclick="return doclink('link-154', '_indent_genbank', 'link-154');">_indent_genbank</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-155" class="py-name"><a title="Bio.EUtils.POM.ElementNode.comment
Bio.Enzyme._RecordConsumer.comment
Bio.GenBank._FeatureConsumer.comment
Bio.GenBank._RecordConsumer.comment
Bio.IntelliGenetics._RecordConsumer.comment
Bio.NBRF._RecordConsumer.comment
Bio.PopGen.GenePop._RecordConsumer.comment
Bio.Prosite._RecordConsumer.comment
Bio.SwissProt.SProt._RecordConsumer.comment
Bio.SwissProt.SProt._SequenceConsumer.comment
Bio.expressions.swissprot.sprot38.comment
Martel.test.test_swissprot38.comment
Martel.test.testformats.swissprot38.comment" class="py-name" href="#" onclick="return doclink('link-155', 'comment', 'link-51');">comment</a></tt><tt class="py-op">,</tt> </tt>
<a name="L362"></a><tt class="py-lineno">362</tt> <tt class="py-line"> <tt id="link-156" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-156', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-157" class="py-name"><a title="Bio.GenBank.Record.Record.GB_BASE_INDENT" class="py-name" href="#" onclick="return doclink('link-157', 'GB_BASE_INDENT', 'link-10');">GB_BASE_INDENT</a></tt><tt class="py-op">)</tt> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">output</tt> </tt>
</div><a name="L364"></a><tt class="py-lineno">364</tt> <tt class="py-line"> </tt>
<a name="Record._features_line"></a><div id="Record._features_line-def"><a name="L365"></a><tt class="py-lineno">365</tt> <a class="py-toggle" href="#" id="Record._features_line-toggle" onclick="return toggle('Record._features_line');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GenBank.Record.Record-class.html#_features_line">_features_line</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._features_line-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Record._features_line-expanded"><a name="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"> <tt class="py-docstring">"""Output for the FEATURES line.</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-name">output</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L369"></a><tt class="py-lineno">369</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">self</tt><tt class="py-op">.</tt><tt id="link-158" class="py-name"><a title="Bio.GFF.Segment.features
BioSQL.BioSeq.DBSeqRecord.features
Martel.Expression.Expression.features
Martel.Expression.ExpressionList.features
Martel.Expression.FastFeature.features
Martel.Expression.Group.features
Martel.Expression.HeaderFooter.features
Martel.Expression.MaxRepeat.features
Martel.Expression.ParseRecords.features
Martel.Expression.PassThrough.features" class="py-name" href="#" onclick="return doclink('link-158', 'features', 'link-52');">features</a></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="L370"></a><tt class="py-lineno">370</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt id="link-159" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-159', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-160" class="py-name"><a title="Bio.GenBank.Record.Record.BASE_FEATURE_FORMAT" class="py-name" href="#" onclick="return doclink('link-160', 'BASE_FEATURE_FORMAT', 'link-26');">BASE_FEATURE_FORMAT</a></tt> <tt class="py-op">%</tt> <tt class="py-string">"FEATURES"</tt> </tt>
<a name="L371"></a><tt class="py-lineno">371</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-string">"Location/Qualifiers\n"</tt> </tt>
<a name="L372"></a><tt class="py-lineno">372</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">output</tt> </tt>
</div><a name="L373"></a><tt class="py-lineno">373</tt> <tt class="py-line"> </tt>
<a name="Record._base_count_line"></a><div id="Record._base_count_line-def"><a name="L374"></a><tt class="py-lineno">374</tt> <a class="py-toggle" href="#" id="Record._base_count_line-toggle" onclick="return toggle('Record._base_count_line');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GenBank.Record.Record-class.html#_base_count_line">_base_count_line</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._base_count_line-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Record._base_count_line-expanded"><a name="L375"></a><tt class="py-lineno">375</tt> <tt class="py-line"> <tt class="py-docstring">"""Output for the BASE COUNT line with base information.</tt> </tt>
<a name="L376"></a><tt class="py-lineno">376</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L377"></a><tt class="py-lineno">377</tt> <tt class="py-line"> <tt class="py-name">output</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-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">base_counts</tt><tt class="py-op">:</tt> </tt>
<a name="L379"></a><tt class="py-lineno">379</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt id="link-161" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-161', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-162" class="py-name"><a title="Bio.GenBank.Record.Record.BASE_FORMAT" class="py-name" href="#" onclick="return doclink('link-162', 'BASE_FORMAT', 'link-16');">BASE_FORMAT</a></tt> <tt class="py-op">%</tt> <tt class="py-string">"BASE COUNT "</tt> </tt>
<a name="L380"></a><tt class="py-lineno">380</tt> <tt class="py-line"> <tt class="py-comment"># split up the base counts into their individual parts</tt> </tt>
<a name="L381"></a><tt class="py-lineno">381</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">count_parts</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">base_counts</tt><tt class="py-op">.</tt><tt id="link-163" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-163', 'split', 'link-4');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">" "</tt><tt class="py-op">)</tt> </tt>
<a name="L382"></a><tt class="py-lineno">382</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-string">''</tt> <tt class="py-keyword">in</tt> <tt class="py-name">count_parts</tt><tt class="py-op">:</tt> </tt>
<a name="L383"></a><tt class="py-lineno">383</tt> <tt class="py-line"> <tt class="py-name">count_parts</tt><tt class="py-op">.</tt><tt id="link-164" class="py-name" targets="Method Bio.Crystal.Chain.remove()=Bio.Crystal.Chain-class.html#remove,Method Bio.GFF.GenericTools.TempFile.remove()=Bio.GFF.GenericTools.TempFile-class.html#remove,Method Bio.Graphics.BasicChromosome._ChromosomeComponent.remove()=Bio.Graphics.BasicChromosome._ChromosomeComponent-class.html#remove,Method Bio.Pathway.Rep.HashSet.HashSet.remove()=Bio.Pathway.Rep.HashSet.HashSet-class.html#remove,Method Bio.Restriction.Restriction.RestrictionBatch.remove()=Bio.Restriction.Restriction.RestrictionBatch-class.html#remove,Method Bio.Seq.MutableSeq.remove()=Bio.Seq.MutableSeq-class.html#remove,Method BioSQL.Loader.DatabaseRemover.remove()=BioSQL.Loader.DatabaseRemover-class.html#remove"><a title="Bio.Crystal.Chain.remove
Bio.GFF.GenericTools.TempFile.remove
Bio.Graphics.BasicChromosome._ChromosomeComponent.remove
Bio.Pathway.Rep.HashSet.HashSet.remove
Bio.Restriction.Restriction.RestrictionBatch.remove
Bio.Seq.MutableSeq.remove
BioSQL.Loader.DatabaseRemover.remove" class="py-name" href="#" onclick="return doclink('link-164', 'remove', 'link-164');">remove</a></tt><tt class="py-op">(</tt><tt class="py-string">''</tt><tt class="py-op">)</tt> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt> <tt class="py-line"> <tt class="py-comment"># deal with the standard case, with a normal origin line</tt> </tt>
<a name="L385"></a><tt class="py-lineno">385</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># like: 474 a 356 c 428 g 364 t</tt> </tt>
