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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.GFF-module.html">Package GFF</a> ::
Module easy
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<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module easy</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.GFF.easy-pysrc.html">source code</a></span></p>
<p>Bio.GFF.easy: some functions to ease the use of Biopython</p>
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<div class="fields"> <p><strong>Version:</strong>
$Revision: 1.9 $
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<a href="Bio.GFF.easy.FeatureDict-class.html" class="summary-name">FeatureDict</a><br />
JH: accessing feature.qualifiers as a list is stupid.
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<a href="Bio.GFF.easy.Location-class.html" class="summary-name">Location</a><br />
this is really best interfaced through LocationFromString fuzzy: <
or > join: {0 = no join, 1 = join, 2 = order}
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<a href="Bio.GFF.easy.LocationFromString-class.html" class="summary-name">LocationFromString</a>
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<td><span class="summary-sig"><a name="_hashname"></a><span class="summary-sig-name">_hashname</span>(<span class="summary-sig-arg">location</span>)</span></td>
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<td><span class="summary-sig"><a name="fasta_single"></a><span class="summary-sig-name">fasta_single</span>(<span class="summary-sig-arg">filename</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">string</span>=<span class="summary-sig-default">None</span>)</span></td>
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<td><span class="summary-sig"><a name="fasta_multi"></a><span class="summary-sig-name">fasta_multi</span>(<span class="summary-sig-arg">filename</span>=<span class="summary-sig-default">None</span>)</span></td>
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<span class="codelink"><a href="Bio.GFF.easy-pysrc.html#fasta_multi">source code</a></span>
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<td><span class="summary-sig"><a name="fasta_readrecords"></a><span class="summary-sig-name">fasta_readrecords</span>(<span class="summary-sig-arg">filename</span>=<span class="summary-sig-default">None</span>)</span></td>
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<span class="codelink"><a href="Bio.GFF.easy-pysrc.html#fasta_readrecords">source code</a></span>
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<td><span class="summary-sig"><a name="fasta_write"></a><span class="summary-sig-name">fasta_write</span>(<span class="summary-sig-arg">filename</span>,
<span class="summary-sig-arg">records</span>)</span></td>
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<span class="codelink"><a href="Bio.GFF.easy-pysrc.html#fasta_write">source code</a></span>
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<td><span class="summary-sig"><a name="genbank_single"></a><span class="summary-sig-name">genbank_single</span>(<span class="summary-sig-arg">filename</span>)</span></td>
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<td><span class="summary-sig"><a name="record_subseq"></a><span class="summary-sig-name">record_subseq</span>(<span class="summary-sig-arg">record</span>,
<span class="summary-sig-arg">location</span>,
<span class="summary-sig-arg">*args</span>,
<span class="summary-sig-arg">**keywds</span>)</span></td>
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<td><span class="summary-sig"><a href="Bio.GFF.easy-module.html#record_sequence" class="summary-sig-name">record_sequence</a>(<span class="summary-sig-arg">record</span>)</span><br />
returns the sequence of a record</td>
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<span class="codelink"><a href="Bio.GFF.easy-pysrc.html#record_sequence">source code</a></span>
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<td><span class="summary-sig"><a name="record_coords"></a><span class="summary-sig-name">record_coords</span>(<span class="summary-sig-arg">record</span>,
<span class="summary-sig-arg">start</span>,
<span class="summary-sig-arg">end</span>,
<span class="summary-sig-arg">strand</span>=<span class="summary-sig-default">0</span>,
<span class="summary-sig-arg">upper</span>=<span class="summary-sig-default">0</span>)</span></td>
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<td><span class="summary-sig"><a name="_test"></a><span class="summary-sig-name">_test</span>(<span class="summary-sig-arg">*args</span>,
<span class="summary-sig-arg">**keywds</span>)</span></td>
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<span class="codelink"><a href="Bio.GFF.easy-pysrc.html#_test">source code</a></span>
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<a name="re_complement"></a><span class="summary-name">re_complement</span> = <code title="re.compile(r"^complement\((.*)\)$")">re.compile(r"^complement\((.*)\)$")</code>
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<a href="Bio.GFF.easy-module.html#re_seqname" class="summary-name">re_seqname</a> = <code title="re.compile(r"^(?!join|order|complement)([^\:]+?):(.*)$")">re.compile(r"^(?!join|order|complement)([^\:]+?):<code class="variable-ellipsis">...</code></code>
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<a name="re_join"></a><span class="summary-name">re_join</span> = <code title="re.compile(r"^(join|order)\((.*)\)$")">re.compile(r"^(join|order)\((.*)\)$")</code>
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<a name="re_dotdot"></a><span class="summary-name">re_dotdot</span> = <code title="re.compile(r"^([><]*\d+)\.\.([><]*\d+)$")">re.compile(r"^([><]*\d+)\.\.([><]*\d+)$")</code>
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<a name="re_fuzzy"></a><span class="summary-name">re_fuzzy</span> = <code title="re.compile(r"^([><])(\d+)")">re.compile(r"^([><])(\d+)")</code>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">record_sequence</span>(<span class="sig-arg">record</span>)</span>
</h3>
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><span class="codelink"><a href="Bio.GFF.easy-pysrc.html#record_sequence">source code</a></span>
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<p>returns the sequence of a record</p>
<p>can be Bio.SeqRecord.SeqRecord or Bio.GenBank.Record.Record</p>
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<h3 class="epydoc">re_seqname</h3>
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<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
re.compile(r"^(?!join|order|complement)([^\:]+?):(.*)$")
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