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        <a href="Bio-module.html">Package&nbsp;Bio</a> ::
        Module&nbsp;utils
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<h1 class="epydoc">Source Code for <a href="Bio.utils-module.html">Module Bio.utils</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno">  1</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">string</tt> </tt>
<a name="L2"></a><tt class="py-lineno">  2</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-0" class="py-name" targets="Module Bio.Seq=Bio.Seq-module.html,Class Bio.Seq.Seq=Bio.Seq.Seq-class.html,Class Martel.Expression.Seq=Martel.Expression.Seq-class.html,Function Martel.Seq()=Martel-module.html#Seq"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-0', 'Seq', 'link-0');">Seq</a></tt> </tt>
<a name="L3"></a><tt class="py-lineno">  3</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-1" class="py-name" targets="Package Bio.Alphabet=Bio.Alphabet-module.html,Class Bio.Alphabet.Alphabet=Bio.Alphabet.Alphabet-class.html"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-1', 'Alphabet', 'link-1');">Alphabet</a></tt> </tt>
<a name="L4"></a><tt class="py-lineno">  4</tt>  <tt class="py-line"> </tt>
<a name="L5"></a><tt class="py-lineno">  5</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-2" class="py-name" targets="Module Bio.PropertyManager=Bio.PropertyManager-module.html,Class Bio.PropertyManager.PropertyManager=Bio.PropertyManager.PropertyManager-class.html"><a title="Bio.PropertyManager
Bio.PropertyManager.PropertyManager" class="py-name" href="#" onclick="return doclink('link-2', 'PropertyManager', 'link-2');">PropertyManager</a></tt> <tt class="py-keyword">import</tt> <tt id="link-3" class="py-name" targets="Variable Bio.PropertyManager.default_manager=Bio.PropertyManager-module.html#default_manager"><a title="Bio.PropertyManager.default_manager" class="py-name" href="#" onclick="return doclink('link-3', 'default_manager', 'link-3');">default_manager</a></tt> </tt>
<a name="L6"></a><tt class="py-lineno">  6</tt>  <tt class="py-line"> </tt>
<a name="translate"></a><div id="translate-def"><a name="L7"></a><tt class="py-lineno">  7</tt> <a class="py-toggle" href="#" id="translate-toggle" onclick="return toggle('translate');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.utils-module.html#translate">translate</a><tt class="py-op">(</tt><tt class="py-param">seq</tt><tt class="py-op">,</tt> <tt class="py-param">id</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="translate-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="translate-expanded"><a name="L8"></a><tt class="py-lineno">  8</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt id="link-4" class="py-name" targets="Variable Bio.Data.CodonTable.id=Bio.Data.CodonTable-module.html#id,Variable Bio.Encodings.IUPACEncoding.id=Bio.Encodings.IUPACEncoding-module.html#id,Method Bio.GFF.Feature.id()=Bio.GFF.Feature-class.html#id"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-4', 'id', 'link-4');">id</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L9"></a><tt class="py-lineno">  9</tt>  <tt class="py-line">        <tt id="link-5" class="py-name" targets="Variable Martel.test.test_swissprot38.s=Martel.test.test_swissprot38-module.html#s"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-5', 's', 'link-5');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"translator"</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt>  <tt class="py-line">        <tt id="link-6" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-6', 's', 'link-5');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"translator.id.%d"</tt> <tt class="py-op">%</tt> <tt id="link-7" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-7', 'id', 'link-4');">id</a></tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt>  <tt class="py-line">    <tt class="py-name">translator</tt> <tt class="py-op">=</tt> <tt id="link-8" class="py-name"><a title="Bio.PropertyManager.default_manager" class="py-name" href="#" onclick="return doclink('link-8', 'default_manager', 'link-3');">default_manager</a></tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Method Bio.Parsers.spark.GenericASTMatcher.resolve()=Bio.Parsers.spark.GenericASTMatcher-class.html#resolve,Method Bio.Parsers.spark.GenericParser.resolve()=Bio.Parsers.spark.GenericParser-class.html#resolve,Method Bio.PropertyManager.PropertyManager.resolve()=Bio.PropertyManager.PropertyManager-class.html#resolve"><a title="Bio.Parsers.spark.GenericASTMatcher.resolve
Bio.Parsers.spark.GenericParser.resolve
Bio.PropertyManager.PropertyManager.resolve" class="py-name" href="#" onclick="return doclink('link-9', 'resolve', 'link-9');">resolve</a></tt><tt class="py-op">(</tt><tt id="link-10" class="py-name" targets="Method Bio.GFF.Feature.seq()=Bio.GFF.Feature-class.html#seq,Method Bio.GFF.FeatureAggregate.seq()=Bio.GFF.FeatureAggregate-class.html#seq,Variable BioSQL.BioSeq.DBSeqRecord.seq=BioSQL.BioSeq.DBSeqRecord-class.html#seq"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-10', 'seq', 'link-10');">seq</a></tt><tt class="py-op">.</tt><tt id="link-11" class="py-name" targets="Variable Bio.Prosite.Pattern.Prosite.alphabet=Bio.Prosite.Pattern.Prosite-class.html#alphabet,Function Bio.Std.alphabet()=Bio.Std-module.html#alphabet"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-11', 'alphabet', 'link-11');">alphabet</a></tt><tt class="py-op">,</tt> <tt id="link-12" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-12', 's', 'link-5');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">translator</tt><tt class="py-op">.</tt><tt id="link-13" class="py-name" targets="Method Bio.GFF.Feature.translate()=Bio.GFF.Feature-class.html#translate,Method Bio.GFF.FeatureAggregate.translate()=Bio.GFF.FeatureAggregate-class.html#translate,Function Bio.Seq.translate()=Bio.Seq-module.html#translate,Function Bio.SeqUtils.translate()=Bio.SeqUtils-module.html#translate,Method Bio.Translate.Translator.translate()=Bio.Translate.Translator-class.html#translate,Function Bio.utils.translate()=Bio.utils-module.html#translate"><a title="Bio.GFF.Feature.translate
