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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.SeqIO-module.html">Package SeqIO</a> ::
Module PhdIO
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<h1 class="epydoc">Source Code for <a href="Bio.SeqIO.PhdIO-module.html">Module Bio.SeqIO.PhdIO</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright 2008-2010 by Peter Cock. All rights reserved.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"># Revisions copyright 2009 by Cymon J. Cox. All rights reserved.</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">"""Bio.SeqIO support for the "phd" file format.</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring">PHD files are output by PHRED and used by PHRAP and CONSED.</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring">You are expected to use this module via the Bio.SeqIO functions, under the</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring">format name "phd". See also the underlying Bio.Sequencing.Phd module.</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring">For example, using Bio.SeqIO we can read in one of the example PHRED files</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring">from the Biopython unit tests:</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring"> >>> from Bio import SeqIO</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-docstring"> >>> for record in SeqIO.parse(open("Phd/phd1"), "phd"):</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring"> ... print record.id</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-docstring"> ... print record.seq[:10], "..."</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-docstring"> ... print record.letter_annotations["phred_quality"][:10], "..."</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring"> 34_222_(80-A03-19).b.ab1</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring"> ctccgtcgga ...</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring"> [9, 9, 10, 19, 22, 37, 28, 28, 24, 22] ...</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring"> 425_103_(81-A03-19).g.ab1</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring"> cgggatccca ...</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-docstring"> [14, 17, 22, 10, 10, 10, 15, 8, 8, 9] ...</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-docstring"> 425_7_(71-A03-19).b.ab1</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring"> acataaatca ...</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-docstring"> [10, 10, 10, 10, 8, 8, 6, 6, 6, 6] ...</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-docstring">Since PHRED files contain quality scores, you can save them as FASTQ or as</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-docstring">QUAL files, for example using Bio.SeqIO.write(...), or simply with the format</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-docstring">method of the SeqRecord object:</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-docstring"> >>> print record[:50].format("fastq")</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-docstring"> @425_7_(71-A03-19).b.ab1</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-docstring"> acataaatcaaattactnaccaacacacaaaccngtctcgcgtagtggag</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-docstring"> +</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"><tt class="py-docstring"> ++++))'''')(''')$!$''')''''(+.''$!