Sophie

Sophie

distrib > Mandriva > 2008.1 > x86_64 > by-pkgid > 763d6289e1351f2d34257ce697a3ccb7 > files > 169

biopython-doc-1.47-2mdv2008.1.x86_64.rpm

<?xml version="1.0" encoding="ascii"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
          "DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
  <title>Bio.CAPS</title>
  <link rel="stylesheet" href="epydoc.css" type="text/css" />
  <script type="text/javascript" src="epydoc.js"></script>
</head>

<body bgcolor="white" text="black" link="blue" vlink="#204080"
      alink="#204080">
<!-- ==================== NAVIGATION BAR ==================== -->
<table class="navbar" border="0" width="100%" cellpadding="0"
       bgcolor="#a0c0ff" cellspacing="0">
  <tr valign="middle">

  <!-- Tree link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="module-tree.html">Trees</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Index link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="identifier-index.html">Indices</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Help link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="help.html">Help</a>&nbsp;&nbsp;&nbsp;</th>

      <th class="navbar" width="100%"></th>
  </tr>
</table>
<table width="100%" cellpadding="0" cellspacing="0">
  <tr valign="top">
    <td width="100%">
      <span class="breadcrumbs">
        <a href="Bio-module.html">Package&nbsp;Bio</a> ::
        Package&nbsp;CAPS
      </span>
    </td>
    <td>
      <table cellpadding="0" cellspacing="0">
        <!-- hide/show private -->
        <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
    onclick="toggle_private();">hide&nbsp;private</a>]</span></td></tr>
        <tr><td align="right"><span class="options"
            >[<a href="frames.html" target="_top">frames</a
            >]&nbsp;|&nbsp;<a href="Bio.CAPS-pysrc.html"
            target="_top">no&nbsp;frames</a>]</span></td></tr>
      </table>
    </td>
  </tr>
</table>
<h1 class="epydoc">Source Code for <a href="Bio.CAPS-module.html">Package Bio.CAPS</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno">  1</tt>  <tt class="py-line"><tt class="py-docstring">"""This module deals with CAPS markers.</tt> </tt>
<a name="L2"></a><tt class="py-lineno">  2</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L3"></a><tt class="py-lineno">  3</tt>  <tt class="py-line"><tt class="py-docstring">A CAPS marker is a location a DifferentialCutsite as described below and a</tt> </tt>
<a name="L4"></a><tt class="py-lineno">  4</tt>  <tt class="py-line"><tt class="py-docstring">set of primers that can be used to visualize this.  More information can</tt> </tt>
<a name="L5"></a><tt class="py-lineno">  5</tt>  <tt class="py-line"><tt class="py-docstring">be found in the paper located at:</tt> </tt>
<a name="L6"></a><tt class="py-lineno">  6</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L7"></a><tt class="py-lineno">  7</tt>  <tt class="py-line"><tt class="py-docstring">http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=8106085&amp;dopt=Abstract</tt> </tt>
<a name="L8"></a><tt class="py-lineno">  8</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L9"></a><tt class="py-lineno">  9</tt>  <tt class="py-line"><tt class="py-docstring">Copyright Jonathan Taylor 2005</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt>  <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt>  <tt class="py-line"> </tt>
<a name="DifferentialCutsite"></a><div id="DifferentialCutsite-def"><a name="L12"></a><tt class="py-lineno"> 12</tt> <a class="py-toggle" href="#" id="DifferentialCutsite-toggle" onclick="return toggle('DifferentialCutsite');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.CAPS.DifferentialCutsite-class.html">DifferentialCutsite</a><tt class="py-op">:</tt> </tt>
</div><div id="DifferentialCutsite-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="DifferentialCutsite-expanded"><a name="L13"></a><tt class="py-lineno"> 13</tt>  <tt class="py-line">  <tt class="py-docstring">"""A differential cutsite is a location in an alignment where an enzyme cuts</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt>  <tt class="py-line"><tt class="py-docstring">  at least one sequence and also cannot cut at least one other sequence.</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt>  <tt class="py-line"><tt class="py-docstring">  Members:</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt>  <tt class="py-line"><tt class="py-docstring">  start       Where it lives in the alignment.</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt>  <tt class="py-line"><tt class="py-docstring">  enzyme      The enzyme that causes this.