<a name="L386"></a><tt class="py-lineno">386</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">count_parts</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-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L387"></a><tt class="py-lineno">387</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">count_parts</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="L388"></a><tt class="py-lineno">388</tt> <tt class="py-line"> <tt class="py-name">count_info</tt> <tt class="py-op">=</tt> <tt class="py-name">count_parts</tt><tt class="py-op">.</tt><tt id="link-165" class="py-name" targets="Method Bio.Seq.MutableSeq.pop()=Bio.Seq.MutableSeq-class.html#pop"><a title="Bio.Seq.MutableSeq.pop" class="py-name" href="#" onclick="return doclink('link-165', 'pop', 'link-165');">pop</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L389"></a><tt class="py-lineno">389</tt> <tt class="py-line"> <tt class="py-name">count_type</tt> <tt class="py-op">=</tt> <tt class="py-name">count_parts</tt><tt class="py-op">.</tt><tt id="link-166" class="py-name"><a title="Bio.Seq.MutableSeq.pop" class="py-name" href="#" onclick="return doclink('link-166', 'pop', 'link-165');">pop</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L390"></a><tt class="py-lineno">390</tt> <tt class="py-line"> </tt>
<a name="L391"></a><tt class="py-lineno">391</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-string">"%7s %s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">count_info</tt><tt class="py-op">,</tt> <tt class="py-name">count_type</tt><tt class="py-op">)</tt> </tt>
<a name="L392"></a><tt class="py-lineno">392</tt> <tt class="py-line"> <tt class="py-comment"># deal with ugly ORIGIN lines like:</tt> </tt>
<a name="L393"></a><tt class="py-lineno">393</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># 1311257 a2224835 c2190093 g1309889 t</tt> </tt>
<a name="L394"></a><tt class="py-lineno">394</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># by just outputting the raw information</tt> </tt>
<a name="L395"></a><tt class="py-lineno">395</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L396"></a><tt class="py-lineno">396</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">base_counts</tt> </tt>
<a name="L397"></a><tt class="py-lineno">397</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-string">"\n"</tt> </tt>
<a name="L398"></a><tt class="py-lineno">398</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">output</tt> </tt>
</div><a name="L399"></a><tt class="py-lineno">399</tt> <tt class="py-line"> </tt>
<a name="Record._origin_line"></a><div id="Record._origin_line-def"><a name="L400"></a><tt class="py-lineno">400</tt> <a class="py-toggle" href="#" id="Record._origin_line-toggle" onclick="return toggle('Record._origin_line');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GenBank.Record.Record-class.html#_origin_line">_origin_line</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._origin_line-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Record._origin_line-expanded"><a name="L401"></a><tt class="py-lineno">401</tt> <tt class="py-line"> <tt class="py-docstring">"""Output for the ORIGIN line</tt> </tt>
<a name="L402"></a><tt class="py-lineno">402</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L403"></a><tt class="py-lineno">403</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L404"></a><tt class="py-lineno">404</tt> <tt class="py-line"> <tt class="py-comment"># only output the ORIGIN line if we have a sequence</tt> </tt>
<a name="L405"></a><tt class="py-lineno">405</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-167" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-167', 'sequence', 'link-53');">sequence</a></tt><tt class="py-op">:</tt> </tt>
<a name="L406"></a><tt class="py-lineno">406</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt id="link-168" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-168', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-169" class="py-name"><a title="Bio.GenBank.Record.Record.BASE_FORMAT" class="py-name" href="#" onclick="return doclink('link-169', 'BASE_FORMAT', 'link-16');">BASE_FORMAT</a></tt> <tt class="py-op">%</tt> <tt class="py-string">"ORIGIN"</tt> </tt>
<a name="L407"></a><tt class="py-lineno">407</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">origin</tt><tt class="py-op">:</tt> </tt>
<a name="L408"></a><tt class="py-lineno">408</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt id="link-170" class="py-name"><a title="Bio.GenBank.Record._wrapped_genbank" class="py-name" href="#" onclick="return doclink('link-170', '_wrapped_genbank', 'link-92');">_wrapped_genbank</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">origin</tt><tt class="py-op">,</tt> </tt>
<a name="L409"></a><tt class="py-lineno">409</tt> <tt class="py-line"> <tt id="link-171" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-171', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-172" class="py-name"><a title="Bio.GenBank.Record.Record.GB_BASE_INDENT" class="py-name" href="#" onclick="return doclink('link-172', 'GB_BASE_INDENT', 'link-10');">GB_BASE_INDENT</a></tt><tt class="py-op">)</tt> </tt>
<a name="L410"></a><tt class="py-lineno">410</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L411"></a><tt class="py-lineno">411</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-string">"\n"</tt> </tt>
<a name="L412"></a><tt class="py-lineno">412</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">output</tt> </tt>
</div><a name="L413"></a><tt class="py-lineno">413</tt> <tt class="py-line"> </tt>
<a name="Record._sequence_line"></a><div id="Record._sequence_line-def"><a name="L414"></a><tt class="py-lineno">414</tt> <a class="py-toggle" href="#" id="Record._sequence_line-toggle" onclick="return toggle('Record._sequence_line');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GenBank.Record.Record-class.html#_sequence_line">_sequence_line</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._sequence_line-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Record._sequence_line-expanded"><a name="L415"></a><tt class="py-lineno">415</tt> <tt class="py-line"> <tt class="py-docstring">"""Output for all of the sequence.</tt> </tt>
<a name="L416"></a><tt class="py-lineno">416</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L417"></a><tt class="py-lineno">417</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L418"></a><tt class="py-lineno">418</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-173" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-173', 'sequence', 'link-53');">sequence</a></tt><tt class="py-op">:</tt> </tt>
<a name="L419"></a><tt class="py-lineno">419</tt> <tt class="py-line"> <tt class="py-name">cur_seq_pos</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L420"></a><tt class="py-lineno">420</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-name">cur_seq_pos</tt> <tt class="py-op"><</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-174" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-174', 'sequence', 'link-53');">sequence</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L421"></a><tt class="py-lineno">421</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt id="link-175" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-175', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-176" class="py-name"><a title="Bio.GenBank.Record.Record.SEQUENCE_FORMAT" class="py-name" href="#" onclick="return doclink('link-176', 'SEQUENCE_FORMAT', 'link-32');">SEQUENCE_FORMAT</a></tt> <tt class="py-op">%</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">cur_seq_pos</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L422"></a><tt class="py-lineno">422</tt> <tt class="py-line"> </tt>
<a name="L423"></a><tt class="py-lineno">423</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">section</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</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="L424"></a><tt class="py-lineno">424</tt> <tt class="py-line"> <tt class="py-name">start_pos</tt> <tt class="py-op">=</tt> <tt class="py-name">cur_seq_pos</tt> <tt class="py-op">+</tt> <tt class="py-name">section</tt> <tt class="py-op">*</tt> <tt class="py-number">10</tt> </tt>
<a name="L425"></a><tt class="py-lineno">425</tt> <tt class="py-line"> <tt class="py-name">end_pos</tt> <tt class="py-op">=</tt> <tt class="py-name">start_pos</tt> <tt class="py-op">+</tt> <tt class="py-number">10</tt> </tt>
<a name="L426"></a><tt class="py-lineno">426</tt> <tt class="py-line"> <tt class="py-name">seq_section</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-177" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-177', 'sequence', 'link-53');">sequence</a></tt><tt class="py-op">[</tt><tt class="py-name">start_pos</tt><tt class="py-op">:</tt><tt class="py-name">end_pos</tt><tt class="py-op">]</tt> </tt>