$))))+)))'''''''</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-docstring"> <BLANKLINE></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">Or,</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-docstring"> >>> print record[:50].format("qual")</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-docstring"> >425_7_(71-A03-19).b.ab1</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"><tt class="py-docstring"> 10 10 10 10 8 8 6 6 6 6 8 7 6 6 6 8 3 0 3 6 6 6 8 6 6 6 6 7</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-docstring"> 10 13 6 6 3 0 3 8 8 8 8 10 8 8 8 6 6 6 6 6 6 6</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-docstring"> <BLANKLINE></tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"><tt class="py-docstring">Note these examples only show the first 50 bases to keep the output short.</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Module Bio.SeqRecord=Bio.SeqRecord-module.html,Class Bio.SeqRecord.SeqRecord=Bio.SeqRecord.SeqRecord-class.html"><a title="Bio.SeqRecord
Bio.SeqRecord.SeqRecord" class="py-name" href="#" onclick="return doclink('link-1', 'SeqRecord', 'link-1');">SeqRecord</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name"><a title="Bio.SeqRecord
Bio.SeqRecord.SeqRecord" class="py-name" href="#" onclick="return doclink('link-2', 'SeqRecord', 'link-1');">SeqRecord</a></tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-3" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-3', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Package Bio.Sequencing=Bio.Sequencing-module.html"><a title="Bio.Sequencing" class="py-name" href="#" onclick="return doclink('link-4', 'Sequencing', 'link-4');">Sequencing</a></tt> <tt class="py-keyword">import</tt> <tt id="link-5" class="py-name" targets="Module Bio.Sequencing.Phd=Bio.Sequencing.Phd-module.html"><a title="Bio.Sequencing.Phd" class="py-name" href="#" onclick="return doclink('link-5', 'Phd', 'link-5');">Phd</a></tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-6" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-6', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-7" class="py-name" targets="Package Bio.SeqIO=Bio.SeqIO-module.html"><a title="Bio.SeqIO" class="py-name" href="#" onclick="return doclink('link-7', 'SeqIO', 'link-7');">SeqIO</a></tt><tt class="py-op">.</tt><tt id="link-8" class="py-name" targets="Module Bio.AlignIO.Interfaces=Bio.AlignIO.Interfaces-module.html,Module Bio.SeqIO.Interfaces=Bio.SeqIO.Interfaces-module.html"><a title="Bio.AlignIO.Interfaces
Bio.SeqIO.Interfaces" class="py-name" href="#" onclick="return doclink('link-8', 'Interfaces', 'link-8');">Interfaces</a></tt> <tt class="py-keyword">import</tt> <tt id="link-9" class="py-name" targets="Class Bio.SeqIO.Interfaces.SequentialSequenceWriter=Bio.SeqIO.Interfaces.SequentialSequenceWriter-class.html"><a title="Bio.SeqIO.Interfaces.SequentialSequenceWriter" class="py-name" href="#" onclick="return doclink('link-9', 'SequentialSequenceWriter', 'link-9');">SequentialSequenceWriter</a></tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-10" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-10', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-11" class="py-name"><a title="Bio.SeqIO" class="py-name" href="#" onclick="return doclink('link-11', 'SeqIO', 'link-7');">SeqIO</a></tt> <tt class="py-keyword">import</tt> <tt id="link-12" class="py-name" targets="Module Bio.SeqIO.QualityIO=Bio.SeqIO.QualityIO-module.html"><a title="Bio.SeqIO.QualityIO" class="py-name" href="#" onclick="return doclink('link-12', 'QualityIO', 'link-12');">QualityIO</a></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-comment">#This is a generator function!</tt> </tt>