</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt>  <tt class="py-line"><tt class="py-docstring">  cuts_in     A list of sequences (as indexes into the alignment) the</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt>  <tt class="py-line"><tt class="py-docstring">              enzyme cuts in.</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt>  <tt class="py-line"><tt class="py-docstring">  blocked_in  A list of sequences (as indexes into the alignment) the</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt>  <tt class="py-line"><tt class="py-docstring">              enzyme is blocked in.</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt>  <tt class="py-line"><tt class="py-docstring">  """</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt>  <tt class="py-line"> </tt>
<a name="DifferentialCutsite.__init__"></a><div id="DifferentialCutsite.__init__-def"><a name="L26"></a><tt class="py-lineno"> 26</tt> <a class="py-toggle" href="#" id="DifferentialCutsite.__init__-toggle" onclick="return toggle('DifferentialCutsite.__init__');">-</a><tt class="py-line">  <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.CAPS.DifferentialCutsite-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-param">kwds</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DifferentialCutsite.__init__-collapsed" style="display:none;" pad="+++" indent="++++++"></div><div id="DifferentialCutsite.__init__-expanded"><a name="L27"></a><tt class="py-lineno"> 27</tt>  <tt class="py-line">    <tt class="py-docstring">"""Initialize a DifferentialCutsite.</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt>  <tt class="py-line"><tt class="py-docstring">    Each member (as listed in the class description) should be included as a</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt>  <tt class="py-line"><tt class="py-docstring">    keyword.</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt>  <tt class="py-line">     </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt>  <tt class="py-line">    <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-0" class="py-name" targets="Method Bio.GFF.easy.Location.start()=Bio.GFF.easy.Location-class.html#start,Method Bio.Prosite.Pattern.PrositeMatch.start()=Bio.Prosite.Pattern.PrositeMatch-class.html#start,Variable Bio.Restriction._Update.RestrictionCompiler.start=Bio.Restriction._Update.RestrictionCompiler-module.html#start,Method Martel.LAX.LAX.start()=Martel.LAX.LAX-class.html#start"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-0', 'start', 'link-0');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">kwds</tt><tt class="py-op">[</tt><tt class="py-string">"start"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt>  <tt class="py-line">    <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Method Bio.MetaTool._RecordConsumer.enzyme()=Bio.MetaTool._RecordConsumer-class.html#enzyme,Variable Bio.MetaTool.metatool_format.enzyme=Bio.MetaTool.metatool_format-module.html#enzyme"><a title="Bio.MetaTool._RecordConsumer.enzyme
Bio.MetaTool.metatool_format.enzyme" class="py-name" href="#" onclick="return doclink('link-1', 'enzyme', 'link-1');">enzyme</a></tt> <tt class="py-op">=</tt> <tt class="py-name">kwds</tt><tt class="py-op">[</tt><tt class="py-string">"enzyme"</tt><tt class="py-op">]</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt>  <tt class="py-line">    <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">cuts_in</tt> <tt class="py-op">=</tt> <tt class="py-name">kwds</tt><tt class="py-op">[</tt><tt class="py-string">"cuts_in"</tt><tt class="py-op">]</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt>  <tt class="py-line">    <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">blocked_in</tt> <tt class="py-op">=</tt> <tt class="py-name">kwds</tt><tt class="py-op">[</tt><tt class="py-string">"blocked_in"</tt><tt class="py-op">]</tt> </tt>
</div></div><a name="L37"></a><tt class="py-lineno"> 37</tt>  <tt class="py-line"> </tt>
<a name="AlignmentHasDifferentLengthsError"></a><div id="AlignmentHasDifferentLengthsError-def"><a name="L38"></a><tt class="py-lineno"> 38</tt> <a class="py-toggle" href="#" id="AlignmentHasDifferentLengthsError-toggle" onclick="return toggle('AlignmentHasDifferentLengthsError');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.CAPS.AlignmentHasDifferentLengthsError-class.html">AlignmentHasDifferentLengthsError</a><tt class="py-op">(</tt><tt class="py-base-class">Exception</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="AlignmentHasDifferentLengthsError-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="AlignmentHasDifferentLengthsError-expanded"><a name="L39"></a><tt class="py-lineno"> 39</tt>  <tt class="py-line">  <tt class="py-keyword">pass</tt> </tt>