Bio.GFF.FeatureAggregate.translate
Bio.Seq.translate
Bio.SeqUtils.translate
Bio.Translate.Translator.translate
Bio.utils.translate" class="py-name" href="#" onclick="return doclink('link-13', 'translate', 'link-13');">translate</a></tt><tt class="py-op">(</tt><tt id="link-14" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-14', 'seq', 'link-10');">seq</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L14"></a><tt class="py-lineno"> 14</tt>  <tt class="py-line"> </tt>
<a name="translate_to_stop"></a><div id="translate_to_stop-def"><a name="L15"></a><tt class="py-lineno"> 15</tt> <a class="py-toggle" href="#" id="translate_to_stop-toggle" onclick="return toggle('translate_to_stop');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.utils-module.html#translate_to_stop">translate_to_stop</a><tt class="py-op">(</tt><tt class="py-param">seq</tt><tt class="py-op">,</tt> <tt class="py-param">id</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="translate_to_stop-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="translate_to_stop-expanded"><a name="L16"></a><tt class="py-lineno"> 16</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt id="link-15" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-15', 'id', 'link-4');">id</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt>  <tt class="py-line">        <tt id="link-16" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-16', 's', 'link-5');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"translator"</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt>  <tt class="py-line">        <tt id="link-17" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-17', 's', 'link-5');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"translator.id.%d"</tt> <tt class="py-op">%</tt> <tt id="link-18" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-18', 'id', 'link-4');">id</a></tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt>  <tt class="py-line">    <tt class="py-name">translator</tt> <tt class="py-op">=</tt> <tt id="link-19" class="py-name"><a title="Bio.PropertyManager.default_manager" class="py-name" href="#" onclick="return doclink('link-19', 'default_manager', 'link-3');">default_manager</a></tt><tt class="py-op">.</tt><tt id="link-20" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.resolve
Bio.Parsers.spark.GenericParser.resolve
Bio.PropertyManager.PropertyManager.resolve" class="py-name" href="#" onclick="return doclink('link-20', 'resolve', 'link-9');">resolve</a></tt><tt class="py-op">(</tt><tt id="link-21" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-21', 'seq', 'link-10');">seq</a></tt><tt class="py-op">.</tt><tt id="link-22" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-22', 'alphabet', 'link-11');">alphabet</a></tt><tt class="py-op">,</tt> <tt id="link-23" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-23', 's', 'link-5');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">translator</tt><tt class="py-op">.</tt><tt id="link-24" class="py-name" targets="Method Bio.Translate.Translator.translate_to_stop()=Bio.Translate.Translator-class.html#translate_to_stop,Function Bio.utils.translate_to_stop()=Bio.utils-module.html#translate_to_stop"><a title="Bio.Translate.Translator.translate_to_stop
Bio.utils.translate_to_stop" class="py-name" href="#" onclick="return doclink('link-24', 'translate_to_stop', 'link-24');">translate_to_stop</a></tt><tt class="py-op">(</tt><tt id="link-25" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-25', 'seq', 'link-10');">seq</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L22"></a><tt class="py-lineno"> 22</tt>  <tt class="py-line"> </tt>
<a name="back_translate"></a><div id="back_translate-def"><a name="L23"></a><tt class="py-lineno"> 23</tt> <a class="py-toggle" href="#" id="back_translate-toggle" onclick="return toggle('back_translate');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.utils-module.html#back_translate">back_translate</a><tt class="py-op">(</tt><tt class="py-param">seq</tt><tt class="py-op">,</tt> <tt class="py-param">id</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="back_translate-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="back_translate-expanded"><a name="L24"></a><tt class="py-lineno"> 24</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt id="link-26" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-26', 'id', 'link-4');">id</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt>  <tt class="py-line">        <tt id="link-27" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-27', 's', 'link-5');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"translator"</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt>  <tt class="py-line">        <tt id="link-28" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-28', 's', 'link-5');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"translator.id.%d"</tt> <tt class="py-op">%</tt> <tt id="link-29" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-29', 'id', 'link-4');">id</a></tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt>  <tt class="py-line">    <tt class="py-name">translator</tt> <tt class="py-op">=</tt> <tt id="link-30" class="py-name"><a title="Bio.PropertyManager.default_manager" class="py-name" href="#" onclick="return doclink('link-30', 'default_manager', 'link-3');">default_manager</a></tt><tt class="py-op">.</tt><tt id="link-31" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.resolve