<a name="PhdIterator"></a><div id="PhdIterator-def"><a name="L61"></a><tt class="py-lineno"> 61</tt> <a class="py-toggle" href="#" id="PhdIterator-toggle" onclick="return toggle('PhdIterator');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqIO.PhdIO-module.html#PhdIterator">PhdIterator</a><tt class="py-op">(</tt><tt class="py-param">handle</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PhdIterator-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="PhdIterator-expanded"><a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns SeqRecord objects from a PHD file.</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"><tt class="py-docstring"> This uses the Bio.Sequencing.Phd module to do the hard work.</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-name">phd_records</tt> <tt class="py-op">=</tt> <tt id="link-13" class="py-name"><a title="Bio.Sequencing.Phd" class="py-name" href="#" onclick="return doclink('link-13', 'Phd', 'link-5');">Phd</a></tt><tt class="py-op">.</tt><tt id="link-14" class="py-name" targets="Method Bio.Affy.CelFile.CelParser.parse()=Bio.Affy.CelFile.CelParser-class.html#parse,Function Bio.AlignIO.parse()=Bio.AlignIO-module.html#parse,Method Bio.Blast.NCBIStandalone.BlastErrorParser.parse()=Bio.Blast.NCBIStandalone.BlastErrorParser-class.html#parse,Method Bio.Blast.NCBIStandalone.BlastParser.parse()=Bio.Blast.NCBIStandalone.BlastParser-class.html#parse,Method Bio.Blast.NCBIStandalone.PSIBlastParser.parse()=Bio.Blast.NCBIStandalone.PSIBlastParser-class.html#parse,Function Bio.Blast.NCBIXML.parse()=Bio.Blast.NCBIXML-module.html#parse,Method Bio.Compass.RecordParser.parse()=Bio.Compass.RecordParser-class.html#parse,Function Bio.Compass.parse()=Bio.Compass-module.html#parse,Function Bio.Emboss.Primer3.parse()=Bio.Emboss.Primer3-module.html#parse,Method Bio.Entrez.Parser.DataHandler.parse()=Bio.Entrez.Parser.DataHandler-class.html#parse,Function Bio.Entrez.parse()=Bio.Entrez-module.html#parse,Function Bio.ExPASy.Enzyme.parse()=Bio.ExPASy.Enzyme-module.html#parse,Function Bio.ExPASy.Prodoc.parse()=Bio.ExPASy.Prodoc-module.html#parse,Function Bio.ExPASy.Prosite.parse()=Bio.ExPASy.Prosite-module.html#parse,Method Bio.GenBank.FeatureParser.parse()=Bio.GenBank.FeatureParser-class.html#parse,Function Bio.GenBank.LocationParser.parse()=Bio.GenBank.LocationParser-module.html#parse,Method Bio.GenBank.RecordParser.parse()=Bio.GenBank.RecordParser-class.html#parse,Method Bio.GenBank.Scanner.InsdcScanner.parse()=Bio.GenBank.Scanner.InsdcScanner-class.html#parse,Function Bio.Geo.parse()=Bio.Geo-module.html#parse,Function Bio.KEGG.Compound.parse()=Bio.KEGG.Compound-module.html#parse,Function Bio.KEGG.Enzyme.parse()=Bio.KEGG.Enzyme-module.html#parse,Function Bio.KEGG.Map.parse()=Bio.KEGG.Map-module.html#parse,Function Bio.Medline.parse()=Bio.Medline-module.html#parse,Function Bio.Motif.parse()=Bio.Motif-module.html#parse,Method Bio.ParserSupport.AbstractParser.parse()=Bio.ParserSupport.AbstractParser-class.html#parse,Method Bio.Parsers.spark.GenericParser.parse()=Bio.Parsers.spark.GenericParser-class.html#parse,Method Bio.Phylo.NewickIO.Parser.parse()=Bio.Phylo.NewickIO.Parser-class.html#parse,Function Bio.Phylo.NewickIO.parse()=Bio.Phylo.NewickIO-module.html#parse,Function Bio.Phylo.NexusIO.parse()=Bio.Phylo.NexusIO-module.html#parse,Method Bio.Phylo.PhyloXMLIO.Parser.parse()=Bio.Phylo.PhyloXMLIO.Parser-class.html#parse,Function Bio.Phylo.PhyloXMLIO.parse()=Bio.Phylo.PhyloXMLIO-module.html#parse,Function Bio.Phylo._io.parse()=Bio.Phylo._io-module.html#parse,Function Bio.SCOP.Cla.parse()=Bio.SCOP.Cla-module.html#parse,Function Bio.SCOP.Des.parse()=Bio.SCOP.Des-module.html#parse,Function Bio.SCOP.Dom.parse()=Bio.SCOP.Dom-module.html#parse,Function Bio.SCOP.Hie.parse()=Bio.SCOP.Hie-module.html#parse,Function Bio.SCOP.Raf.parse()=Bio.SCOP.Raf-module.html#parse,Method Bio.SeqIO.UniprotIO.Parser.parse()=Bio.SeqIO.UniprotIO.Parser-class.html#parse,Function Bio.SeqIO.parse()=Bio.SeqIO-module.html#parse,Function Bio.Sequencing.Ace.parse()=Bio.Sequencing.Ace-module.html#parse,Function Bio.Sequencing.Phd.parse()=Bio.Sequencing.Phd-module.html#parse,Function Bio.SwissProt.KeyWList.parse()=Bio.SwissProt.KeyWList-module.html#parse,Function Bio.SwissProt.parse()=Bio.SwissProt-module.html#parse,Method Bio.UniGene.RecordParser.parse()=Bio.UniGene.RecordParser-class.html#parse,Method Bio.UniGene.UniGene.UniGeneParser.parse()=Bio.UniGene.UniGene.UniGeneParser-class.html#parse,Function Bio.UniGene.parse()=Bio.UniGene-module.html#parse,Function Bio.Wise.psw.parse()=Bio.Wise.psw-module.html#parse"><a title="Bio.Affy.CelFile.CelParser.parse