<a name="L427"></a><tt class="py-lineno">427</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-string">" %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">seq_section</tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L428"></a><tt class="py-lineno">428</tt> <tt class="py-line"> </tt>
<a name="L429"></a><tt class="py-lineno">429</tt> <tt class="py-line"> <tt class="py-comment"># stop looping if we are out of sequence</tt> </tt>
<a name="L430"></a><tt class="py-lineno">430</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">end_pos</tt> <tt class="py-op">></tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-178" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-178', 'sequence', 'link-53');">sequence</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L431"></a><tt class="py-lineno">431</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L432"></a><tt class="py-lineno">432</tt> <tt class="py-line"> </tt>
<a name="L433"></a><tt class="py-lineno">433</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-string">"\n"</tt> </tt>
<a name="L434"></a><tt class="py-lineno">434</tt> <tt class="py-line"> <tt class="py-name">cur_seq_pos</tt> <tt class="py-op">+=</tt> <tt class="py-number">60</tt> </tt>
<a name="L435"></a><tt class="py-lineno">435</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">output</tt> </tt>
</div><a name="L436"></a><tt class="py-lineno">436</tt> <tt class="py-line"> </tt>
<a name="Record._contig_line"></a><div id="Record._contig_line-def"><a name="L437"></a><tt class="py-lineno">437</tt> <a class="py-toggle" href="#" id="Record._contig_line-toggle" onclick="return toggle('Record._contig_line');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GenBank.Record.Record-class.html#_contig_line">_contig_line</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._contig_line-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Record._contig_line-expanded"><a name="L438"></a><tt class="py-lineno">438</tt> <tt class="py-line"> <tt class="py-docstring">"""Output for CONTIG location information from RefSeq.</tt> </tt>
<a name="L439"></a><tt class="py-lineno">439</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L440"></a><tt class="py-lineno">440</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L441"></a><tt class="py-lineno">441</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">contig</tt><tt class="py-op">:</tt> </tt>
<a name="L442"></a><tt class="py-lineno">442</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt id="link-179" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-179', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-180" class="py-name"><a title="Bio.GenBank.Record.Record.BASE_FORMAT" class="py-name" href="#" onclick="return doclink('link-180', 'BASE_FORMAT', 'link-16');">BASE_FORMAT</a></tt> <tt class="py-op">%</tt> <tt class="py-string">"CONTIG"</tt> </tt>
<a name="L443"></a><tt class="py-lineno">443</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt id="link-181" class="py-name"><a title="Bio.GenBank.Record._wrapped_genbank" class="py-name" href="#" onclick="return doclink('link-181', '_wrapped_genbank', 'link-92');">_wrapped_genbank</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">contig</tt><tt class="py-op">,</tt> </tt>
<a name="L444"></a><tt class="py-lineno">444</tt> <tt class="py-line"> <tt id="link-182" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-182', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-183" class="py-name"><a title="Bio.GenBank.Record.Record.GB_BASE_INDENT" class="py-name" href="#" onclick="return doclink('link-183', 'GB_BASE_INDENT', 'link-10');">GB_BASE_INDENT</a></tt><tt class="py-op">,</tt> <tt class="py-name">split_char</tt> <tt class="py-op">=</tt> <tt class="py-string">','</tt><tt class="py-op">)</tt> </tt>
<a name="L445"></a><tt class="py-lineno">445</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">output</tt> </tt>
</div></div><a name="L446"></a><tt class="py-lineno">446</tt> <tt class="py-line"> </tt>
<a name="Reference"></a><div id="Reference-def"><a name="L447"></a><tt class="py-lineno">447</tt> <a class="py-toggle" href="#" id="Reference-toggle" onclick="return toggle('Reference');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.GenBank.Record.Reference-class.html">Reference</a><tt class="py-op">:</tt> </tt>
</div><div id="Reference-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Reference-expanded"><a name="L448"></a><tt class="py-lineno">448</tt> <tt class="py-line"> <tt class="py-docstring">"""Hold information from a GenBank reference.</tt> </tt>
<a name="L449"></a><tt class="py-lineno">449</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L450"></a><tt class="py-lineno">450</tt> <tt class="py-line"><tt class="py-docstring"> Attributes:</tt> </tt>
<a name="L451"></a><tt class="py-lineno">451</tt> <tt class="py-line"><tt class="py-docstring"> o number - The number of the reference in the listing of references.</tt> </tt>
<a name="L452"></a><tt class="py-lineno">452</tt> <tt class="py-line"><tt class="py-docstring"> o bases - The bases in the sequence the reference refers to.</tt> </tt>
<a name="L453"></a><tt class="py-lineno">453</tt> <tt class="py-line"><tt class="py-docstring"> o authors - String with all of the authors.</tt> </tt>
<a name="L454"></a><tt class="py-lineno">454</tt> <tt class="py-line"><tt class="py-docstring"> o consrtm - Consortium the authors belong to. </tt> </tt>
<a name="L455"></a><tt class="py-lineno">455</tt> <tt class="py-line"><tt class="py-docstring"> o title - The title of the reference.</tt> </tt>
<a name="L456"></a><tt class="py-lineno">456</tt> <tt class="py-line"><tt class="py-docstring"> o journal - Information about the journal where the reference appeared.</tt> </tt>
<a name="L457"></a><tt class="py-lineno">457</tt> <tt class="py-line"><tt class="py-docstring"> o medline_id - The medline id for the reference.</tt> </tt>
<a name="L458"></a><tt class="py-lineno">458</tt> <tt class="py-line"><tt class="py-docstring"> o pubmed_id - The pubmed_id for the reference.</tt> </tt>
<a name="L459"></a><tt class="py-lineno">459</tt> <tt class="py-line"><tt class="py-docstring"> o remark - Free-form remarks about the reference.</tt> </tt>
<a name="L460"></a><tt class="py-lineno">460</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="Reference.__init__"></a><div id="Reference.__init__-def"><a name="L461"></a><tt class="py-lineno">461</tt> <a class="py-toggle" href="#" id="Reference.__init__-toggle" onclick="return toggle('Reference.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GenBank.Record.Reference-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="Reference.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Reference.__init__-expanded"><a name="L462"></a><tt class="py-lineno">462</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">number</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L463"></a><tt class="py-lineno">463</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">bases</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L464"></a><tt class="py-lineno">464</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-184" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.authors()=Bio.GenBank._FeatureConsumer-class.html#authors,Method Bio.GenBank._RecordConsumer.authors()=Bio.GenBank._RecordConsumer-class.html#authors"><a title="Bio.GenBank._FeatureConsumer.authors
Bio.GenBank._RecordConsumer.authors" class="py-name" href="#" onclick="return doclink('link-184', 'authors', 'link-184');">authors</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</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-185" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.consrtm()=Bio.GenBank._FeatureConsumer-class.html#consrtm,Method Bio.GenBank._RecordConsumer.consrtm()=Bio.GenBank._RecordConsumer-class.html#consrtm"><a title="Bio.GenBank._FeatureConsumer.consrtm
