516 lines
26 KiB
HTML
516 lines
26 KiB
HTML
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Package obitools
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<!-- ==================== PACKAGE DESCRIPTION ==================== -->
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<h1 class="epydoc">Package obitools</h1><p class="nomargin-top"><span class="codelink"><a href="obitools-pysrc.html">source code</a></span></p>
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<!-- ==================== SUBMODULES ==================== -->
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<a name="section-Submodules"></a>
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<table class="summary" border="1" cellpadding="3"
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cellspacing="0" width="100%" bgcolor="white">
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<td align="left"><span class="table-header">Submodules</span></td>
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<td align="right" valign="top"
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><span class="options">[<a href="#section-Submodules"
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<ul class="nomargin">
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<li> <strong class="uidlink"><a href="obitools.SVGdraw-module.html">obitools.SVGdraw</a></strong>: <em class="summary">Use SVGdraw to generate your SVGdrawings.</em> </li>
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<li> <strong class="uidlink"><a href="obitools.align-module.html">obitools.align</a></strong>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.align.homopolymere-module.html">obitools.align.homopolymere</a></strong>: <em class="summary">Created on 14 mai 2009</em> </li>
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<li> <strong class="uidlink"><a href="obitools.align.ssearch-module.html">obitools.align.ssearch</a></strong> </li>
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</ul>
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</li>
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<li> <strong class="uidlink"><a href="obitools.alignment-module.html">obitools.alignment</a></strong>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.alignment.ace-module.html">obitools.alignment.ace</a></strong> </li>
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</ul>
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</li>
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<li> <strong class="uidlink"><a href="obitools.blast-module.html">obitools.blast</a></strong> </li>
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<li> <strong class="uidlink"><a href="obitools.carto-module.html">obitools.carto</a></strong> </li>
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<li> <strong class="uidlink"><a href="obitools.cns-module.html">obitools.cns</a></strong>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.cns.fasta-module.html">obitools.cns.fasta</a></strong> </li>
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<li> <strong class="uidlink"><a href="obitools.cns.quality-module.html">obitools.cns.quality</a></strong> </li>
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</ul>
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</li>
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<li> <strong class="uidlink"><a href="obitools.decorator-module.html">obitools.decorator</a></strong> </li>
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<li> <strong class="uidlink"><a href="obitools.distances-module.html">obitools.distances</a></strong>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.distances.observed-module.html">obitools.distances.observed</a></strong>: <em class="summary">Module dedicated to compute observed divergeances from an
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alignment.</em> </li>
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<li> <strong class="uidlink"><a href="obitools.distances.phylip-module.html">obitools.distances.phylip</a></strong> </li>
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<li> <strong class="uidlink"><a href="obitools.distances.r-module.html">obitools.distances.r</a></strong> </li>
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</ul>
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</li>
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<li> <strong class="uidlink"><a href="obitools.dnahash-module.html">obitools.dnahash</a></strong> </li>
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<li> <strong class="uidlink"><a href="obitools.ecopcr-module.html">obitools.ecopcr</a></strong>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.ecopcr.annotation-module.html">obitools.ecopcr.annotation</a></strong> </li>
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<li> <strong class="uidlink"><a href="obitools.ecopcr.sequence-module.html">obitools.ecopcr.sequence</a></strong> </li>
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<li> <strong class="uidlink"><a href="obitools.ecopcr.taxonomy-module.html">obitools.ecopcr.taxonomy</a></strong> </li>
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</ul>
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</li>
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<li> <strong class="uidlink"><a href="obitools.ecotag-module.html">obitools.ecotag</a></strong>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.ecotag.parser-module.html">obitools.ecotag.parser</a></strong> </li>
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</ul>
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</li>
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<li> <strong class="uidlink"><a href="obitools.eutils-module.html">obitools.eutils</a></strong> </li>
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<li> <strong class="uidlink"><a href="obitools.fast-module.html">obitools.fast</a></strong>: <em class="summary">implement fastn/fastp sililarity search algorithm for BioSequence.</em> </li>
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<li> <strong class="uidlink"><a href="obitools.fasta-module.html">obitools.fasta</a></strong>: <em class="summary">fasta module provides functions to read and write sequences in
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fasta format.</em> </li>
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<li> <strong class="uidlink"><a href="obitools.format-module.html">obitools.format</a></strong>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.format.genericparser-module.html">obitools.format.genericparser</a></strong> </li>
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<li> <strong class="uidlink"><a href="obitools.format.ontology-module.html">obitools.format.ontology</a></strong>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.format.ontology.go_obo-module.html">obitools.format.ontology.go_obo</a></strong> </li>
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<li> <strong class="uidlink"><a href="obitools.format.ontology.obo-module.html">obitools.format.ontology.obo</a></strong> </li>
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</ul>