Bio.Parsers.spark.GenericParser.resolve
Bio.PropertyManager.PropertyManager.resolve" class="py-name" href="#" onclick="return doclink('link-31', 'resolve', 'link-9');">resolve</a></tt><tt class="py-op">(</tt><tt id="link-32" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-32', 'seq', 'link-10');">seq</a></tt><tt class="py-op">.</tt><tt id="link-33" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-33', 'alphabet', 'link-11');">alphabet</a></tt><tt class="py-op">,</tt> <tt id="link-34" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-34', 's', 'link-5');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">translator</tt><tt class="py-op">.</tt><tt id="link-35" class="py-name" targets="Method Bio.Translate.Translator.back_translate()=Bio.Translate.Translator-class.html#back_translate,Function Bio.utils.back_translate()=Bio.utils-module.html#back_translate"><a title="Bio.Translate.Translator.back_translate
Bio.utils.back_translate" class="py-name" href="#" onclick="return doclink('link-35', 'back_translate', 'link-35');">back_translate</a></tt><tt class="py-op">(</tt><tt id="link-36" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-36', 'seq', 'link-10');">seq</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L30"></a><tt class="py-lineno"> 30</tt>  <tt class="py-line"> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt>  <tt class="py-line"> </tt>
<a name="transcribe"></a><div id="transcribe-def"><a name="L32"></a><tt class="py-lineno"> 32</tt> <a class="py-toggle" href="#" id="transcribe-toggle" onclick="return toggle('transcribe');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.utils-module.html#transcribe">transcribe</a><tt class="py-op">(</tt><tt class="py-param">seq</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="transcribe-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="transcribe-expanded"><a name="L33"></a><tt class="py-lineno"> 33</tt>  <tt class="py-line">    <tt class="py-name">transcriber</tt> <tt class="py-op">=</tt> <tt id="link-37" class="py-name"><a title="Bio.PropertyManager.default_manager" class="py-name" href="#" onclick="return doclink('link-37', 'default_manager', 'link-3');">default_manager</a></tt><tt class="py-op">.</tt><tt id="link-38" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.resolve
Bio.Parsers.spark.GenericParser.resolve
Bio.PropertyManager.PropertyManager.resolve" class="py-name" href="#" onclick="return doclink('link-38', 'resolve', 'link-9');">resolve</a></tt><tt class="py-op">(</tt><tt id="link-39" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-39', 'seq', 'link-10');">seq</a></tt><tt class="py-op">.</tt><tt id="link-40" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-40', 'alphabet', 'link-11');">alphabet</a></tt><tt class="py-op">,</tt> <tt class="py-string">"transcriber"</tt><tt class="py-op">)</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">transcriber</tt><tt class="py-op">.</tt><tt id="link-41" class="py-name" targets="Function Bio.Seq.transcribe()=Bio.Seq-module.html#transcribe,Method Bio.Transcribe.Transcribe.transcribe()=Bio.Transcribe.Transcribe-class.html#transcribe,Function Bio.utils.transcribe()=Bio.utils-module.html#transcribe"><a title="Bio.Seq.transcribe
Bio.Transcribe.Transcribe.transcribe
Bio.utils.transcribe" class="py-name" href="#" onclick="return doclink('link-41', 'transcribe', 'link-41');">transcribe</a></tt><tt class="py-op">(</tt><tt id="link-42" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-42', 'seq', 'link-10');">seq</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L35"></a><tt class="py-lineno"> 35</tt>  <tt class="py-line"> </tt>
<a name="back_transcribe"></a><div id="back_transcribe-def"><a name="L36"></a><tt class="py-lineno"> 36</tt> <a class="py-toggle" href="#" id="back_transcribe-toggle" onclick="return toggle('back_transcribe');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.utils-module.html#back_transcribe">back_transcribe</a><tt class="py-op">(</tt><tt class="py-param">seq</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="back_transcribe-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="back_transcribe-expanded"><a name="L37"></a><tt class="py-lineno"> 37</tt>  <tt class="py-line">    <tt class="py-name">transcriber</tt> <tt class="py-op">=</tt> <tt id="link-43" class="py-name"><a title="Bio.PropertyManager.default_manager" class="py-name" href="#" onclick="return doclink('link-43', 'default_manager', 'link-3');">default_manager</a></tt><tt class="py-op">.</tt><tt id="link-44" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.resolve
Bio.Parsers.spark.GenericParser.resolve
Bio.PropertyManager.PropertyManager.resolve" class="py-name" href="#" onclick="return doclink('link-44', 'resolve', 'link-9');">resolve</a></tt><tt class="py-op">(</tt><tt id="link-45" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-45', 'seq', 'link-10');">seq</a></tt><tt class="py-op">.</tt><tt id="link-46" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-46', 'alphabet', 'link-11');">alphabet</a></tt><tt class="py-op">,</tt> <tt class="py-string">"transcriber"</tt><tt class="py-op">)</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">transcriber</tt><tt class="py-op">.</tt><tt id="link-47" class="py-name" targets="Function Bio.Seq.back_transcribe()=Bio.Seq-module.html#back_transcribe,Method Bio.Transcribe.Transcribe.back_transcribe()=Bio.Transcribe.Transcribe-class.html#back_transcribe,Function Bio.utils.back_transcribe()=Bio.utils-module.html#back_transcribe"><a title="Bio.Seq.back_transcribe
Bio.Transcribe.Transcribe.back_transcribe