Bio.GenBank._RecordConsumer.consrtm" class="py-name" href="#" onclick="return doclink('link-185', 'consrtm', 'link-185');">consrtm</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-186" 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,Method Bio.Medline._RecordConsumer.title()=Bio.Medline._RecordConsumer-class.html#title,Variable Bio.expressions.fasta.title=Bio.expressions.fasta-module.html#title"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title
Bio.Medline._RecordConsumer.title
Bio.expressions.fasta.title" class="py-name" href="#" onclick="return doclink('link-186', 'title', 'link-186');">title</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 id="link-187" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.journal()=Bio.GenBank._FeatureConsumer-class.html#journal,Method Bio.GenBank._RecordConsumer.journal()=Bio.GenBank._RecordConsumer-class.html#journal"><a title="Bio.GenBank._FeatureConsumer.journal
Bio.GenBank._RecordConsumer.journal" class="py-name" href="#" onclick="return doclink('link-187', 'journal', 'link-187');">journal</a></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 id="link-188" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.medline_id()=Bio.GenBank._FeatureConsumer-class.html#medline_id,Method Bio.GenBank._RecordConsumer.medline_id()=Bio.GenBank._RecordConsumer-class.html#medline_id"><a title="Bio.GenBank._FeatureConsumer.medline_id
Bio.GenBank._RecordConsumer.medline_id" class="py-name" href="#" onclick="return doclink('link-188', 'medline_id', 'link-188');">medline_id</a></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-name">self</tt><tt class="py-op">.</tt><tt id="link-189" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.pubmed_id()=Bio.GenBank._FeatureConsumer-class.html#pubmed_id,Method Bio.GenBank._RecordConsumer.pubmed_id()=Bio.GenBank._RecordConsumer-class.html#pubmed_id,Method Bio.Medline._RecordConsumer.pubmed_id()=Bio.Medline._RecordConsumer-class.html#pubmed_id"><a title="Bio.GenBank._FeatureConsumer.pubmed_id
Bio.GenBank._RecordConsumer.pubmed_id
Bio.Medline._RecordConsumer.pubmed_id" class="py-name" href="#" onclick="return doclink('link-189', 'pubmed_id', 'link-189');">pubmed_id</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L470"></a><tt class="py-lineno">470</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-190" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.remark()=Bio.GenBank._FeatureConsumer-class.html#remark,Method Bio.GenBank._RecordConsumer.remark()=Bio.GenBank._RecordConsumer-class.html#remark"><a title="Bio.GenBank._FeatureConsumer.remark
Bio.GenBank._RecordConsumer.remark" class="py-name" href="#" onclick="return doclink('link-190', 'remark', 'link-190');">remark</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
</div><a name="L471"></a><tt class="py-lineno">471</tt> <tt class="py-line"> </tt>
<a name="Reference.__str__"></a><div id="Reference.__str__-def"><a name="L472"></a><tt class="py-lineno">472</tt> <a class="py-toggle" href="#" id="Reference.__str__-toggle" onclick="return toggle('Reference.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GenBank.Record.Reference-class.html#__str__">__str__</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="Reference.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Reference.__str__-expanded"><a name="L473"></a><tt class="py-lineno">473</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-191" class="py-name" targets="Method Bio.GenBank.Record.Reference._reference_line()=Bio.GenBank.Record.Reference-class.html#_reference_line"><a title="Bio.GenBank.Record.Reference._reference_line" class="py-name" href="#" onclick="return doclink('link-191', '_reference_line', 'link-191');">_reference_line</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L474"></a><tt class="py-lineno">474</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-192" class="py-name" targets="Method Bio.GenBank.Record.Reference._authors_line()=Bio.GenBank.Record.Reference-class.html#_authors_line"><a title="Bio.GenBank.Record.Reference._authors_line" class="py-name" href="#" onclick="return doclink('link-192', '_authors_line', 'link-192');">_authors_line</a></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 class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-193" class="py-name" targets="Method Bio.GenBank.Record.Reference._consrtm_line()=Bio.GenBank.Record.Reference-class.html#_consrtm_line"><a title="Bio.GenBank.Record.Reference._consrtm_line" class="py-name" href="#" onclick="return doclink('link-193', '_consrtm_line', 'link-193');">_consrtm_line</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L476"></a><tt class="py-lineno">476</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-194" class="py-name" targets="Method Bio.GenBank.Record.Reference._title_line()=Bio.GenBank.Record.Reference-class.html#_title_line"><a title="Bio.GenBank.Record.Reference._title_line" class="py-name" href="#" onclick="return doclink('link-194', '_title_line', 'link-194');">_title_line</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L477"></a><tt class="py-lineno">477</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-195" class="py-name" targets="Method Bio.GenBank.Record.Reference._journal_line()=Bio.GenBank.Record.Reference-class.html#_journal_line"><a title="Bio.GenBank.Record.Reference._journal_line" class="py-name" href="#" onclick="return doclink('link-195', '_journal_line', 'link-195');">_journal_line</a></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">output</tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-196" class="py-name" targets="Method Bio.GenBank.Record.Reference._medline_line()=Bio.GenBank.Record.Reference-class.html#_medline_line"><a title="Bio.GenBank.Record.Reference._medline_line" class="py-name" href="#" onclick="return doclink('link-196', '_medline_line', 'link-196');">_medline_line</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L479"></a><tt class="py-lineno">479</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-197" class="py-name" targets="Method Bio.GenBank.Record.Reference._pubmed_line()=Bio.GenBank.Record.Reference-class.html#_pubmed_line"><a title="Bio.GenBank.Record.Reference._pubmed_line" class="py-name" href="#" onclick="return doclink('link-197', '_pubmed_line', 'link-197');">_pubmed_line</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L480"></a><tt class="py-lineno">480</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-198" class="py-name" targets="Method Bio.GenBank.Record.Reference._remark_line()=Bio.GenBank.Record.Reference-class.html#_remark_line"><a title="Bio.GenBank.Record.Reference._remark_line" class="py-name" href="#" onclick="return doclink('link-198', '_remark_line', 'link-198');">_remark_line</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L481"></a><tt class="py-lineno">481</tt> <tt class="py-line"> </tt>
<a name="L482"></a><tt class="py-lineno">482</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">output</tt> </tt>
</div><a name="L483"></a><tt class="py-lineno">483</tt> <tt class="py-line"> </tt>
<a name="Reference._reference_line"></a><div id="Reference._reference_line-def"><a name="L484"></a><tt class="py-lineno">484</tt> <a class="py-toggle" href="#" id="Reference._reference_line-toggle" onclick="return toggle('Reference._reference_line');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GenBank.Record.Reference-class.html#_reference_line">_reference_line</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="Reference._reference_line-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Reference._reference_line-expanded"><a name="L485"></a><tt class="py-lineno">485</tt> <tt class="py-line"> <tt class="py-docstring">"""Output for REFERENCE lines.</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-name">output</tt> <tt class="py-op">=</tt> <tt id="link-199" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-199', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-200" class="py-name"><a title="Bio.GenBank.Record.Record.BASE_FORMAT" class="py-name" href="#" onclick="return doclink('link-200', 'BASE_FORMAT', 'link-16');">BASE_FORMAT</a></tt> <tt class="py-op">%</tt> <tt class="py-string">"REFERENCE"</tt> </tt>
<a name="L488"></a><tt class="py-lineno">488</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">number</tt><tt class="py-op">:</tt> </tt>