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</li>
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<li> <strong class="uidlink"><a href="obitools.format.sequence-module.html">obitools.format.sequence</a></strong>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.format.sequence.embl-module.html">obitools.format.sequence.embl</a></strong> </li>
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<li> <strong class="uidlink"><a href="obitools.format.sequence.fasta-module.html">obitools.format.sequence.fasta</a></strong> </li>
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<li> <strong class="uidlink"><a href="obitools.format.sequence.genbank-module.html">obitools.format.sequence.genbank</a></strong> </li>
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<li> <strong class="uidlink"><a href="obitools.format.sequence.tagmatcher-module.html">obitools.format.sequence.tagmatcher</a></strong> </li>
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</ul>
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</li>
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</ul>
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</li>
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<li> <strong class="uidlink"><a href="obitools.genbank-module.html">obitools.genbank</a></strong>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.genbank.ncbi-module.html">obitools.genbank.ncbi</a></strong> </li>
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</ul>
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</li>
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<li> <strong class="uidlink"><a href="obitools.goa-module.html">obitools.goa</a></strong>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.goa.parser-module.html">obitools.goa.parser</a></strong> </li>
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</ul>
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</li>
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<li> <strong class="uidlink"><a href="obitools.graph-module.html">obitools.graph</a></strong>: <em class="summary">This module offert classes to manipulate graphs</em>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.graph.algorithms-module.html">obitools.graph.algorithms</a></strong>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.graph.algorithms.clique-module.html">obitools.graph.algorithms.clique</a></strong> </li>
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<li> <strong class="uidlink"><a href="obitools.graph.algorithms.compact-module.html">obitools.graph.algorithms.compact</a></strong> </li>
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<li> <strong class="uidlink"><a href="obitools.graph.algorithms.component-module.html">obitools.graph.algorithms.component</a></strong> </li>
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</ul>
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</li>
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<li> <strong class="uidlink"><a href="obitools.graph.dag-module.html">obitools.graph.dag</a></strong> </li>
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<li> <strong class="uidlink"><a href="obitools.graph.layout-module.html">obitools.graph.layout</a></strong>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.graph.layout.radialtree-module.html">obitools.graph.layout.radialtree</a></strong> </li>
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</ul>
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</li>
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<li> <strong class="uidlink"><a href="obitools.graph.rootedtree-module.html">obitools.graph.rootedtree</a></strong> </li>
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<li> <strong class="uidlink"><a href="obitools.graph.tree-module.html">obitools.graph.tree</a></strong> </li>
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</ul>
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</li>
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<li> <strong class="uidlink"><a href="obitools.gzip-module.html">obitools.gzip</a></strong>: <em class="summary">Functions that read and write gzipped files.</em> </li>
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<li> <strong class="uidlink"><a href="obitools.location-module.html">obitools.location</a></strong>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.location.feature-module.html">obitools.location.feature</a></strong> </li>
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</ul>
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</li>
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<li> <strong class="uidlink"><a href="obitools.nucdb-module.html">obitools.nucdb</a></strong>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.nucdb.genbank-module.html">obitools.nucdb.genbank</a></strong>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.nucdb.genbank.ncbi-module.html">obitools.nucdb.genbank.ncbi</a></strong> </li>
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<li> <strong class="uidlink"><a href="obitools.nucdb.genbank.parser-module.html">obitools.nucdb.genbank.parser</a></strong> </li>
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</ul>
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</li>
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</ul>
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</li>
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<li> <strong class="uidlink"><a href="obitools.obischemas-module.html">obitools.obischemas</a></strong>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.obischemas.kb-module.html">obitools.obischemas.kb</a></strong>: <em class="summary">kb package is devoted to manage access to postgresql database from
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python script</em>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.obischemas.kb.extern-module.html">obitools.obischemas.kb.extern</a></strong>: <em class="summary">Module : KB.extern Author : Eric Coissac Date : 03/05/2004</em> </li>
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</ul>
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</li>
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<li> <strong class="uidlink"><a href="obitools.obischemas.options-module.html">obitools.obischemas.options</a></strong> </li>
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</ul>
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</li>
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<li> <strong class="uidlink"><a href="obitools.obo-module.html">obitools.obo</a></strong>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.obo.go-module.html">obitools.obo.go</a></strong>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.obo.go.parser-module.html">obitools.obo.go.parser</a></strong> </li>
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</ul>
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</li>
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<li> <strong class="uidlink"><a href="obitools.obo.parser-module.html">obitools.obo.parser</a></strong> </li>
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</ul>
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</li>