</div><a name="L40"></a><tt class="py-lineno"> 40</tt>  <tt class="py-line"> </tt>
<a name="CAPSMap"></a><div id="CAPSMap-def"><a name="L41"></a><tt class="py-lineno"> 41</tt> <a class="py-toggle" href="#" id="CAPSMap-toggle" onclick="return toggle('CAPSMap');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.CAPS.CAPSMap-class.html">CAPSMap</a><tt class="py-op">:</tt> </tt>
</div><div id="CAPSMap-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="CAPSMap-expanded"><a name="L42"></a><tt class="py-lineno"> 42</tt>  <tt class="py-line">  <tt class="py-docstring">"""A map of an alignment showing all possible dcuts.</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt>  <tt class="py-line"><tt class="py-docstring">  Members:</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt>  <tt class="py-line"><tt class="py-docstring">  alignment  The alignment that is mapped.</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt>  <tt class="py-line"><tt class="py-docstring">  dcuts      A list of possible CAPS markers in the form of </tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt>  <tt class="py-line"><tt class="py-docstring">             DifferentialCutsites.</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt>  <tt class="py-line"><tt class="py-docstring">  """</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt>  <tt class="py-line"> </tt>
<a name="CAPSMap.__init__"></a><div id="CAPSMap.__init__-def"><a name="L50"></a><tt class="py-lineno"> 50</tt> <a class="py-toggle" href="#" id="CAPSMap.__init__-toggle" onclick="return toggle('CAPSMap.__init__');">-</a><tt class="py-line">  <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.CAPS.CAPSMap-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">alignment</tt><tt class="py-op">,</tt> <tt class="py-param">enzymes</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CAPSMap.__init__-collapsed" style="display:none;" pad="+++" indent="++++++"></div><div id="CAPSMap.__init__-expanded"><a name="L51"></a><tt class="py-lineno"> 51</tt>  <tt class="py-line">    <tt class="py-docstring">"""Initialize the CAPSMap</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt>  <tt class="py-line"><tt class="py-docstring">    Required:</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt>  <tt class="py-line"><tt class="py-docstring">    alignment    The alignment to be mapped.</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt>  <tt class="py-line"><tt class="py-docstring">    Optional:</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt>  <tt class="py-line"><tt class="py-docstring">    enzymes      The enzymes to be used to create the map.</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt>  <tt class="py-line"> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt>  <tt class="py-line">    <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Method Bio.AlignAce.Parser.AlignAceConsumer.sequences()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#sequences"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequences" class="py-name" href="#" onclick="return doclink('link-2', 'sequences', 'link-2');">sequences</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">rec</tt><tt class="py-op">.</tt><tt id="link-3" 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-3', 'seq', 'link-3');">seq</a></tt> <tt class="py-keyword">for</tt> <tt class="py-name">rec</tt> <tt class="py-keyword">in</tt> <tt id="link-4" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.alignment=Bio.expressions.blast.ncbiblast-module.html#alignment"><a title="Bio.expressions.blast.ncbiblast.alignment" class="py-name" href="#" onclick="return doclink('link-4', 'alignment', 'link-4');">alignment</a></tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Method Bio.Align.Generic.Alignment.get_all_seqs()=Bio.Align.Generic.Alignment-class.html#get_all_seqs"><a title="Bio.Align.Generic.Alignment.get_all_seqs" class="py-name" href="#" onclick="return doclink('link-5', 'get_all_seqs', 'link-5');">get_all_seqs</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt>  <tt class="py-line">    <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-6" 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-6', 'size', 'link-6');">size</a></tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequences" class="py-name" href="#" onclick="return doclink('link-7', 'sequences', 'link-2');">sequences</a></tt><tt class="py-op">)</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt>  <tt class="py-line">    <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-8" class="py-name" targets="Method Bio.Blast.NCBIStandalone._AlignmentConsumer.length()=Bio.Blast.NCBIStandalone._AlignmentConsumer-class.html#length,Method Bio.GFF.easy.Location.length()=Bio.GFF.easy.Location-class.html#length"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-8', 'length', 'link-8');">length</a></tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequences" class="py-name" href="#" onclick="return doclink('link-9', 'sequences', 'link-2');">sequences</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt id="link-10" 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-10', 'seq', 'link-3');">seq</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-11" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequences" class="py-name" href="#" onclick="return doclink('link-11', 'sequences', 'link-2');">sequences</a></tt><tt class="py-op">:</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt>  <tt class="py-line">      <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-12" 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-12', 'seq', 'link-3');">seq</a></tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-13" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-13', 'length', 'link-8');">length</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-keyword">raise</tt> <tt id="link-14" class="py-name" targets="Class Bio.CAPS.AlignmentHasDifferentLengthsError=Bio.CAPS.AlignmentHasDifferentLengthsError-class.html"><a title="Bio.CAPS.AlignmentHasDifferentLengthsError" class="py-name" href="#" onclick="return doclink('link-14', 'AlignmentHasDifferentLengthsError', 'link-14');">AlignmentHasDifferentLengthsError</a></tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt>  <tt class="py-line"> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt>  <tt class="py-line">    <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name"><a title="Bio.expressions.blast.ncbiblast.alignment" class="py-name" href="#" onclick="return doclink('link-15', 'alignment', 'link-4');">alignment</a></tt> <tt class="py-op">=</tt> <tt id="link-16" class="py-name"><a title="Bio.expressions.blast.ncbiblast.alignment" class="py-name" href="#" onclick="return doclink('link-16', 'alignment', 'link-4');">alignment</a></tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt>  <tt class="py-line">    <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">enzymes</tt> <tt class="py-op">=</tt> <tt class="py-name">enzymes</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt>  <tt class="py-line"> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt>  <tt class="py-line">    <tt class="py-comment"># look for dcuts</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name" targets="Method Bio.CAPS.CAPSMap._digest()=Bio.CAPS.CAPSMap-class.html#_digest"><a title="Bio.CAPS.CAPSMap._digest" class="py-name" href="#" onclick="return doclink('link-17', '_digest', 'link-17');">_digest</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L72"></a><tt class="py-lineno"> 72</tt>  <tt class="py-line">   </tt>
<a name="CAPSMap._digest_with"></a><div id="CAPSMap._digest_with-def"><a name="L73"></a><tt class="py-lineno"> 73</tt> <a class="py-toggle" href="#" id="CAPSMap._digest_with-toggle" onclick="return toggle('CAPSMap._digest_with');">-</a><tt class="py-line">  <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.CAPS.CAPSMap-class.html#_digest_with">_digest_with</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">enzyme</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CAPSMap._digest_with-collapsed" style="display:none;" pad="+++" indent="++++++"></div><div id="CAPSMap._digest_with-expanded"><a name="L74"></a><tt class="py-lineno"> 74</tt>  <tt class="py-line">    <tt class="py-name">cuts</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt>  <tt class="py-line">    <tt class="py-name">all</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt>  <tt class="py-line"> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt>  <tt class="py-line">    <tt class="py-comment"># go through each sequence</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-keyword">for</tt> <tt id="link-18" 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-18', 'seq', 'link-3');">seq</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequences" class="py-name" href="#" onclick="return doclink('link-19', 'sequences', 'link-2');">sequences</a></tt><tt class="py-op">:</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt>  <tt class="py-line"> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt>  <tt class="py-line">      <tt class="py-comment"># grab all the cuts in the sequence</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt>  <tt class="py-line"><tt class="py-comment"></tt>      <tt class="py-name">cuts</tt><tt class="py-op">[</tt><tt id="link-20" 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-20', 'seq', 'link-3');">seq</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">cut</tt> <tt class="py-op">-</tt> <tt id="link-21" class="py-name"><a title="Bio.MetaTool._RecordConsumer.enzyme