<a name="L489"></a><tt class="py-lineno">489</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">bases</tt><tt class="py-op">:</tt> </tt>
<a name="L490"></a><tt class="py-lineno">490</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-string">"%-3s"</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">number</tt> </tt>
<a name="L491"></a><tt class="py-lineno">491</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-string">"%s"</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">bases</tt> </tt>
<a name="L492"></a><tt class="py-lineno">492</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L493"></a><tt class="py-lineno">493</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-string">"%s"</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">number</tt> </tt>
<a name="L494"></a><tt class="py-lineno">494</tt> <tt class="py-line"> </tt>
<a name="L495"></a><tt class="py-lineno">495</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-string">"\n"</tt> </tt>
<a name="L496"></a><tt class="py-lineno">496</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">output</tt> </tt>
</div><a name="L497"></a><tt class="py-lineno">497</tt> <tt class="py-line"> </tt>
<a name="Reference._authors_line"></a><div id="Reference._authors_line-def"><a name="L498"></a><tt class="py-lineno">498</tt> <a class="py-toggle" href="#" id="Reference._authors_line-toggle" onclick="return toggle('Reference._authors_line');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GenBank.Record.Reference-class.html#_authors_line">_authors_line</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="Reference._authors_line-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Reference._authors_line-expanded"><a name="L499"></a><tt class="py-lineno">499</tt> <tt class="py-line"> <tt class="py-docstring">"""Output for AUTHORS information.</tt> </tt>
<a name="L500"></a><tt class="py-lineno">500</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L501"></a><tt class="py-lineno">501</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L502"></a><tt class="py-lineno">502</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-201" class="py-name"><a title="Bio.GenBank._FeatureConsumer.authors
Bio.GenBank._RecordConsumer.authors" class="py-name" href="#" onclick="return doclink('link-201', 'authors', 'link-184');">authors</a></tt><tt class="py-op">:</tt> </tt>
<a name="L503"></a><tt class="py-lineno">503</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt id="link-202" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-202', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-203" class="py-name"><a title="Bio.GenBank.Record.Record.INTERNAL_FORMAT" class="py-name" href="#" onclick="return doclink('link-203', 'INTERNAL_FORMAT', 'link-18');">INTERNAL_FORMAT</a></tt> <tt class="py-op">%</tt> <tt class="py-string">"AUTHORS"</tt> </tt>
<a name="L504"></a><tt class="py-lineno">504</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt id="link-204" class="py-name"><a title="Bio.GenBank.Record._wrapped_genbank" class="py-name" href="#" onclick="return doclink('link-204', '_wrapped_genbank', 'link-92');">_wrapped_genbank</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-205" class="py-name"><a title="Bio.GenBank._FeatureConsumer.authors
Bio.GenBank._RecordConsumer.authors" class="py-name" href="#" onclick="return doclink('link-205', 'authors', 'link-184');">authors</a></tt><tt class="py-op">,</tt> <tt id="link-206" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-206', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-207" class="py-name"><a title="Bio.GenBank.Record.Record.GB_BASE_INDENT" class="py-name" href="#" onclick="return doclink('link-207', 'GB_BASE_INDENT', 'link-10');">GB_BASE_INDENT</a></tt><tt class="py-op">)</tt> </tt>
<a name="L505"></a><tt class="py-lineno">505</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">output</tt> </tt>
</div><a name="L506"></a><tt class="py-lineno">506</tt> <tt class="py-line"> </tt>
<a name="Reference._consrtm_line"></a><div id="Reference._consrtm_line-def"><a name="L507"></a><tt class="py-lineno">507</tt> <a class="py-toggle" href="#" id="Reference._consrtm_line-toggle" onclick="return toggle('Reference._consrtm_line');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GenBank.Record.Reference-class.html#_consrtm_line">_consrtm_line</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="Reference._consrtm_line-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Reference._consrtm_line-expanded"><a name="L508"></a><tt class="py-lineno">508</tt> <tt class="py-line"> <tt class="py-docstring">"""Output for CONSRTM information.</tt> </tt>
<a name="L509"></a><tt class="py-lineno">509</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L510"></a><tt class="py-lineno">510</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L511"></a><tt class="py-lineno">511</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-208" class="py-name"><a title="Bio.GenBank._FeatureConsumer.consrtm
Bio.GenBank._RecordConsumer.consrtm" class="py-name" href="#" onclick="return doclink('link-208', 'consrtm', 'link-185');">consrtm</a></tt><tt class="py-op">:</tt> </tt>
<a name="L512"></a><tt class="py-lineno">512</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt id="link-209" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-209', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-210" class="py-name"><a title="Bio.GenBank.Record.Record.INTERNAL_FORMAT" class="py-name" href="#" onclick="return doclink('link-210', 'INTERNAL_FORMAT', 'link-18');">INTERNAL_FORMAT</a></tt> <tt class="py-op">%</tt> <tt class="py-string">"CONSRTM"</tt> </tt>
<a name="L513"></a><tt class="py-lineno">513</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt id="link-211" class="py-name"><a title="Bio.GenBank.Record._wrapped_genbank" class="py-name" href="#" onclick="return doclink('link-211', '_wrapped_genbank', 'link-92');">_wrapped_genbank</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-212" class="py-name"><a title="Bio.GenBank._FeatureConsumer.consrtm
Bio.GenBank._RecordConsumer.consrtm" class="py-name" href="#" onclick="return doclink('link-212', 'consrtm', 'link-185');">consrtm</a></tt><tt class="py-op">,</tt> <tt id="link-213" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-213', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-214" class="py-name"><a title="Bio.GenBank.Record.Record.GB_BASE_INDENT" class="py-name" href="#" onclick="return doclink('link-214', 'GB_BASE_INDENT', 'link-10');">GB_BASE_INDENT</a></tt><tt class="py-op">)</tt> </tt>
<a name="L514"></a><tt class="py-lineno">514</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">output</tt> </tt>
</div><a name="L515"></a><tt class="py-lineno">515</tt> <tt class="py-line"> </tt>
<a name="Reference._title_line"></a><div id="Reference._title_line-def"><a name="L516"></a><tt class="py-lineno">516</tt> <a class="py-toggle" href="#" id="Reference._title_line-toggle" onclick="return toggle('Reference._title_line');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GenBank.Record.Reference-class.html#_title_line">_title_line</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="Reference._title_line-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Reference._title_line-expanded"><a name="L517"></a><tt class="py-lineno">517</tt> <tt class="py-line"> <tt class="py-docstring">"""Output for TITLE information.</tt> </tt>
<a name="L518"></a><tt class="py-lineno">518</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L519"></a><tt class="py-lineno">519</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L520"></a><tt class="py-lineno">520</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-215" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title
Bio.Medline._RecordConsumer.title
Bio.expressions.fasta.title" class="py-name" href="#" onclick="return doclink('link-215', 'title', 'link-186');">title</a></tt><tt class="py-op">:</tt> </tt>
