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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.formatdefs-module.html">Package formatdefs</a> ::
Module genbank
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<h1 class="epydoc">Source Code for <a href="Bio.formatdefs.genbank-module.html">Module Bio.formatdefs.genbank</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Package Bio.config=Bio.config-module.html"><a title="Bio.config" class="py-name" href="#" onclick="return doclink('link-1', 'config', 'link-1');">config</a></tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Module Bio.config.FormatRegistry=Bio.config.FormatRegistry-module.html,Class Bio.config.FormatRegistry.FormatRegistry=Bio.config.FormatRegistry.FormatRegistry-class.html"><a title="Bio.config.FormatRegistry
Bio.config.FormatRegistry.FormatRegistry" class="py-name" href="#" onclick="return doclink('link-2', 'FormatRegistry', 'link-2');">FormatRegistry</a></tt> <tt class="py-keyword">import</tt> <tt id="link-3" class="py-name" targets="Class Bio.config.FormatRegistry.FormatObject=Bio.config.FormatRegistry.FormatObject-class.html"><a title="Bio.config.FormatRegistry.FormatObject" class="py-name" href="#" onclick="return doclink('link-3', 'FormatObject', 'link-3');">FormatObject</a></tt><tt class="py-op">,</tt> <tt id="link-4" class="py-name" targets="Class Bio.config.FormatRegistry.FormatGroup=Bio.config.FormatRegistry.FormatGroup-class.html"><a title="Bio.config.FormatRegistry.FormatGroup" class="py-name" href="#" onclick="return doclink('link-4', 'FormatGroup', 'link-4');">FormatGroup</a></tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"># This is a sequence of genbank records</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-5" class="py-name" targets="Variable Bio.formatdefs.genbank.genbank_records=Bio.formatdefs.genbank-module.html#genbank_records"><a title="Bio.formatdefs.genbank.genbank_records" class="py-name" href="#" onclick="return doclink('link-5', 'genbank_records', 'link-5');">genbank_records</a></tt> <tt class="py-op">=</tt> <tt id="link-6" class="py-name"><a title="Bio.config.FormatRegistry.FormatObject" class="py-name" href="#" onclick="return doclink('link-6', 'FormatObject', 'link-3');">FormatObject</a></tt><tt class="py-op">(</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"> <tt id="link-7" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.name=Bio.Encodings.IUPACEncoding-module.html#name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-7', 'name', 'link-7');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"genbank-records"</tt><tt class="py-op">,</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"> <tt class="py-name">abbrev</tt> <tt class="py-op">=</tt> <tt class="py-string">"genbank_records"</tt><tt class="py-op">,</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"> <tt class="py-name">expression</tt> <tt class="py-op">=</tt> <tt class="py-string">"Bio.expressions.genbank.format"</tt><tt class="py-op">,</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"> </tt>
<a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"><tt class="py-comment"># This is the format as released by NCBI. It includes</tt> </tt>
<a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># the header information.</tt> </tt>
<a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-8" class="py-name" targets="Variable Bio.formatdefs.genbank.genbank_release=Bio.formatdefs.genbank-module.html#genbank_release"><a title="Bio.formatdefs.genbank.genbank_release" class="py-name" href="#" onclick="return doclink('link-8', 'genbank_release', 'link-8');">genbank_release</a></tt> <tt class="py-op">=</tt> <tt id="link-9" class="py-name"><a title="Bio.config.FormatRegistry.FormatObject" class="py-name" href="#" onclick="return doclink('link-9', 'FormatObject', 'link-3');">FormatObject</a></tt><tt class="py-op">(</tt> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"> <tt id="link-10" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-10', 'name', 'link-7');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"genbank-release"</tt><tt class="py-op">,</tt> </tt>