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<li> <strong class="uidlink"><a href="obitools.oligo-module.html">obitools.oligo</a></strong>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.oligo.options-module.html">obitools.oligo.options</a></strong> </li>
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<li> <strong class="uidlink"><a href="obitools.oligo.predicat-module.html">obitools.oligo.predicat</a></strong> </li>
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</ul>
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</li>
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<li> <strong class="uidlink"><a href="obitools.options-module.html">obitools.options</a></strong>: <em class="summary">Module providing high level functions to manage command line
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options.</em>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.options.bioseqcutter-module.html">obitools.options.bioseqcutter</a></strong> </li>
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<li> <strong class="uidlink"><a href="obitools.options.bioseqedittag-module.html">obitools.options.bioseqedittag</a></strong> </li>
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<li> <strong class="uidlink"><a href="obitools.options.bioseqfilter-module.html">obitools.options.bioseqfilter</a></strong> </li>
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<li> <strong class="uidlink"><a href="obitools.options.taxonomyfilter-module.html">obitools.options.taxonomyfilter</a></strong> </li>
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</ul>
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</li>
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<li> <strong class="uidlink"><a href="obitools.parallel-module.html">obitools.parallel</a></strong>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.parallel.jobqueue-module.html">obitools.parallel.jobqueue</a></strong> </li>
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</ul>
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</li>
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<li> <strong class="uidlink"><a href="obitools.phylogeny-module.html">obitools.phylogeny</a></strong>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.phylogeny.newick-module.html">obitools.phylogeny.newick</a></strong> </li>
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</ul>
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</li>
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<li> <strong class="uidlink"><a href="obitools.seqdb-module.html">obitools.seqdb</a></strong>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.seqdb.blastdb-module.html">obitools.seqdb.blastdb</a></strong> </li>
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<li> <strong class="uidlink"><a href="obitools.seqdb.dnaparser-module.html">obitools.seqdb.dnaparser</a></strong> </li>
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<li> <strong class="uidlink"><a href="obitools.seqdb.embl-module.html">obitools.seqdb.embl</a></strong>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.seqdb.embl.parser-module.html">obitools.seqdb.embl.parser</a></strong> </li>
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</ul>
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</li>
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<li> <strong class="uidlink"><a href="obitools.seqdb.genbank-module.html">obitools.seqdb.genbank</a></strong>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.graph-module.html">obitools.seqdb.genbank.graph</a></strong>: <em class="summary">This module offert classes to manipulate graphs</em>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.graph.algorithms-module.html">obitools.seqdb.genbank.graph.algorithms</a></strong>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.graph.algorithms.clique-module.html">obitools.seqdb.genbank.graph.algorithms.clique</a></strong> </li>
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<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.graph.algorithms.component-module.html">obitools.seqdb.genbank.graph.algorithms.component</a></strong> </li>
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</ul>
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</li>
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<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.graph.dag-module.html">obitools.seqdb.genbank.graph.dag</a></strong> </li>
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<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.graph.rootedtree-module.html">obitools.seqdb.genbank.graph.rootedtree</a></strong> </li>
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<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.graph.tree-module.html">obitools.seqdb.genbank.graph.tree</a></strong> </li>
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</ul>
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</li>
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<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.ncbi-module.html">obitools.seqdb.genbank.ncbi</a></strong> </li>
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<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.parser-module.html">obitools.seqdb.genbank.parser</a></strong> </li>
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</ul>
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</li>
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</ul>
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</li>
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<li> <strong class="uidlink"><a href="obitools.sequenceencoder-module.html">obitools.sequenceencoder</a></strong> </li>
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<li> <strong class="uidlink"><a href="obitools.solexa-module.html">obitools.solexa</a></strong> </li>
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<li> <strong class="uidlink"><a href="obitools.statistics-module.html">obitools.statistics</a></strong>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.statistics.hypergeometric-module.html">obitools.statistics.hypergeometric</a></strong>: <em class="summary">Module de calcules statistiques.</em> </li>
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<li> <strong class="uidlink"><a href="obitools.statistics.noncentralhypergeo-module.html">obitools.statistics.noncentralhypergeo</a></strong> </li>
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</ul>
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</li>
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<li> <strong class="uidlink"><a href="obitools.svg-module.html">obitools.svg</a></strong>: <em class="summary">SVG.py - Construct/display SVG scenes.</em> </li>
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<li> <strong class="uidlink"><a href="obitools.table-module.html">obitools.table</a></strong>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.table.csv-module.html">obitools.table.csv</a></strong>: <em class="summary">obitools.table.csv module provides an iterator adapter allowing to
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parse csv (comma separatted value) file</em> </li>