Bio.MetaTool.metatool_format.enzyme" class="py-name" href="#" onclick="return doclink('link-21', 'enzyme', 'link-1');">enzyme</a></tt><tt class="py-op">.</tt><tt class="py-name">fst5</tt> <tt class="py-keyword">for</tt> <tt class="py-name">cut</tt> <tt class="py-keyword">in</tt> <tt id="link-22" class="py-name"><a title="Bio.MetaTool._RecordConsumer.enzyme
Bio.MetaTool.metatool_format.enzyme" class="py-name" href="#" onclick="return doclink('link-22', 'enzyme', 'link-1');">enzyme</a></tt><tt class="py-op">.</tt><tt id="link-23" class="py-name" targets="Method Bio.EUtils.DBIdsClient.DBIdsClient.search()=Bio.EUtils.DBIdsClient.DBIdsClient-class.html#search,Method Bio.EUtils.HistoryClient.HistoryClient.search()=Bio.EUtils.HistoryClient.HistoryClient-class.html#search,Method Bio.KDTree.KDTree.KDTree.search()=Bio.KDTree.KDTree.KDTree-class.html#search,Method Bio.PDB.NeighborSearch.NeighborSearch.search()=Bio.PDB.NeighborSearch.NeighborSearch-class.html#search,Method Bio.Prosite.Pattern.Prosite.search()=Bio.Prosite.Pattern.Prosite-class.html#search,Class Method Bio.Restriction.Restriction.AbstractCut.search()=Bio.Restriction.Restriction.AbstractCut-class.html#search,Method Bio.Restriction.Restriction.RestrictionBatch.search()=Bio.Restriction.Restriction.RestrictionBatch-class.html#search,Function Bio.SCOP.search()=Bio.SCOP-module.html#search,Module Bio.builders.Search.search=Bio.builders.Search.search-module.html,Module Bio.formatdefs.search=Bio.formatdefs.search-module.html,Variable Bio.formatdefs.search.search=Bio.formatdefs.search-module.html#search"><a title="Bio.EUtils.DBIdsClient.DBIdsClient.search
Bio.EUtils.HistoryClient.HistoryClient.search
Bio.KDTree.KDTree.KDTree.search
Bio.PDB.NeighborSearch.NeighborSearch.search
Bio.Prosite.Pattern.Prosite.search
Bio.Restriction.Restriction.AbstractCut.search
Bio.Restriction.Restriction.RestrictionBatch.search
Bio.SCOP.search
Bio.builders.Search.search
Bio.formatdefs.search
Bio.formatdefs.search.search" class="py-name" href="#" onclick="return doclink('link-23', 'search', 'link-23');">search</a></tt><tt class="py-op">(</tt><tt id="link-24" 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-24', 'seq', 'link-3');">seq</a></tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt>  <tt class="py-line"> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt>  <tt class="py-line">      <tt class="py-comment"># maintain a list of all cuts in all sequences</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt>  <tt class="py-line"><tt class="py-comment"></tt>      <tt class="py-name">all</tt><tt class="py-op">.</tt><tt id="link-25" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.extend()=Bio.EUtils.POM.ElementNode-class.html#extend,Method Bio.SCOP.Raf.SeqMap.extend()=Bio.SCOP.Raf.SeqMap-class.html#extend,Method Bio.Seq.MutableSeq.extend()=Bio.Seq.MutableSeq-class.html#extend"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-25', 'extend', 'link-25');">extend</a></tt><tt class="py-op">(</tt><tt class="py-name">cuts</tt><tt class="py-op">[</tt><tt id="link-26" 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-26', 'seq', 'link-3');">seq</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt>  <tt class="py-line"> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt>  <tt class="py-line">    <tt class="py-comment"># we sort the all list and remove duplicates</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-name">all</tt><tt class="py-op">.</tt><tt id="link-27" class="py-name" targets="Method Bio.PDB.Residue.DisorderedResidue.sort()=Bio.PDB.Residue.DisorderedResidue-class.html#sort,Method Bio.PDB.Residue.Residue.sort()=Bio.PDB.Residue.Residue-class.html#sort,Method Bio.Sequencing.Ace.ACEFileRecord.sort()=Bio.Sequencing.Ace.ACEFileRecord-class.html#sort"><a title="Bio.PDB.Residue.DisorderedResidue.sort
Bio.PDB.Residue.Residue.sort
Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-27', 'sort', 'link-27');">sort</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt>  <tt class="py-line">     </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt>  <tt class="py-line">    <tt class="py-name">last</tt> <tt class="py-op">=</tt> <tt class="py-op">-</tt><tt class="py-number">999</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt>  <tt class="py-line">    <tt class="py-name">new</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">cut</tt> <tt class="py-keyword">in</tt> <tt class="py-name">all</tt><tt class="py-op">:</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt>  <tt class="py-line">      <tt class="py-keyword">if</tt> <tt class="py-name">cut</tt> <tt class="py-op">!=</tt> <tt class="py-name">last</tt><tt class="py-op">:</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt>  <tt class="py-line">        <tt class="py-name">new</tt><tt class="py-op">.</tt><tt id="link-28" 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-28', 'append', 'link-28');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">cut</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">last</tt> <tt class="py-op">=</tt> <tt class="py-name">cut</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt>  <tt class="py-line"> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt>  <tt class="py-line">    <tt class="py-name">all</tt> <tt class="py-op">=</tt> <tt class="py-name">new</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt>  <tt class="py-line">    <tt class="py-comment"># all now has indices for all sequences in the alignment</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">cut</tt> <tt class="py-keyword">in</tt> <tt class="py-name">all</tt><tt class="py-op">:</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt>  <tt class="py-line">      <tt class="py-comment"># test for dcuts</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt>  <tt class="py-line">      <tt class="py-name">cuts_in</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt>  <tt class="py-line">      <tt class="py-name">blocked_in</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt>  <tt class="py-line"> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt>  <tt class="py-line">      <tt class="py-keyword">for</tt> <tt id="link-29" class="py-name" targets="Variable Bio.PDB.Polypeptide.i=Bio.PDB.Polypeptide-module.html#i"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-29', 'i', 'link-29');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-30" class="py-name"><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-30', 'size', 'link-6');">size</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt>  <tt class="py-line">        <tt id="link-31" 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-31', 'seq', 'link-3');">seq</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-32" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequences" class="py-name" href="#" onclick="return doclink('link-32', 'sequences', 'link-2');">sequences</a></tt><tt class="py-op">[</tt><tt id="link-33" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-33', 'i', 'link-29');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">cut</tt> <tt class="py-keyword">in</tt> <tt class="py-name">cuts</tt><tt class="py-op">[</tt><tt id="link-34" 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-34', 'seq', 'link-3');">seq</a></tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt>  <tt class="py-line">          <tt class="py-name">cuts_in</tt><tt class="py-op">.</tt><tt id="link-35" class="py-name"><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-35', 'append', 'link-28');">append</a></tt><tt class="py-op">(</tt><tt id="link-36" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-36', 'i', 'link-29');">i</a></tt><tt class="py-op">)</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt>  <tt class="py-line">        <tt class="py-keyword">else</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">blocked_in</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name"><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-37', 'append', 'link-28');">append</a></tt><tt class="py-op">(</tt><tt id="link-38" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-38', 'i', 'link-29');">i</a></tt><tt class="py-op">)</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt>  <tt class="py-line"> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt>  <tt class="py-line">      <tt class="py-keyword">if</tt> <tt class="py-name">cuts_in</tt> <tt class="py-op">!=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> <tt class="py-keyword">and</tt> <tt class="py-name">blocked_in</tt> <tt class="py-op">!=</tt> <tt class="py-op">[</tt><tt class="py-op">]</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">self</tt><tt class="py-op">.</tt><tt class="py-name">dcuts</tt><tt class="py-op">.</tt><tt id="link-39" class="py-name"><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-39', 'append', 'link-28');">append</a></tt><tt class="py-op">(</tt><tt id="link-40" class="py-name" targets="Class Bio.CAPS.DifferentialCutsite=Bio.CAPS.DifferentialCutsite-class.html"><a title="Bio.CAPS.DifferentialCutsite" class="py-name" href="#" onclick="return doclink('link-40', 'DifferentialCutsite', 'link-40');">DifferentialCutsite</a></tt><tt class="py-op">(</tt><tt id="link-41" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-41', 'start', 'link-0');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-name">cut</tt><tt class="py-op">,</tt> <tt id="link-42" class="py-name"><a title="Bio.MetaTool._RecordConsumer.enzyme