<a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"> <tt class="py-name">abbrev</tt> <tt class="py-op">=</tt> <tt class="py-string">"genbank_release"</tt><tt class="py-op">,</tt> </tt>
<a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"> <tt class="py-name">expression</tt> <tt class="py-op">=</tt> <tt class="py-string">"Bio.expressions.genbank.ncbi_format"</tt><tt class="py-op">,</tt> </tt>
<a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
<a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"> </tt>
<a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"><tt id="link-11" class="py-name" targets="Module Bio.dbdefs.genbank=Bio.dbdefs.genbank-module.html,Module Bio.expressions.genbank=Bio.expressions.genbank-module.html,Module Bio.formatdefs.genbank=Bio.formatdefs.genbank-module.html,Variable Bio.formatdefs.genbank.genbank=Bio.formatdefs.genbank-module.html#genbank"><a title="Bio.dbdefs.genbank
Bio.expressions.genbank
Bio.formatdefs.genbank
Bio.formatdefs.genbank.genbank" class="py-name" href="#" onclick="return doclink('link-11', 'genbank', 'link-11');">genbank</a></tt> <tt class="py-op">=</tt> <tt id="link-12" class="py-name"><a title="Bio.config.FormatRegistry.FormatGroup" class="py-name" href="#" onclick="return doclink('link-12', 'FormatGroup', 'link-4');">FormatGroup</a></tt><tt class="py-op">(</tt> </tt>
<a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"> <tt id="link-13" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-13', 'name', 'link-7');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"genbank"</tt><tt class="py-op">,</tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"><tt id="link-14" class="py-name"><a title="Bio.dbdefs.genbank
Bio.expressions.genbank
Bio.formatdefs.genbank
Bio.formatdefs.genbank.genbank" class="py-name" href="#" onclick="return doclink('link-14', 'genbank', 'link-11');">genbank</a></tt><tt class="py-op">.</tt><tt id="link-15" class="py-name" targets="Variable Bio.Affy.CelFile.add=Bio.Affy.CelFile-module.html#add,Method Bio.EUtils.POM.ElementNode.add()=Bio.EUtils.POM.ElementNode-class.html#add,Method Bio.GFF.easy.Location.add()=Bio.GFF.easy.Location-class.html#add,Method Bio.Graphics.BasicChromosome._ChromosomeComponent.add()=Bio.Graphics.BasicChromosome._ChromosomeComponent-class.html#add,Variable Bio.LogisticRegression.add=Bio.LogisticRegression-module.html#add,Variable Bio.MarkovModel.add=Bio.MarkovModel-module.html#add,Variable Bio.MaxEntropy.add=Bio.MaxEntropy-module.html#add,Variable Bio.NaiveBayes.add=Bio.NaiveBayes-module.html#add,Method Bio.Nexus.Nexus.StepMatrix.add()=Bio.Nexus.Nexus.StepMatrix-class.html#add,Method Bio.Nexus.Nodes.Chain.add()=Bio.Nexus.Nodes.Chain-class.html#add,Method Bio.PDB.Entity.Entity.add()=Bio.PDB.Entity.Entity-class.html#add,Method Bio.PDB.Residue.DisorderedResidue.add()=Bio.PDB.Residue.DisorderedResidue-class.html#add,Method Bio.PDB.Residue.Residue.add()=Bio.PDB.Residue.Residue-class.html#add,Method Bio.Pathway.Rep.HashSet.HashSet.add()=Bio.Pathway.Rep.HashSet.HashSet-class.html#add,Method Bio.Restriction.Restriction.RestrictionBatch.add()=Bio.Restriction.Restriction.RestrictionBatch-class.html#add,Variable Bio.Statistics.lowess.add=Bio.Statistics.lowess-module.html#add,Method Bio.config.FormatRegistry.FormatGroup.add()=Bio.config.FormatRegistry.FormatGroup-class.html#add,Method Bio.config.Registry.RegisterableGroup.add()=Bio.config.Registry.RegisterableGroup-class.html#add,Variable Bio.distance.add=Bio.distance-module.html#add,Variable Bio.kNN.add=Bio.kNN-module.html#add,Method Martel.Dispatch.MulticallEnd.add()=Martel.Dispatch.MulticallEnd-class.html#add,Method Martel.Dispatch.MulticallStart.add()=Martel.Dispatch.MulticallStart-class.html#add"><a title="Bio.Affy.CelFile.add
Bio.EUtils.POM.ElementNode.add
Bio.GFF.easy.Location.add
Bio.Graphics.BasicChromosome._ChromosomeComponent.add
Bio.LogisticRegression.add
Bio.MarkovModel.add
Bio.MaxEntropy.add
Bio.NaiveBayes.add
Bio.Nexus.Nexus.StepMatrix.add
Bio.Nexus.Nodes.Chain.add
Bio.PDB.Entity.Entity.add
Bio.PDB.Residue.DisorderedResidue.add
Bio.PDB.Residue.Residue.add
Bio.Pathway.Rep.HashSet.HashSet.add