Bio.utils.back_transcribe" class="py-name" href="#" onclick="return doclink('link-47', 'back_transcribe', 'link-47');">back_transcribe</a></tt><tt class="py-op">(</tt><tt id="link-48" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-48', 'seq', 'link-10');">seq</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L39"></a><tt class="py-lineno"> 39</tt>  <tt class="py-line"> </tt>
<a name="ungap"></a><div id="ungap-def"><a name="L40"></a><tt class="py-lineno"> 40</tt> <a class="py-toggle" href="#" id="ungap-toggle" onclick="return toggle('ungap');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.utils-module.html#ungap">ungap</a><tt class="py-op">(</tt><tt class="py-param">seq</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ungap-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="ungap-expanded"><a name="L41"></a><tt class="py-lineno"> 41</tt>  <tt class="py-line">    <tt class="py-docstring">"""given a sequence with gap encoding, return the ungapped sequence"""</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt>  <tt class="py-line">    <tt class="py-name">gap</tt> <tt class="py-op">=</tt> <tt id="link-49" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-49', 'seq', 'link-10');">seq</a></tt><tt class="py-op">.</tt><tt class="py-name">gap_char</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt>  <tt class="py-line">    <tt id="link-50" class="py-name" targets="Variable Bio.Alphabet.Alphabet.letters=Bio.Alphabet.Alphabet-class.html#letters,Variable Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters=Bio.Alphabet.IUPAC.ExtendedIUPACDNA-class.html#letters,Variable Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters=Bio.Alphabet.IUPAC.ExtendedIUPACProtein-class.html#letters,Variable Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters=Bio.Alphabet.IUPAC.IUPACAmbiguousDNA-class.html#letters,Variable Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters=Bio.Alphabet.IUPAC.IUPACAmbiguousRNA-class.html#letters,Variable Bio.Alphabet.IUPAC.IUPACProtein.letters=Bio.Alphabet.IUPAC.IUPACProtein-class.html#letters,Variable Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters=Bio.Alphabet.IUPAC.IUPACUnambiguousDNA-class.html#letters,Variable Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters=Bio.Alphabet.IUPAC.IUPACUnambiguousRNA-class.html#letters,Variable Bio.Alphabet.Reduced.HPModel.letters=Bio.Alphabet.Reduced.HPModel-class.html#letters,Variable Bio.Alphabet.Reduced.Murphy10.letters=Bio.Alphabet.Reduced.Murphy10-class.html#letters,Variable Bio.Alphabet.Reduced.Murphy15.letters=Bio.Alphabet.Reduced.Murphy15-class.html#letters,Variable Bio.Alphabet.Reduced.Murphy4.letters=Bio.Alphabet.Reduced.Murphy4-class.html#letters,Variable Bio.Alphabet.Reduced.Murphy8.letters=Bio.Alphabet.Reduced.Murphy8-class.html#letters,Variable Bio.Alphabet.Reduced.PC5.letters=Bio.Alphabet.Reduced.PC5-class.html#letters,Variable Bio.Alphabet.SecondaryStructure.letters=Bio.Alphabet.SecondaryStructure-class.html#letters,Variable Bio.Alphabet.SingleLetterAlphabet.letters=Bio.Alphabet.SingleLetterAlphabet-class.html#letters,Variable Bio.Alphabet.ThreeLetterProtein.letters=Bio.Alphabet.ThreeLetterProtein-class.html#letters,Variable Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters=Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet-class.html#letters,Variable Bio.SeqUtils.ProteinX.letters=Bio.SeqUtils.ProteinX-class.html#letters"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters
Bio.SeqUtils.ProteinX.letters" class="py-name" href="#" onclick="return doclink('link-50', 'letters', 'link-50');">letters</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">c</tt> <tt class="py-keyword">in</tt> <tt id="link-51" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-51', 'seq', 'link-10');">seq</a></tt><tt class="py-op">.</tt><tt id="link-52" class="py-name" targets="Variable BioSQL.BioSeq.DBSeq.data=BioSQL.BioSeq.DBSeq-class.html#data"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-52', 'data', 'link-52');">data</a></tt><tt class="py-op">:</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">c</tt> <tt class="py-op">!=</tt> <tt class="py-name">gap</tt><tt class="py-op">:</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt>  <tt class="py-line">            <tt id="link-53" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters
Bio.SeqUtils.ProteinX.letters" class="py-name" href="#" onclick="return doclink('link-53', 'letters', 'link-50');">letters</a></tt><tt class="py-op">.</tt><tt id="link-54" 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-54', 'append', 'link-54');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">c</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">return</tt> <tt id="link-55" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-55', 'Seq', 'link-0');">Seq</a></tt><tt class="py-op">.</tt><tt id="link-56" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-56', 'Seq', 'link-0');">Seq</a></tt><tt class="py-op">(</tt><tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt id="link-57" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters
Bio.SeqUtils.ProteinX.letters" class="py-name" href="#" onclick="return doclink('link-57', 'letters', 'link-50');">letters</a></tt><tt class="py-op">,</tt> <tt class="py-string">""</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-58" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-58', 'seq', 'link-10');">seq</a></tt><tt class="py-op">.</tt><tt id="link-59" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-59', 'alphabet', 'link-11');">alphabet</a></tt><tt class="py-op">.</tt><tt id="link-60" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-60', 'alphabet', 'link-11');">alphabet</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L48"></a><tt class="py-lineno"> 48</tt>  <tt class="py-line"> </tt>