Bio.AlignIO.parse
Bio.Blast.NCBIStandalone.BlastErrorParser.parse
Bio.Blast.NCBIStandalone.BlastParser.parse
Bio.Blast.NCBIStandalone.PSIBlastParser.parse
Bio.Blast.NCBIXML.parse
Bio.Compass.RecordParser.parse
Bio.Compass.parse
Bio.Emboss.Primer3.parse
Bio.Entrez.Parser.DataHandler.parse
Bio.Entrez.parse
Bio.ExPASy.Enzyme.parse
Bio.ExPASy.Prodoc.parse
Bio.ExPASy.Prosite.parse
Bio.GenBank.FeatureParser.parse
Bio.GenBank.LocationParser.parse
Bio.GenBank.RecordParser.parse
Bio.GenBank.Scanner.InsdcScanner.parse
Bio.Geo.parse
Bio.KEGG.Compound.parse
Bio.KEGG.Enzyme.parse
Bio.KEGG.Map.parse
Bio.Medline.parse
Bio.Motif.parse
Bio.ParserSupport.AbstractParser.parse
Bio.Parsers.spark.GenericParser.parse
Bio.Phylo.NewickIO.Parser.parse
Bio.Phylo.NewickIO.parse
Bio.Phylo.NexusIO.parse
Bio.Phylo.PhyloXMLIO.Parser.parse
Bio.Phylo.PhyloXMLIO.parse
Bio.Phylo._io.parse
Bio.SCOP.Cla.parse
Bio.SCOP.Des.parse
Bio.SCOP.Dom.parse
Bio.SCOP.Hie.parse
Bio.SCOP.Raf.parse
Bio.SeqIO.UniprotIO.Parser.parse
Bio.SeqIO.parse
Bio.Sequencing.Ace.parse
Bio.Sequencing.Phd.parse
Bio.SwissProt.KeyWList.parse
Bio.SwissProt.parse
Bio.UniGene.RecordParser.parse
Bio.UniGene.UniGene.UniGeneParser.parse
Bio.UniGene.parse
Bio.Wise.psw.parse" class="py-name" href="#" onclick="return doclink('link-14', 'parse', 'link-14');">parse</a></tt><tt class="py-op">(</tt><tt id="link-15" class="py-name" targets="Variable Bio.UniGene.UniGene.handle=Bio.UniGene.UniGene-module.html#handle"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-15', 'handle', 'link-15');">handle</a></tt><tt class="py-op">)</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">phd_record</tt> <tt class="py-keyword">in</tt> <tt class="py-name">phd_records</tt><tt class="py-op">:</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-comment">#Convert the PHY record into a SeqRecord...</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt class="py-comment">#The "filename" can contain spaces, e.g. 'HWI-EAS94_4_1_1_602_99 1'</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-comment">#from unit test example file phd_solexa.</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-comment">#This will cause problems if used as the record identifier</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-comment">#(e.g. output for FASTQ format).</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt id="link-16" class="py-name" targets="Method Bio.Phylo.PhyloXMLIO.Writer.name()=Bio.Phylo.PhyloXMLIO.Writer-class.html#name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-16', 'name', 'link-16');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-name">phd_record</tt><tt class="py-op">.</tt><tt class="py-name">file_name</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name" targets="Method Bio.Nexus.Trees.Tree.split()=Bio.Nexus.Trees.Tree-class.html#split,Method Bio.Phylo.BaseTree.TreeMixin.split()=Bio.Phylo.BaseTree.TreeMixin-class.html#split,Method Bio.Restriction.Restriction.RestrictionBatch.split()=Bio.Restriction.Restriction.RestrictionBatch-class.html#split,Method Bio.Seq.Seq.split()=Bio.Seq.Seq-class.html#split"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.split" class="py-name" href="#" onclick="return doclink('link-17', 'split', 'link-17');">split</a></tt><tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-name">seq_record</tt> <tt class="py-op">=</tt> <tt id="link-18" class="py-name"><a title="Bio.SeqRecord