Bio.MetaTool.metatool_format.enzyme" class="py-name" href="#" onclick="return doclink('link-42', 'enzyme', 'link-1');">enzyme</a></tt> <tt class="py-op">=</tt> <tt id="link-43" class="py-name"><a title="Bio.MetaTool._RecordConsumer.enzyme
Bio.MetaTool.metatool_format.enzyme" class="py-name" href="#" onclick="return doclink('link-43', 'enzyme', 'link-1');">enzyme</a></tt><tt class="py-op">,</tt> <tt class="py-name">cuts_in</tt> <tt class="py-op">=</tt> <tt class="py-name">cuts_in</tt><tt class="py-op">,</tt> <tt class="py-name">blocked_in</tt> <tt class="py-op">=</tt> <tt class="py-name">blocked_in</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L114"></a><tt class="py-lineno">114</tt>  <tt class="py-line"> </tt>
<a name="CAPSMap._digest"></a><div id="CAPSMap._digest-def"><a name="L115"></a><tt class="py-lineno">115</tt> <a class="py-toggle" href="#" id="CAPSMap._digest-toggle" onclick="return toggle('CAPSMap._digest');">-</a><tt class="py-line">  <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.CAPS.CAPSMap-class.html#_digest">_digest</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CAPSMap._digest-collapsed" style="display:none;" pad="+++" indent="++++++"></div><div id="CAPSMap._digest-expanded"><a name="L116"></a><tt class="py-lineno">116</tt>  <tt class="py-line">    <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dcuts</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt>  <tt class="py-line"> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt id="link-44" class="py-name"><a title="Bio.MetaTool._RecordConsumer.enzyme
Bio.MetaTool.metatool_format.enzyme" class="py-name" href="#" onclick="return doclink('link-44', 'enzyme', 'link-1');">enzyme</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">enzymes</tt><tt class="py-op">:</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt>  <tt class="py-line">      <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-45" class="py-name" targets="Method Bio.CAPS.CAPSMap._digest_with()=Bio.CAPS.CAPSMap-class.html#_digest_with"><a title="Bio.CAPS.CAPSMap._digest_with" class="py-name" href="#" onclick="return doclink('link-45', '_digest_with', 'link-45');">_digest_with</a></tt><tt class="py-op">(</tt><tt id="link-46" class="py-name"><a title="Bio.MetaTool._RecordConsumer.enzyme
Bio.MetaTool.metatool_format.enzyme" class="py-name" href="#" onclick="return doclink('link-46', 'enzyme', 'link-1');">enzyme</a></tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L120"></a><tt class="py-lineno">120</tt>  <tt class="py-line"> </tt><script type="text/javascript">
<!--
expandto(location.href);
// -->
</script>
</pre>
<br />
<!-- ==================== NAVIGATION BAR ==================== -->
<table class="navbar" border="0" width="100%" cellpadding="0"
       bgcolor="#a0c0ff" cellspacing="0">
  <tr valign="middle">

  <!-- Tree link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="module-tree.html">Trees</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Index link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="identifier-index.html">Indices</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Help link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="help.html">Help</a>&nbsp;&nbsp;&nbsp;</th>

      <th class="navbar" width="100%"></th>
  </tr>
</table>
<table border="0" cellpadding="0" cellspacing="0" width="100%%">
  <tr>
    <td align="left" class="footer">
    Generated by Epydoc 3.0.1 on Mon Sep 15 09:28:08 2008
    </td>
    <td align="right" class="footer">
      <a target="mainFrame" href="http://epydoc.sourceforge.net"
        >http://epydoc.sourceforge.net</a>
    </td>
  </tr>
</table>

<script type="text/javascript">
  <!--
  // Private objects are initially displayed (because if
  // javascript is turned off then we want them to be
  // visible); but by default, we want to hide them.  So hide
  // them unless we have a cookie that says to show them.
  checkCookie();
  // -->
</script>
</body>
</html>

Perl :: Catalyst :: PostgreSQL :: RPM Valid HTML 4.01 Transitional