<a name="verify_alphabet"></a><div id="verify_alphabet-def"><a name="L49"></a><tt class="py-lineno"> 49</tt> <a class="py-toggle" href="#" id="verify_alphabet-toggle" onclick="return toggle('verify_alphabet');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.utils-module.html#verify_alphabet">verify_alphabet</a><tt class="py-op">(</tt><tt class="py-param">seq</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="verify_alphabet-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="verify_alphabet-expanded"><a name="L50"></a><tt class="py-lineno"> 50</tt>  <tt class="py-line">    <tt id="link-61" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters
Bio.SeqUtils.ProteinX.letters" class="py-name" href="#" onclick="return doclink('link-61', 'letters', 'link-50');">letters</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">c</tt> <tt class="py-keyword">in</tt> <tt id="link-62" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-62', 'seq', 'link-10');">seq</a></tt><tt class="py-op">.</tt><tt id="link-63" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-63', 'alphabet', 'link-11');">alphabet</a></tt><tt class="py-op">.</tt><tt id="link-64" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters
Bio.SeqUtils.ProteinX.letters" class="py-name" href="#" onclick="return doclink('link-64', 'letters', 'link-50');">letters</a></tt><tt class="py-op">:</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt>  <tt class="py-line">        <tt id="link-65" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters
Bio.SeqUtils.ProteinX.letters" class="py-name" href="#" onclick="return doclink('link-65', 'letters', 'link-50');">letters</a></tt><tt class="py-op">[</tt><tt class="py-name">c</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt>  <tt class="py-line">    <tt class="py-keyword">try</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">for</tt> <tt class="py-name">c</tt> <tt class="py-keyword">in</tt> <tt id="link-66" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-66', 'seq', 'link-10');">seq</a></tt><tt class="py-op">.</tt><tt id="link-67" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-67', 'data', 'link-52');">data</a></tt><tt class="py-op">:</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt>  <tt class="py-line">            <tt id="link-68" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters
Bio.SeqUtils.ProteinX.letters" class="py-name" href="#" onclick="return doclink('link-68', 'letters', 'link-50');">letters</a></tt><tt class="py-op">[</tt><tt class="py-name">c</tt><tt class="py-op">]</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt>  <tt class="py-line">    <tt class="py-keyword">except</tt> <tt class="py-name">KeyError</tt><tt class="py-op">:</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
</div><a name="L59"></a><tt class="py-lineno"> 59</tt>  <tt class="py-line"> </tt>
<a name="count_monomers"></a><div id="count_monomers-def"><a name="L60"></a><tt class="py-lineno"> 60</tt> <a class="py-toggle" href="#" id="count_monomers-toggle" onclick="return toggle('count_monomers');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.utils-module.html#count_monomers">count_monomers</a><tt class="py-op">(</tt><tt class="py-param">seq</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="count_monomers-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="count_monomers-expanded"><a name="L61"></a><tt class="py-lineno"> 61</tt>  <tt class="py-line">    <tt class="py-name">dict</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt>  <tt class="py-line"><tt class="py-comment">#    bugfix: string.count(s,c) raises an AttributeError. Iddo Friedberg 16 Mar. 04</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#    s = buffer(seq.data)  # works for strings and array.arrays</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-keyword">for</tt> <tt class="py-name">c</tt> <tt class="py-keyword">in</tt> <tt id="link-69" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-69', 'seq', 'link-10');">seq</a></tt><tt class="py-op">.</tt><tt id="link-70" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-70', 'alphabet', 'link-11');">alphabet</a></tt><tt class="py-op">.</tt><tt id="link-71" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters
Bio.SeqUtils.ProteinX.letters" class="py-name" href="#" onclick="return doclink('link-71', 'letters', 'link-50');">letters</a></tt><tt class="py-op">:</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt>  <tt class="py-line">        <tt class="py-name">dict</tt><tt class="py-op">[</tt><tt class="py-name">c</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt id="link-72" class="py-name" targets="Method Bio.Crystal.Chain.count()=Bio.Crystal.Chain-class.html#count,Method Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count()=Bio.NeuralNetwork.Gene.Pattern.PatternRepository-class.html#count,Method Bio.Seq.MutableSeq.count()=Bio.Seq.MutableSeq-class.html#count,Method Bio.Seq.Seq.count()=Bio.Seq.Seq-class.html#count,Function Bio.listfns.count()=Bio.listfns-module.html#count"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-72', 'count', 'link-72');">count</a></tt><tt class="py-op">(</tt><tt id="link-73" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-73', 'seq', 'link-10');">seq</a></tt><tt class="py-op">.</tt><tt id="link-74" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-74', 'data', 'link-52');">data</a></tt><tt class="py-op">,</tt> <tt class="py-name">c</tt><tt class="py-op">)</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">dict</tt> </tt>
</div><a name="L67"></a><tt class="py-lineno"> 67</tt>  <tt class="py-line"> </tt>