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</ul>
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</li>
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<li> <strong class="uidlink"><a href="obitools.tagmatcher-module.html">obitools.tagmatcher</a></strong>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.tagmatcher.options-module.html">obitools.tagmatcher.options</a></strong> </li>
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<li> <strong class="uidlink"><a href="obitools.tagmatcher.parser-module.html">obitools.tagmatcher.parser</a></strong> </li>
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</ul>
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</li>
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<li> <strong class="uidlink"><a href="obitools.tree-module.html">obitools.tree</a></strong>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.tree.dot-module.html">obitools.tree.dot</a></strong> </li>
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<li> <strong class="uidlink"><a href="obitools.tree.layout-module.html">obitools.tree.layout</a></strong> </li>
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<li> <strong class="uidlink"><a href="obitools.tree.newick-module.html">obitools.tree.newick</a></strong> </li>
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<li> <strong class="uidlink"><a href="obitools.tree.svg-module.html">obitools.tree.svg</a></strong> </li>
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<li> <strong class="uidlink"><a href="obitools.tree.unrooted-module.html">obitools.tree.unrooted</a></strong> </li>
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</ul>
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</li>
|
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<li> <strong class="uidlink"><a href="obitools.unit-module.html">obitools.unit</a></strong>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.unit.obitools-module.html">obitools.unit.obitools</a></strong> </li>
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</ul>
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</li>
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<li> <strong class="uidlink"><a href="obitools.utils-module.html">obitools.utils</a></strong>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.utils.bioseq-module.html">obitools.utils.bioseq</a></strong> </li>
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<li> <strong class="uidlink"><a href="obitools.utils.crc64-module.html">obitools.utils.crc64</a></strong> </li>
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<li> <strong class="uidlink"><a href="obitools.utils.iterator-module.html">obitools.utils.iterator</a></strong> </li>
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</ul>
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</li>
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|
<li> <strong class="uidlink"><a href="obitools.word-module.html">obitools.word</a></strong>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.word.options-module.html">obitools.word.options</a></strong> </li>
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<li> <strong class="uidlink"><a href="obitools.word.predicat-module.html">obitools.word.predicat</a></strong> </li>
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</ul>
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</li>
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<li> <strong class="uidlink"><a href="obitools.zipfile-module.html">obitools.zipfile</a></strong>: <em class="summary">Read and write ZIP files.</em> </li>
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</ul></td></tr>
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</table>
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<br />
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<!-- ==================== CLASSES ==================== -->
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<a name="section-Classes"></a>
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<table class="summary" border="1" cellpadding="3"
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cellspacing="0" width="100%" bgcolor="white">
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<tr bgcolor="#70b0f0" class="table-header">
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<td colspan="2" class="table-header">
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<table border="0" cellpadding="0" cellspacing="0" width="100%">
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<tr valign="top">
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<td align="left"><span class="table-header">Classes</span></td>
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<td align="right" valign="top"
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><span class="options">[<a href="#section-Classes"
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class="privatelink" onclick="toggle_private();"
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>hide private</a>]</span></td>
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</tr>
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</table>
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</td>
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</tr>
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<tr>
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<td width="15%" align="right" valign="top" class="summary">
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<span class="summary-type"> </span>
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</td><td class="summary">
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<a href="obitools.WrapperSetIterator-class.html" class="summary-name">WrapperSetIterator</a>
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</td>
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</tr>
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<tr>
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<td width="15%" align="right" valign="top" class="summary">
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<span class="summary-type"> </span>
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</td><td class="summary">
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<a href="obitools.WrapperSet-class.html" class="summary-name">WrapperSet</a>
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</td>
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</tr>
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<tr>
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<td width="15%" align="right" valign="top" class="summary">
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<span class="summary-type"> </span>
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</td><td class="summary">
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<a href="obitools.BioSequence-class.html" class="summary-name">BioSequence</a><br />
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BioSequence class is the base class for biological sequence
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|
representation.