Bio.Restriction.Restriction.RestrictionBatch.add
Bio.Statistics.lowess.add
Bio.config.FormatRegistry.FormatGroup.add
Bio.config.Registry.RegisterableGroup.add
Bio.distance.add
Bio.kNN.add
Martel.Dispatch.MulticallEnd.add
Martel.Dispatch.MulticallStart.add" class="py-name" href="#" onclick="return doclink('link-15', 'add', 'link-15');">add</a></tt><tt class="py-op">(</tt><tt id="link-16" class="py-name"><a title="Bio.formatdefs.genbank.genbank_records" class="py-name" href="#" onclick="return doclink('link-16', 'genbank_records', 'link-5');">genbank_records</a></tt><tt class="py-op">)</tt> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"><tt id="link-17" class="py-name"><a title="Bio.dbdefs.genbank
Bio.expressions.genbank
Bio.formatdefs.genbank
Bio.formatdefs.genbank.genbank" class="py-name" href="#" onclick="return doclink('link-17', 'genbank', 'link-11');">genbank</a></tt><tt class="py-op">.</tt><tt id="link-18" class="py-name"><a title="Bio.Affy.CelFile.add
Bio.EUtils.POM.ElementNode.add
Bio.GFF.easy.Location.add
Bio.Graphics.BasicChromosome._ChromosomeComponent.add
Bio.LogisticRegression.add
Bio.MarkovModel.add
Bio.MaxEntropy.add
Bio.NaiveBayes.add
Bio.Nexus.Nexus.StepMatrix.add
Bio.Nexus.Nodes.Chain.add
Bio.PDB.Entity.Entity.add
Bio.PDB.Residue.DisorderedResidue.add
Bio.PDB.Residue.Residue.add
Bio.Pathway.Rep.HashSet.HashSet.add
Bio.Restriction.Restriction.RestrictionBatch.add
Bio.Statistics.lowess.add
Bio.config.FormatRegistry.FormatGroup.add
Bio.config.Registry.RegisterableGroup.add
Bio.distance.add
Bio.kNN.add
Martel.Dispatch.MulticallEnd.add
Martel.Dispatch.MulticallStart.add" class="py-name" href="#" onclick="return doclink('link-18', 'add', 'link-15');">add</a></tt><tt class="py-op">(</tt><tt id="link-19" class="py-name"><a title="Bio.formatdefs.genbank.genbank_release" class="py-name" href="#" onclick="return doclink('link-19', 'genbank_release', 'link-8');">genbank_release</a></tt><tt class="py-op">)</tt> </tt>
<a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"> </tt>
<a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-20" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-20', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-21" class="py-name" targets="Package Bio.formatdefs=Bio.formatdefs-module.html"><a title="Bio.formatdefs" class="py-name" href="#" onclick="return doclink('link-21', 'formatdefs', 'link-21');">formatdefs</a></tt> <tt class="py-keyword">import</tt> <tt id="link-22" 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-22', 'sequence', 'link-22');">sequence</a></tt> </tt>
<a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"><tt id="link-23" 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-23', 'sequence', 'link-22');">sequence</a></tt><tt class="py-op">.</tt><tt id="link-24" 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-24', 'sequence', 'link-22');">sequence</a></tt><tt class="py-op">.</tt><tt id="link-25" class="py-name"><a title="Bio.Affy.CelFile.add
Bio.EUtils.POM.ElementNode.add
Bio.GFF.easy.Location.add
Bio.Graphics.BasicChromosome._ChromosomeComponent.add
Bio.LogisticRegression.add
Bio.MarkovModel.add
Bio.MaxEntropy.add
Bio.NaiveBayes.add
Bio.Nexus.Nexus.StepMatrix.add
Bio.Nexus.Nodes.Chain.add
Bio.PDB.Entity.Entity.add
Bio.PDB.Residue.DisorderedResidue.add
Bio.PDB.Residue.Residue.add
Bio.Pathway.Rep.HashSet.HashSet.add
Bio.Restriction.Restriction.RestrictionBatch.add
Bio.Statistics.lowess.add
Bio.config.FormatRegistry.FormatGroup.add
Bio.config.Registry.RegisterableGroup.add
Bio.distance.add
Bio.kNN.add
Martel.Dispatch.MulticallEnd.add
Martel.Dispatch.MulticallStart.add" class="py-name" href="#" onclick="return doclink('link-25', 'add', 'link-15');">add</a></tt><tt class="py-op">(</tt><tt id="link-26" class="py-name"><a title="Bio.dbdefs.genbank
Bio.expressions.genbank
Bio.formatdefs.genbank
Bio.formatdefs.genbank.genbank" class="py-name" href="#" onclick="return doclink('link-26', 'genbank', 'link-11');">genbank</a></tt><tt class="py-op">)</tt> </tt>
<a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"> </tt><script type="text/javascript">
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