<a name="percent_monomers"></a><div id="percent_monomers-def"><a name="L68"></a><tt class="py-lineno"> 68</tt> <a class="py-toggle" href="#" id="percent_monomers-toggle" onclick="return toggle('percent_monomers');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.utils-module.html#percent_monomers">percent_monomers</a><tt class="py-op">(</tt><tt class="py-param">seq</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="percent_monomers-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="percent_monomers-expanded"><a name="L69"></a><tt class="py-lineno"> 69</tt>  <tt class="py-line">   <tt class="py-name">dict2</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt>  <tt class="py-line">   <tt class="py-name">seq_len</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-75" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-75', 'seq', 'link-10');">seq</a></tt><tt class="py-op">)</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt>  <tt class="py-line">   <tt class="py-name">dict</tt> <tt class="py-op">=</tt> <tt id="link-76" class="py-name" targets="Function Bio.utils.count_monomers()=Bio.utils-module.html#count_monomers"><a title="Bio.utils.count_monomers" class="py-name" href="#" onclick="return doclink('link-76', 'count_monomers', 'link-76');">count_monomers</a></tt><tt class="py-op">(</tt><tt id="link-77" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-77', 'seq', 'link-10');">seq</a></tt><tt class="py-op">)</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt>  <tt class="py-line">   <tt class="py-keyword">for</tt> <tt class="py-name">m</tt> <tt class="py-keyword">in</tt> <tt class="py-name">dict</tt><tt class="py-op">:</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt>  <tt class="py-line">      <tt class="py-name">dict2</tt><tt class="py-op">[</tt><tt class="py-name">m</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">dict</tt><tt class="py-op">[</tt><tt class="py-name">m</tt><tt class="py-op">]</tt> <tt class="py-op">*</tt> <tt class="py-number">100.</tt> <tt class="py-op">/</tt> <tt class="py-name">seq_len</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt>  <tt class="py-line">   <tt class="py-keyword">return</tt> <tt class="py-name">dict2</tt> </tt>
</div><a name="L75"></a><tt class="py-lineno"> 75</tt>  <tt class="py-line"> </tt>
<a name="sum"></a><div id="sum-def"><a name="L76"></a><tt class="py-lineno"> 76</tt> <a class="py-toggle" href="#" id="sum-toggle" onclick="return toggle('sum');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.utils-module.html#sum">sum</a><tt class="py-op">(</tt><tt class="py-param">seq</tt><tt class="py-op">,</tt> <tt class="py-param">table</tt><tt class="py-op">,</tt> <tt class="py-param">zero</tt> <tt class="py-op">=</tt> <tt class="py-number">0.0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="sum-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="sum-expanded"><a name="L77"></a><tt class="py-lineno"> 77</tt>  <tt class="py-line">    <tt class="py-name">total</tt> <tt class="py-op">=</tt> <tt class="py-name">zero</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">c</tt> <tt class="py-keyword">in</tt> <tt class="py-name">getattr</tt><tt class="py-op">(</tt><tt id="link-78" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-78', 'seq', 'link-10');">seq</a></tt><tt class="py-op">,</tt> <tt class="py-string">"data"</tt><tt class="py-op">,</tt> <tt id="link-79" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-79', 'seq', 'link-10');">seq</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt>  <tt class="py-line">        <tt class="py-name">total</tt> <tt class="py-op">=</tt> <tt class="py-name">total</tt> <tt class="py-op">+</tt> <tt id="link-80" class="py-name" targets="Variable Bio.CDD.cdd_format.table=Bio.CDD.cdd_format-module.html#table,Variable Bio.expressions.blast.ncbiblast.table=Bio.expressions.blast.ncbiblast-module.html#table"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-80', 'table', 'link-80');">table</a></tt><tt class="py-op">[</tt><tt class="py-name">c</tt><tt class="py-op">]</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">total</tt> </tt>
</div><a name="L81"></a><tt class="py-lineno"> 81</tt>  <tt class="py-line"> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt>  <tt class="py-line"><tt class="py-comment"># For ranged addition</tt> </tt>
<a name="sum_2ple"></a><div id="sum_2ple-def"><a name="L83"></a><tt class="py-lineno"> 83</tt> <a class="py-toggle" href="#" id="sum_2ple-toggle" onclick="return toggle('sum_2ple');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.utils-module.html#sum_2ple">sum_2ple</a><tt class="py-op">(</tt><tt class="py-param">seq</tt><tt class="py-op">,</tt> <tt class="py-param">table</tt><tt class="py-op">,</tt> <tt class="py-param">zero</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-number">0.0</tt><tt class="py-op">,</tt> <tt class="py-number">0.0</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="sum_2ple-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="sum_2ple-expanded"><a name="L84"></a><tt class="py-lineno"> 84</tt>  <tt class="py-line">    <tt id="link-81" class="py-name" targets="Variable Bio.MarkovModel.x=Bio.MarkovModel-module.html#x,Variable Bio.Statistics.lowess.x=Bio.Statistics.lowess-module.html#x"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-81', 'x', 'link-81');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">y</tt> <tt class="py-op">=</tt> <tt class="py-name">zero</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt>  <tt class="py-line">    <tt id="link-82" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-82', 'data', 'link-52');">data</a></tt> <tt class="py-op">=</tt> <tt class="py-name">getattr</tt><tt class="py-op">(</tt><tt id="link-83" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-83', 'seq', 'link-10');">seq</a></tt><tt class="py-op">,</tt> <tt class="py-string">"data"</tt><tt class="py-op">,</tt> <tt id="link-84" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-84', 