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</td>
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</tr>
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<tr>
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<td width="15%" align="right" valign="top" class="summary">
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<span class="summary-type"> </span>
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</td><td class="summary">
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<a href="obitools.NucSequence-class.html" class="summary-name">NucSequence</a>
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</td>
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</tr>
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<tr>
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<td width="15%" align="right" valign="top" class="summary">
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<span class="summary-type"> </span>
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</td><td class="summary">
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<a href="obitools.AASequence-class.html" class="summary-name">AASequence</a>
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</td>
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</tr>
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<tr>
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<td width="15%" align="right" valign="top" class="summary">
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<span class="summary-type"> </span>
|
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</td><td class="summary">
|
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<a href="obitools.WrappedBioSequence-class.html" class="summary-name">WrappedBioSequence</a>
|
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</td>
|
|
</tr>
|
|
<tr>
|
|
<td width="15%" align="right" valign="top" class="summary">
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<span class="summary-type"> </span>
|
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</td><td class="summary">
|
|
<a href="obitools.SubSequence-class.html" class="summary-name">SubSequence</a>
|
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</td>
|
|
</tr>
|
|
<tr>
|
|
<td width="15%" align="right" valign="top" class="summary">
|
|
<span class="summary-type"> </span>
|
|
</td><td class="summary">
|
|
<a href="obitools.DNAComplementSequence-class.html" class="summary-name">DNAComplementSequence</a>
|
|
</td>
|
|
</tr>
|
|
</table>
|
|
<!-- ==================== FUNCTIONS ==================== -->
|
|
<a name="section-Functions"></a>
|
|
<table class="summary" border="1" cellpadding="3"
|
|
cellspacing="0" width="100%" bgcolor="white">
|
|
<tr bgcolor="#70b0f0" class="table-header">
|
|
<td colspan="2" class="table-header">
|
|
<table border="0" cellpadding="0" cellspacing="0" width="100%">
|
|
<tr valign="top">
|
|
<td align="left"><span class="table-header">Functions</span></td>
|
|
<td align="right" valign="top"
|
|
><span class="options">[<a href="#section-Functions"
|
|
class="privatelink" onclick="toggle_private();"
|
|
>hide private</a>]</span></td>
|
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</tr>
|
|
</table>
|
|
</td>
|
|
</tr>
|
|
<tr class="private">
|
|
<td width="15%" align="right" valign="top" class="summary">
|
|
<span class="summary-type"> </span>
|
|
</td><td class="summary">
|
|
<table width="100%" cellpadding="0" cellspacing="0" border="0">
|
|
<tr>
|
|
<td><span class="summary-sig"><a name="_isNucSeq"></a><span class="summary-sig-name">_isNucSeq</span>(<span class="summary-sig-arg">text</span>)</span></td>
|
|
<td align="right" valign="top">
|
|
<span class="codelink"><a href="obitools-pysrc.html#_isNucSeq">source code</a></span>
|
|
|
|
</td>
|
|
</tr>
|
|
</table>
|
|
|
|
</td>
|
|
</tr>
|
|
<tr>
|
|
<td width="15%" align="right" valign="top" class="summary">
|
|
<span class="summary-type"> </span>
|
|
</td><td class="summary">
|
|
<table width="100%" cellpadding="0" cellspacing="0" border="0">
|
|
<tr>
|
|
<td><span class="summary-sig"><a name="bioSeqGenerator"></a><span class="summary-sig-name">bioSeqGenerator</span>(<span class="summary-sig-arg">id</span>,
|
|
<span class="summary-sig-arg">seq</span>,
|
|
<span class="summary-sig-arg">definition</span>=<span class="summary-sig-default">None</span>,
|
|
<span class="summary-sig-arg">**info</span>)</span></td>
|
|
<td align="right" valign="top">
|
|
<span class="codelink"><a href="obitools-pysrc.html#bioSeqGenerator">source code</a></span>
|
|
|
|
</td>
|
|
</tr>
|
|
</table>
|
|
|
|
</td>
|
|
</tr>
|
|
</table>
|
|
<!-- ==================== VARIABLES ==================== -->
|
|
<a name="section-Variables"></a>
|
|
<table class="summary" border="1" cellpadding="3"
|
|
cellspacing="0" width="100%" bgcolor="white">
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<tr bgcolor="#70b0f0" class="table-header">
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<td colspan="2" class="table-header">
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<table border="0" cellpadding="0" cellspacing="0" width="100%">
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|
<tr valign="top">
|
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<td align="left"><span class="table-header">Variables</span></td>
|
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<td align="right" valign="top"
|
|
><span class="options">[<a href="#section-Variables"
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class="privatelink" onclick="toggle_private();"
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>hide private</a>]</span></td>
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</tr>
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</td>
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</tr>
|
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<tr>
|
|
<td width="15%" align="right" valign="top" class="summary">
|
|
<span class="summary-type"> </span>
|
|
</td><td class="summary">
|
|
<a name="__package__"></a><span class="summary-name">__package__</span> = <code title="'obitools'"><code class="variable-quote">'</code><code class="variable-string">obitools</code><code class="variable-quote">'</code></code>
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