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<a href="Bio-module.html">Package Bio</a> ::
Module utils
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<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module utils</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.utils-pysrc.html">source code</a></span></p>
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<td><span class="summary-sig"><a name="translate"></a><span class="summary-sig-name">translate</span>(<span class="summary-sig-arg">seq</span>,
<span class="summary-sig-arg">id</span>=<span class="summary-sig-default">None</span>)</span></td>
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<td><span class="summary-sig"><a name="translate_to_stop"></a><span class="summary-sig-name">translate_to_stop</span>(<span class="summary-sig-arg">seq</span>,
<span class="summary-sig-arg">id</span>=<span class="summary-sig-default">None</span>)</span></td>
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<span class="codelink"><a href="Bio.utils-pysrc.html#translate_to_stop">source code</a></span>
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<td><span class="summary-sig"><a name="back_translate"></a><span class="summary-sig-name">back_translate</span>(<span class="summary-sig-arg">seq</span>,
<span class="summary-sig-arg">id</span>=<span class="summary-sig-default">None</span>)</span></td>
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<span class="codelink"><a href="Bio.utils-pysrc.html#back_translate">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="transcribe"></a><span class="summary-sig-name">transcribe</span>(<span class="summary-sig-arg">seq</span>)</span></td>
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<td><span class="summary-sig"><a name="back_transcribe"></a><span class="summary-sig-name">back_transcribe</span>(<span class="summary-sig-arg">seq</span>)</span></td>
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<span class="codelink"><a href="Bio.utils-pysrc.html#back_transcribe">source code</a></span>
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<td><span class="summary-sig"><a name="ungap"></a><span class="summary-sig-name">ungap</span>(<span class="summary-sig-arg">seq</span>)</span><br />
given a sequence with gap encoding, return the ungapped sequence</td>
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<span class="codelink"><a href="Bio.utils-pysrc.html#ungap">source code</a></span>
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<td><span class="summary-sig"><a name="verify_alphabet"></a><span class="summary-sig-name">verify_alphabet</span>(<span class="summary-sig-arg">seq</span>)</span></td>
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<span class="codelink"><a href="Bio.utils-pysrc.html#verify_alphabet">source code</a></span>
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<td><span class="summary-sig"><a name="count_monomers"></a><span class="summary-sig-name">count_monomers</span>(<span class="summary-sig-arg">seq</span>)</span></td>
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<span class="codelink"><a href="Bio.utils-pysrc.html#count_monomers">source code</a></span>
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<td><span class="summary-sig"><a name="percent_monomers"></a><span class="summary-sig-name">percent_monomers</span>(<span class="summary-sig-arg">seq</span>)</span></td>
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<td><span class="summary-sig"><a name="sum"></a><span class="summary-sig-name">sum</span>(<span class="summary-sig-arg">seq</span>,
<span class="summary-sig-arg">table</span>,
<span class="summary-sig-arg">zero</span>=<span class="summary-sig-default">0.0</span>)</span></td>
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<span class="codelink"><a href="Bio.utils-pysrc.html#sum">source code</a></span>
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<td><span class="summary-sig"><a name="sum_2ple"></a><span class="summary-sig-name">sum_2ple</span>(<span class="summary-sig-arg">seq</span>,
<span class="summary-sig-arg">table</span>,
<span class="summary-sig-arg">zero</span>=<span class="summary-sig-default"><code class="variable-group">(</code>0.0<code class="variable-op">, </code>0.0<code class="variable-group">)</code></span>)</span></td>
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<span class="codelink"><a href="Bio.utils-pysrc.html#sum_2ple">source code</a></span>
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<td><span class="summary-sig"><a name="total_weight"></a><span class="summary-sig-name">total_weight</span>(<span class="summary-sig-arg">seq</span>,
<span class="summary-sig-arg">weight_table</span>=<span class="summary-sig-default">None</span>)</span></td>
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<span class="codelink"><a href="Bio.utils-pysrc.html#total_weight">source code</a></span>
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<td><span class="summary-sig"><a name="total_weight_range"></a><span class="summary-sig-name">total_weight_range</span>(<span class="summary-sig-arg">seq</span>,
<span class="summary-sig-arg">weight_table</span>=<span class="summary-sig-default">None</span>)</span></td>
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<td><span class="summary-sig"><a href="Bio.utils-module.html#reduce_sequence" class="summary-sig-name">reduce_sequence</a>(<span class="summary-sig-arg">seq</span>,
<span class="summary-sig-arg">reduction_table</span>,
<span class="summary-sig-arg">new_alphabet</span>=<span class="summary-sig-default">None</span>)</span><br />
given an amino-acid sequence, return it in reduced alphabet form
based on the letter-translation table passed.</td>
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<span class="codelink"><a href="Bio.utils-pysrc.html#reduce_sequence">source code</a></span>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">reduce_sequence</span>(<span class="sig-arg">seq</span>,
<span class="sig-arg">reduction_table</span>,
<span class="sig-arg">new_alphabet</span>=<span class="sig-default">None</span>)</span>
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<p>given an amino-acid sequence, return it in reduced alphabet form based
on the letter-translation table passed. Some "standard" tables
are in Alphabet.Reduced. seq: a Seq.Seq type sequence reduction_table: a
dictionary whose keys are the "from" alphabet, and values are
the "to" alphabet</p>
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