'seq', 'link-10');">seq</a></tt><tt class="py-op">)</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">c</tt> <tt class="py-keyword">in</tt> <tt id="link-85" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-85', 'data', 'link-52');">data</a></tt><tt class="py-op">:</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt>  <tt class="py-line">        <tt class="py-name">x2</tt><tt class="py-op">,</tt> <tt class="py-name">y2</tt> <tt class="py-op">=</tt> <tt id="link-86" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-86', 'table', 'link-80');">table</a></tt><tt class="py-op">[</tt><tt class="py-name">c</tt><tt class="py-op">]</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt>  <tt class="py-line">        <tt id="link-87" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-87', 'x', 'link-81');">x</a></tt> <tt class="py-op">=</tt> <tt id="link-88" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-88', 'x', 'link-81');">x</a></tt> <tt class="py-op">+</tt> <tt class="py-name">x2</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt>  <tt class="py-line">        <tt class="py-name">y</tt> <tt class="py-op">=</tt> <tt class="py-name">y</tt> <tt class="py-op">+</tt> <tt class="py-name">y2</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt id="link-89" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-89', 'x', 'link-81');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">y</tt><tt class="py-op">)</tt> </tt>
</div><a name="L91"></a><tt class="py-lineno"> 91</tt>  <tt class="py-line"> </tt>
<a name="total_weight"></a><div id="total_weight-def"><a name="L92"></a><tt class="py-lineno"> 92</tt> <a class="py-toggle" href="#" id="total_weight-toggle" onclick="return toggle('total_weight');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.utils-module.html#total_weight">total_weight</a><tt class="py-op">(</tt><tt class="py-param">seq</tt><tt class="py-op">,</tt> <tt class="py-param">weight_table</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="total_weight-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="total_weight-expanded"><a name="L93"></a><tt class="py-lineno"> 93</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">weight_table</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt>  <tt class="py-line">        <tt class="py-name">weight_table</tt> <tt class="py-op">=</tt> <tt id="link-90" class="py-name"><a title="Bio.PropertyManager.default_manager" class="py-name" href="#" onclick="return doclink('link-90', 'default_manager', 'link-3');">default_manager</a></tt><tt class="py-op">.</tt><tt id="link-91" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.resolve
Bio.Parsers.spark.GenericParser.resolve
Bio.PropertyManager.PropertyManager.resolve" class="py-name" href="#" onclick="return doclink('link-91', 'resolve', 'link-9');">resolve</a></tt><tt class="py-op">(</tt><tt id="link-92" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-92', 'seq', 'link-10');">seq</a></tt><tt class="py-op">.</tt><tt id="link-93" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-93', 'alphabet', 'link-11');">alphabet</a></tt><tt class="py-op">,</tt> <tt class="py-string">"weight_table"</tt><tt class="py-op">)</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-94" class="py-name" targets="Method Bio.Nexus.Nexus.StepMatrix.sum()=Bio.Nexus.Nexus.StepMatrix-class.html#sum,Function Bio.utils.sum()=Bio.utils-module.html#sum"><a title="Bio.Nexus.Nexus.StepMatrix.sum
Bio.utils.sum" class="py-name" href="#" onclick="return doclink('link-94', 'sum', 'link-94');">sum</a></tt><tt class="py-op">(</tt><tt id="link-95" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-95', 'seq', 'link-10');">seq</a></tt><tt class="py-op">,</tt> <tt class="py-name">weight_table</tt><tt class="py-op">)</tt> </tt>
</div><a name="L96"></a><tt class="py-lineno"> 96</tt>  <tt class="py-line"> </tt>
<a name="total_weight_range"></a><div id="total_weight_range-def"><a name="L97"></a><tt class="py-lineno"> 97</tt> <a class="py-toggle" href="#" id="total_weight_range-toggle" onclick="return toggle('total_weight_range');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.utils-module.html#total_weight_range">total_weight_range</a><tt class="py-op">(</tt><tt class="py-param">seq</tt><tt class="py-op">,</tt> <tt class="py-param">weight_table</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="total_weight_range-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="total_weight_range-expanded"><a name="L98"></a><tt class="py-lineno"> 98</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">weight_table</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt>  <tt class="py-line">        <tt class="py-name">weight_table</tt> <tt class="py-op">=</tt> <tt id="link-96" class="py-name"><a title="Bio.PropertyManager.default_manager" class="py-name" href="#" onclick="return doclink('link-96', 'default_manager', 'link-3');">default_manager</a></tt><tt class="py-op">.</tt><tt id="link-97" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.resolve
Bio.Parsers.spark.GenericParser.resolve
Bio.PropertyManager.PropertyManager.resolve" class="py-name" href="#" onclick="return doclink('link-97', 'resolve', 'link-9');">resolve</a></tt><tt class="py-op">(</tt><tt id="link-98" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-98', 'seq', 'link-10');">seq</a></tt><tt class="py-op">.</tt><tt id="link-99" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-99', 'alphabet', 'link-11');">alphabet</a></tt><tt class="py-op">,</tt> <tt class="py-string">"weight_range_table"</tt><tt class="py-op">)</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-100" class="py-name" targets="Function Bio.utils.sum_2ple()=Bio.utils-module.html#sum_2ple"><a title="Bio.utils.sum_2ple" class="py-name" href="#" onclick="return doclink('link-100', 'sum_2ple', 'link-100');">sum_2ple</a></tt><tt class="py-op">(</tt><tt id="link-101" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-101', 'seq', 'link-10');">seq</a></tt><tt class="py-op">,</tt> <tt class="py-name">weight_table</tt><tt class="py-op">)</tt> </tt>