<a name="L521"></a><tt class="py-lineno">521</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt id="link-216" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-216', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-217" class="py-name"><a title="Bio.GenBank.Record.Record.INTERNAL_FORMAT" class="py-name" href="#" onclick="return doclink('link-217', 'INTERNAL_FORMAT', 'link-18');">INTERNAL_FORMAT</a></tt> <tt class="py-op">%</tt> <tt class="py-string">"TITLE"</tt> </tt>
<a name="L522"></a><tt class="py-lineno">522</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt id="link-218" class="py-name"><a title="Bio.GenBank.Record._wrapped_genbank" class="py-name" href="#" onclick="return doclink('link-218', '_wrapped_genbank', 'link-92');">_wrapped_genbank</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-219" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title
Bio.Medline._RecordConsumer.title
Bio.expressions.fasta.title" class="py-name" href="#" onclick="return doclink('link-219', 'title', 'link-186');">title</a></tt><tt class="py-op">,</tt> <tt id="link-220" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-220', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-221" class="py-name"><a title="Bio.GenBank.Record.Record.GB_BASE_INDENT" class="py-name" href="#" onclick="return doclink('link-221', 'GB_BASE_INDENT', 'link-10');">GB_BASE_INDENT</a></tt><tt class="py-op">)</tt> </tt>
<a name="L523"></a><tt class="py-lineno">523</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">output</tt> </tt>
</div><a name="L524"></a><tt class="py-lineno">524</tt> <tt class="py-line"> </tt>
<a name="Reference._journal_line"></a><div id="Reference._journal_line-def"><a name="L525"></a><tt class="py-lineno">525</tt> <a class="py-toggle" href="#" id="Reference._journal_line-toggle" onclick="return toggle('Reference._journal_line');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GenBank.Record.Reference-class.html#_journal_line">_journal_line</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="Reference._journal_line-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Reference._journal_line-expanded"><a name="L526"></a><tt class="py-lineno">526</tt> <tt class="py-line"> <tt class="py-docstring">"""Output for JOURNAL information.</tt> </tt>
<a name="L527"></a><tt class="py-lineno">527</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L528"></a><tt class="py-lineno">528</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L529"></a><tt class="py-lineno">529</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-222" class="py-name"><a title="Bio.GenBank._FeatureConsumer.journal
Bio.GenBank._RecordConsumer.journal" class="py-name" href="#" onclick="return doclink('link-222', 'journal', 'link-187');">journal</a></tt><tt class="py-op">:</tt> </tt>
<a name="L530"></a><tt class="py-lineno">530</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt id="link-223" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-223', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-224" class="py-name"><a title="Bio.GenBank.Record.Record.INTERNAL_FORMAT" class="py-name" href="#" onclick="return doclink('link-224', 'INTERNAL_FORMAT', 'link-18');">INTERNAL_FORMAT</a></tt> <tt class="py-op">%</tt> <tt class="py-string">"JOURNAL"</tt> </tt>
<a name="L531"></a><tt class="py-lineno">531</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt id="link-225" class="py-name"><a title="Bio.GenBank.Record._wrapped_genbank" class="py-name" href="#" onclick="return doclink('link-225', '_wrapped_genbank', 'link-92');">_wrapped_genbank</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-226" class="py-name"><a title="Bio.GenBank._FeatureConsumer.journal
Bio.GenBank._RecordConsumer.journal" class="py-name" href="#" onclick="return doclink('link-226', 'journal', 'link-187');">journal</a></tt><tt class="py-op">,</tt> <tt id="link-227" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-227', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-228" class="py-name"><a title="Bio.GenBank.Record.Record.GB_BASE_INDENT" class="py-name" href="#" onclick="return doclink('link-228', 'GB_BASE_INDENT', 'link-10');">GB_BASE_INDENT</a></tt><tt class="py-op">)</tt> </tt>
<a name="L532"></a><tt class="py-lineno">532</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">output</tt> </tt>
</div><a name="L533"></a><tt class="py-lineno">533</tt> <tt class="py-line"> </tt>
<a name="Reference._medline_line"></a><div id="Reference._medline_line-def"><a name="L534"></a><tt class="py-lineno">534</tt> <a class="py-toggle" href="#" id="Reference._medline_line-toggle" onclick="return toggle('Reference._medline_line');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GenBank.Record.Reference-class.html#_medline_line">_medline_line</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="Reference._medline_line-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Reference._medline_line-expanded"><a name="L535"></a><tt class="py-lineno">535</tt> <tt class="py-line"> <tt class="py-docstring">"""Output for MEDLINE information.</tt> </tt>
<a name="L536"></a><tt class="py-lineno">536</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L537"></a><tt class="py-lineno">537</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L538"></a><tt class="py-lineno">538</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-229" class="py-name"><a title="Bio.GenBank._FeatureConsumer.medline_id
Bio.GenBank._RecordConsumer.medline_id" class="py-name" href="#" onclick="return doclink('link-229', 'medline_id', 'link-188');">medline_id</a></tt><tt class="py-op">:</tt> </tt>
<a name="L539"></a><tt class="py-lineno">539</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt id="link-230" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-230', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-231" class="py-name"><a title="Bio.GenBank.Record.Record.INTERNAL_FORMAT" class="py-name" href="#" onclick="return doclink('link-231', 'INTERNAL_FORMAT', 'link-18');">INTERNAL_FORMAT</a></tt> <tt class="py-op">%</tt> <tt class="py-string">"MEDLINE"</tt> </tt>
<a name="L540"></a><tt class="py-lineno">540</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-232" class="py-name"><a title="Bio.GenBank._FeatureConsumer.medline_id
Bio.GenBank._RecordConsumer.medline_id" class="py-name" href="#" onclick="return doclink('link-232', 'medline_id', 'link-188');">medline_id</a></tt> <tt class="py-op">+</tt> <tt class="py-string">"\n"</tt> </tt>
<a name="L541"></a><tt class="py-lineno">541</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">output</tt> </tt>
</div><a name="L542"></a><tt class="py-lineno">542</tt> <tt class="py-line"> </tt>
<a name="Reference._pubmed_line"></a><div id="Reference._pubmed_line-def"><a name="L543"></a><tt class="py-lineno">543</tt> <a class="py-toggle" href="#" id="Reference._pubmed_line-toggle" onclick="return toggle('Reference._pubmed_line');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GenBank.Record.Reference-class.html#_pubmed_line">_pubmed_line</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="Reference._pubmed_line-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Reference._pubmed_line-expanded"><a name="L544"></a><tt class="py-lineno">544</tt> <tt class="py-line"> <tt class="py-docstring">"""Output for PUBMED information.</tt> </tt>
<a name="L545"></a><tt class="py-lineno">545</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L546"></a><tt class="py-lineno">546</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L547"></a><tt class="py-lineno">547</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-233" class="py-name"><a title="Bio.GenBank._FeatureConsumer.pubmed_id
Bio.GenBank._RecordConsumer.pubmed_id
Bio.Medline._RecordConsumer.pubmed_id" class="py-name" href="#" onclick="return doclink('link-233', 'pubmed_id', 'link-189');">pubmed_id</a></tt><tt class="py-op">:</tt> </tt>
<a name="L548"></a><tt class="py-lineno">548</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt id="link-234" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-234', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-235" class="py-name"><a title="Bio.GenBank.Record.Record.OTHER_INTERNAL_FORMAT" class="py-name" href="#" onclick="return doclink('link-235', 'OTHER_INTERNAL_FORMAT', 'link-22');">OTHER_INTERNAL_FORMAT</a></tt> <tt class="py-op">%</tt> <tt class="py-string">"PUBMED"</tt> </tt>
<a name="L549"></a><tt class="py-lineno">549</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-236" class="py-name"><a title="Bio.GenBank._FeatureConsumer.pubmed_id
Bio.GenBank._RecordConsumer.pubmed_id
Bio.Medline._RecordConsumer.pubmed_id" class="py-name" href="#" onclick="return doclink('link-236', 'pubmed_id', 'link-189');">pubmed_id</a></tt> <tt class="py-op">+</tt> <tt class="py-string">"\n"</tt> </tt>
<a name="L550"></a><tt class="py-lineno">550</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">output</tt> </tt>
</div><a name="L551"></a><tt class="py-lineno">551</tt> <tt class="py-line"> </tt>
<a name="Reference._remark_line"></a><div id="Reference._remark_line-def"><a name="L552"></a><tt class="py-lineno">552</tt> <a class="py-toggle" href="#" id="Reference._remark_line-toggle" onclick="return toggle('Reference._remark_line');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GenBank.Record.Reference-class.html#_remark_line">_remark_line</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="Reference._remark_line-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Reference._remark_line-expanded"><a name="L553"></a><tt class="py-lineno">553</tt> <tt class="py-line"> <tt class="py-docstring">"""Output for REMARK information.</tt> </tt>
<a name="L554"></a><tt class="py-lineno">554</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L555"></a><tt class="py-lineno">555</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L556"></a><tt class="py-lineno">556</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-237" class="py-name"><a title="Bio.GenBank._FeatureConsumer.remark
Bio.GenBank._RecordConsumer.remark" class="py-name" href="#" onclick="return doclink('link-237', 'remark', 'link-190');">remark</a></tt><tt class="py-op">:</tt> </tt>
<a name="L557"></a><tt class="py-lineno">557</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt id="link-238" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-238', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-239" class="py-name"><a title="Bio.GenBank.Record.Record.INTERNAL_FORMAT" class="py-name" href="#" onclick="return doclink('link-239', 'INTERNAL_FORMAT', 'link-18');">INTERNAL_FORMAT</a></tt> <tt class="py-op">%</tt> <tt class="py-string">"REMARK"</tt> </tt>
<a name="L558"></a><tt class="py-lineno">558</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt id="link-240" class="py-name"><a title="Bio.GenBank.Record._wrapped_genbank" class="py-name" href="#" onclick="return doclink('link-240', '_wrapped_genbank', 'link-92');">_wrapped_genbank</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-241" class="py-name"><a title="Bio.GenBank._FeatureConsumer.remark
Bio.GenBank._RecordConsumer.remark" class="py-name" href="#" onclick="return doclink('link-241', 'remark', 'link-190');">remark</a></tt><tt class="py-op">,</tt> <tt id="link-242" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-242', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-243" class="py-name"><a title="Bio.GenBank.Record.Record.GB_BASE_INDENT" class="py-name" href="#" onclick="return doclink('link-243', 'GB_BASE_INDENT', 'link-10');">GB_BASE_INDENT</a></tt><tt class="py-op">)</tt> </tt>
<a name="L559"></a><tt class="py-lineno">559</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">output</tt> </tt>
</div></div><a name="L560"></a><tt class="py-lineno">560</tt> <tt class="py-line"> </tt>
<a name="Feature"></a><div id="Feature-def"><a name="L561"></a><tt class="py-lineno">561</tt> <a class="py-toggle" href="#" id="Feature-toggle" onclick="return toggle('Feature');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.GenBank.Record.Feature-class.html">Feature</a><tt class="py-op">:</tt> </tt>
</div><div id="Feature-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Feature-expanded"><a name="L562"></a><tt class="py-lineno">562</tt> <tt class="py-line"> <tt class="py-docstring">"""Hold information about a Feature in the Feature Table of GenBank record.</tt> </tt>
<a name="L563"></a><tt class="py-lineno">563</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L564"></a><tt class="py-lineno">564</tt> <tt class="py-line"><tt class="py-docstring"> Attributes:</tt> </tt>
<a name="L565"></a><tt class="py-lineno">565</tt> <tt class="py-line"><tt class="py-docstring"> o key - The key name of the featue (ie. source)</tt> </tt>
<a name="L566"></a><tt class="py-lineno">566</tt> <tt class="py-line"><tt class="py-docstring"> o location - The string specifying the location of the feature.</tt> </tt>
<a name="L567"></a><tt class="py-lineno">567</tt> <tt class="py-line"><tt class="py-docstring"> o qualfiers - A listing Qualifier objects in the feature.</tt> </tt>
<a name="L568"></a><tt class="py-lineno">568</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="Feature.__init__"></a><div id="Feature.__init__-def"><a name="L569"></a><tt class="py-lineno">569</tt> <a class="py-toggle" href="#" id="Feature.__init__-toggle" onclick="return toggle('Feature.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GenBank.Record.Feature-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="Feature.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Feature.__init__-expanded"><a name="L570"></a><tt class="py-lineno">570</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-244" class="py-name" targets="Variable Bio.Translate.key=Bio.Translate-module.html#key"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-244', 'key', 'link-244');">key</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L571"></a><tt class="py-lineno">571</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-245" class="py-name" targets="Method Bio.GFF.Feature.location()=Bio.GFF.Feature-class.html#location,Method Bio.GFF.FeatureAggregate.location()=Bio.GFF.FeatureAggregate-class.html#location,Method Bio.GenBank._FeatureConsumer.location()=Bio.GenBank._FeatureConsumer-class.html#location,Method Bio.GenBank._RecordConsumer.location()=Bio.GenBank._RecordConsumer-class.html#location,Variable Bio.expressions.genbank.location=Bio.expressions.genbank-module.html#location"><a title="Bio.GFF.Feature.location
Bio.GFF.FeatureAggregate.location
Bio.GenBank._FeatureConsumer.location
Bio.GenBank._RecordConsumer.location
Bio.expressions.genbank.location" class="py-name" href="#" onclick="return doclink('link-245', 'location', 'link-245');">location</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L572"></a><tt class="py-lineno">572</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">qualifiers</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
</div><a name="L573"></a><tt class="py-lineno">573</tt> <tt class="py-line"> </tt>
<a name="Feature.__str__"></a><div id="Feature.__str__-def"><a name="L574"></a><tt class="py-lineno">574</tt> <a class="py-toggle" href="#" id="Feature.__str__-toggle" onclick="return toggle('Feature.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GenBank.Record.Feature-class.html#__str__">__str__</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="Feature.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Feature.__str__-expanded"><a name="L575"></a><tt class="py-lineno">575</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt id="link-246" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-246', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-247" class="py-name"><a title="Bio.GenBank.Record.Record.INTERNAL_FEATURE_FORMAT" class="py-name" href="#" onclick="return doclink('link-247', 'INTERNAL_FEATURE_FORMAT', 'link-28');">INTERNAL_FEATURE_FORMAT</a></tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-248" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-248', 'key', 'link-244');">key</a></tt> </tt>
<a name="L576"></a><tt class="py-lineno">576</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt id="link-249" class="py-name"><a title="Bio.GenBank.Record._wrapped_genbank" class="py-name" href="#" onclick="return doclink('link-249', '_wrapped_genbank', 'link-92');">_wrapped_genbank</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-250" class="py-name"><a title="Bio.GFF.Feature.location
Bio.GFF.FeatureAggregate.location
Bio.GenBank._FeatureConsumer.location