</div><a name="L101"></a><tt class="py-lineno">101</tt>  <tt class="py-line"> </tt>
<a name="reduce_sequence"></a><div id="reduce_sequence-def"><a name="L102"></a><tt class="py-lineno">102</tt> <a class="py-toggle" href="#" id="reduce_sequence-toggle" onclick="return toggle('reduce_sequence');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.utils-module.html#reduce_sequence">reduce_sequence</a><tt class="py-op">(</tt><tt class="py-param">seq</tt><tt class="py-op">,</tt> <tt class="py-param">reduction_table</tt><tt class="py-op">,</tt><tt class="py-param">new_alphabet</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="reduce_sequence-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="reduce_sequence-expanded"><a name="L103"></a><tt class="py-lineno">103</tt>  <tt class="py-line">   <tt class="py-docstring">""" given an amino-acid sequence, return it in reduced alphabet form based</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt>  <tt class="py-line"><tt class="py-docstring">       on the letter-translation table passed. Some "standard" tables are in</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt>  <tt class="py-line"><tt class="py-docstring">       Alphabet.Reduced.</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt>  <tt class="py-line"><tt class="py-docstring">       seq: a Seq.Seq type sequence</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt>  <tt class="py-line"><tt class="py-docstring">       reduction_table: a dictionary whose keys are the "from" alphabet, and values</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt>  <tt class="py-line"><tt class="py-docstring">       are the "to" alphabet"""</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt>  <tt class="py-line">   <tt class="py-keyword">if</tt> <tt class="py-name">new_alphabet</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt>  <tt class="py-line">      <tt class="py-name">new_alphabet</tt> <tt class="py-op">=</tt> <tt id="link-102" class="py-name"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-102', 'Alphabet', 'link-1');">Alphabet</a></tt><tt class="py-op">.</tt><tt id="link-103" class="py-name" targets="Variable Bio.Alphabet.single_letter_alphabet=Bio.Alphabet-module.html#single_letter_alphabet"><a title="Bio.Alphabet.single_letter_alphabet" class="py-name" href="#" onclick="return doclink('link-103', 'single_letter_alphabet', 'link-103');">single_letter_alphabet</a></tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt>  <tt class="py-line">      <tt class="py-name">new_alphabet</tt><tt class="py-op">.</tt><tt id="link-104" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters
Bio.SeqUtils.ProteinX.letters" class="py-name" href="#" onclick="return doclink('link-104', 'letters', 'link-50');">letters</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt>  <tt class="py-line">      <tt class="py-keyword">for</tt> <tt class="py-name">letter</tt> <tt class="py-keyword">in</tt> <tt class="py-name">reduction_table</tt><tt class="py-op">:</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt>  <tt class="py-line">         <tt class="py-name">new_alphabet</tt><tt class="py-op">.</tt><tt id="link-105" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters
Bio.SeqUtils.ProteinX.letters" class="py-name" href="#" onclick="return doclink('link-105', 'letters', 'link-50');">letters</a></tt> <tt class="py-op">+=</tt> <tt class="py-name">letter</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt>  <tt class="py-line">      <tt class="py-name">new_alphabet</tt><tt class="py-op">.</tt><tt id="link-106" 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-106', 'size', 'link-106');">size</a></tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">new_alphabet</tt><tt class="py-op">.</tt><tt id="link-107" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters
Bio.SeqUtils.ProteinX.letters" class="py-name" href="#" onclick="return doclink('link-107', 'letters', 'link-50');">letters</a></tt><tt class="py-op">)</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt>  <tt class="py-line">   <tt class="py-name">new_seq</tt> <tt class="py-op">=</tt> <tt id="link-108" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-108', 'Seq', 'link-0');">Seq</a></tt><tt class="py-op">.</tt><tt id="link-109" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-109', 'Seq', 'link-0');">Seq</a></tt><tt class="py-op">(</tt><tt class="py-string">''</tt><tt class="py-op">,</tt><tt class="py-name">new_alphabet</tt><tt class="py-op">)</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt>  <tt class="py-line">   <tt class="py-keyword">for</tt> <tt class="py-name">letter</tt> <tt class="py-keyword">in</tt> <tt id="link-110" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-110', 'seq', 'link-10');">seq</a></tt><tt class="py-op">:</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt>  <tt class="py-line">      <tt class="py-name">new_seq</tt> <tt class="py-op">+=</tt> <tt class="py-name">reduction_table</tt><tt class="py-op">[</tt><tt class="py-name">letter</tt><tt class="py-op">]</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt>  <tt class="py-line">   <tt class="py-keyword">return</tt> <tt class="py-name">new_seq</tt> </tt>
</div><a name="L119"></a><tt class="py-lineno">119</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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</pre>
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