Bio.GenBank._RecordConsumer.location
Bio.expressions.genbank.location" class="py-name" href="#" onclick="return doclink('link-250', 'location', 'link-245');">location</a></tt><tt class="py-op">,</tt> <tt id="link-251" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-251', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-252" class="py-name"><a title="Bio.GenBank.Record.Record.GB_FEATURE_INDENT" class="py-name" href="#" onclick="return doclink('link-252', 'GB_FEATURE_INDENT', 'link-11');">GB_FEATURE_INDENT</a></tt><tt class="py-op">,</tt> </tt>
<a name="L577"></a><tt class="py-lineno">577</tt> <tt class="py-line"> <tt class="py-name">split_char</tt> <tt class="py-op">=</tt> <tt class="py-string">','</tt><tt class="py-op">)</tt> </tt>
<a name="L578"></a><tt class="py-lineno">578</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-253" class="py-name" targets="Variable Bio.expressions.genbank.qualifier=Bio.expressions.genbank-module.html#qualifier"><a title="Bio.expressions.genbank.qualifier" class="py-name" href="#" onclick="return doclink('link-253', 'qualifier', 'link-253');">qualifier</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">qualifiers</tt><tt class="py-op">:</tt> </tt>
<a name="L579"></a><tt class="py-lineno">579</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-string">" "</tt> <tt class="py-op">*</tt> <tt id="link-254" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-254', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-255" class="py-name"><a title="Bio.GenBank.Record.Record.GB_FEATURE_INDENT" class="py-name" href="#" onclick="return doclink('link-255', 'GB_FEATURE_INDENT', 'link-11');">GB_FEATURE_INDENT</a></tt> </tt>
<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 class="py-comment"># determine whether we can wrap on spaces</tt> </tt>
<a name="L582"></a><tt class="py-lineno">582</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">space_wrap</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L583"></a><tt class="py-lineno">583</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">no_space_key</tt> <tt class="py-keyword">in</tt> \ </tt>
<a name="L584"></a><tt class="py-lineno">584</tt> <tt class="py-line"> <tt id="link-256" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-256', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-257" class="py-name"><a title="Bio.GenBank" class="py-name" href="#" onclick="return doclink('link-257', 'GenBank', 'link-1');">GenBank</a></tt><tt class="py-op">.</tt><tt id="link-258" class="py-name" targets="Class Bio.GenBank._BaseGenBankConsumer=Bio.GenBank._BaseGenBankConsumer-class.html"><a title="Bio.GenBank._BaseGenBankConsumer" class="py-name" href="#" onclick="return doclink('link-258', '_BaseGenBankConsumer', 'link-258');">_BaseGenBankConsumer</a></tt><tt class="py-op">.</tt><tt id="link-259" class="py-name" targets="Variable Bio.GenBank._BaseGenBankConsumer.remove_space_keys=Bio.GenBank._BaseGenBankConsumer-class.html#remove_space_keys"><a title="Bio.GenBank._BaseGenBankConsumer.remove_space_keys" class="py-name" href="#" onclick="return doclink('link-259', 'remove_space_keys', 'link-259');">remove_space_keys</a></tt><tt class="py-op">:</tt> </tt>
<a name="L585"></a><tt class="py-lineno">585</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-260" class="py-name"><a title="Bio.expressions.genbank.qualifier" class="py-name" href="#" onclick="return doclink('link-260', 'qualifier', 'link-253');">qualifier</a></tt><tt class="py-op">.</tt><tt id="link-261" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-261', 'key', 'link-244');">key</a></tt><tt class="py-op">.</tt><tt id="link-262" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-262', 'find', 'link-80');">find</a></tt><tt class="py-op">(</tt><tt class="py-name">no_space_key</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="L586"></a><tt class="py-lineno">586</tt> <tt class="py-line"> <tt class="py-name">space_wrap</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L587"></a><tt class="py-lineno">587</tt> <tt class="py-line"> </tt>
<a name="L588"></a><tt class="py-lineno">588</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt id="link-263" class="py-name"><a title="Bio.GenBank.Record._wrapped_genbank" class="py-name" href="#" onclick="return doclink('link-263', '_wrapped_genbank', 'link-92');">_wrapped_genbank</a></tt><tt class="py-op">(</tt><tt id="link-264" class="py-name"><a title="Bio.expressions.genbank.qualifier" class="py-name" href="#" onclick="return doclink('link-264', 'qualifier', 'link-253');">qualifier</a></tt><tt class="py-op">.</tt><tt id="link-265" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-265', 'key', 'link-244');">key</a></tt> <tt class="py-op">+</tt> <tt id="link-266" class="py-name"><a title="Bio.expressions.genbank.qualifier" class="py-name" href="#" onclick="return doclink('link-266', 'qualifier', 'link-253');">qualifier</a></tt><tt class="py-op">.</tt><tt id="link-267" class="py-name" targets="Variable Bio.Translate.value=Bio.Translate-module.html#value"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-267', 'value', 'link-267');">value</a></tt><tt class="py-op">,</tt> </tt>
<a name="L589"></a><tt class="py-lineno">589</tt> <tt class="py-line"> <tt id="link-268" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-268', 'Record', 'link-2');">Record</a></tt><tt class="py-op">.</tt><tt id="link-269" class="py-name"><a title="Bio.GenBank.Record.Record.GB_FEATURE_INDENT" class="py-name" href="#" onclick="return doclink('link-269', 'GB_FEATURE_INDENT', 'link-11');">GB_FEATURE_INDENT</a></tt><tt class="py-op">,</tt> <tt class="py-name">space_wrap</tt><tt class="py-op">)</tt> </tt>
<a name="L590"></a><tt class="py-lineno">590</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">output</tt> </tt>
</div></div><a name="L591"></a><tt class="py-lineno">591</tt> <tt class="py-line"> </tt>
<a name="Qualifier"></a><div id="Qualifier-def"><a name="L592"></a><tt class="py-lineno">592</tt> <a class="py-toggle" href="#" id="Qualifier-toggle" onclick="return toggle('Qualifier');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.GenBank.Record.Qualifier-class.html">Qualifier</a><tt class="py-op">:</tt> </tt>
</div><div id="Qualifier-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Qualifier-expanded"><a name="L593"></a><tt class="py-lineno">593</tt> <tt class="py-line"> <tt class="py-docstring">"""Hold information about a qualifier in a GenBank feature.</tt> </tt>
<a name="L594"></a><tt class="py-lineno">594</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L595"></a><tt class="py-lineno">595</tt> <tt class="py-line"><tt class="py-docstring"> Attributes:</tt> </tt>
<a name="L596"></a><tt class="py-lineno">596</tt> <tt class="py-line"><tt class="py-docstring"> o key - The key name of the qualifier (ie. /organism=)</tt> </tt>
<a name="L597"></a><tt class="py-lineno">597</tt> <tt class="py-line"><tt class="py-docstring"> o value - The value of the qualifier ("Dictyostelium discoideum").</tt> </tt>
<a name="L598"></a><tt class="py-lineno">598</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="Qualifier.__init__"></a><div id="Qualifier.__init__-def"><a name="L599"></a><tt class="py-lineno">599</tt> <a class="py-toggle" href="#" id="Qualifier.__init__-toggle" onclick="return toggle('Qualifier.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GenBank.Record.Qualifier-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="Qualifier.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Qualifier.__init__-expanded"><a name="L600"></a><tt class="py-lineno">600</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-270" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-270', 'key', 'link-244');">key</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L601"></a><tt class="py-lineno">601</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-271" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-271', 'value', 'link-267');">value</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
</div></div><a name="L602"></a><tt class="py-lineno">602</tt> <tt class="py-line"> </tt><script type="text/javascript">
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