Bio.SeqRecord.SeqRecord" class="py-name" href="#" onclick="return doclink('link-18', 'SeqRecord', 'link-1');">SeqRecord</a></tt><tt class="py-op">(</tt><tt class="py-name">phd_record</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name" targets="Variable Bio.SeqRecord.SeqRecord.seq=Bio.SeqRecord.SeqRecord-class.html#seq,Variable BioSQL.BioSeq.DBSeqRecord.seq=BioSQL.BioSeq.DBSeqRecord-class.html#seq"><a title="Bio.SeqRecord.SeqRecord.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-19', 'seq', 'link-19');">seq</a></tt><tt class="py-op">,</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt id="link-20" class="py-name" targets="Method Bio.Phylo.PhyloXMLIO.Parser.id()=Bio.Phylo.PhyloXMLIO.Parser-class.html#id,Method Bio.Phylo.PhyloXMLIO.Writer.id()=Bio.Phylo.PhyloXMLIO.Writer-class.html#id"><a title="Bio.Phylo.PhyloXMLIO.Parser.id
Bio.Phylo.PhyloXMLIO.Writer.id" class="py-name" href="#" onclick="return doclink('link-20', 'id', 'link-20');">id</a></tt> <tt class="py-op">=</tt> <tt id="link-21" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-21', 'name', 'link-16');">name</a></tt><tt class="py-op">,</tt> <tt id="link-22" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-22', 'name', 'link-16');">name</a></tt> <tt class="py-op">=</tt> <tt id="link-23" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-23', 'name', 'link-16');">name</a></tt><tt class="py-op">,</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt id="link-24" class="py-name" targets="Method Bio.Blast.NCBIStandalone._DescriptionConsumer.description()=Bio.Blast.NCBIStandalone._DescriptionConsumer-class.html#description,Method Bio.Phylo.PhyloXMLIO.Writer.description()=Bio.Phylo.PhyloXMLIO.Writer-class.html#description"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description
Bio.Phylo.PhyloXMLIO.Writer.description" class="py-name" href="#" onclick="return doclink('link-24', 'description', 'link-24');">description</a></tt><tt class="py-op">=</tt> <tt class="py-name">phd_record</tt><tt class="py-op">.</tt><tt class="py-name">file_name</tt><tt class="py-op">)</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-comment">#Just re-use the comments dictionary as the SeqRecord's annotations</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-name">seq_record</tt><tt class="py-op">.</tt><tt id="link-25" class="py-name" targets="Variable BioSQL.BioSeq.DBSeqRecord.annotations=BioSQL.BioSeq.DBSeqRecord-class.html#annotations"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-25', 'annotations', 'link-25');">annotations</a></tt> <tt class="py-op">=</tt> <tt class="py-name">phd_record</tt><tt class="py-op">.</tt><tt class="py-name">comments</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-comment">#And store the qualities and peak locations as per-letter-annotation</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-name">seq_record</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name" targets="Variable Bio.SeqRecord.SeqRecord.letter_annotations=Bio.SeqRecord.SeqRecord-class.html#letter_annotations"><a title="Bio.SeqRecord.SeqRecord.letter_annotations" class="py-name" href="#" onclick="return doclink('link-26', 'letter_annotations', 'link-26');">letter_annotations</a></tt><tt class="py-op">[</tt><tt class="py-string">"phred_quality"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> \ </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-op">[</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-27" class="py-name" targets="Variable Bio.Restriction.Restriction.AanI.site=Bio.Restriction.Restriction.AanI-class.html#site,Variable Bio.Restriction.Restriction.AarI.site=Bio.Restriction.Restriction.AarI-class.html#site,Variable Bio.Restriction.Restriction.AasI.site=Bio.Restriction.Restriction.AasI-class.html#site,Variable Bio.Restriction.Restriction.AatI.site=Bio.Restriction.Restriction.AatI-class.html#site,Variable Bio.Restriction.Restriction.AatII.site=Bio.Restriction.Restriction.AatII-class.html#site,Variable Bio.Restriction.Restriction.AbsI.site=Bio.Restriction.Restriction.AbsI-class.html#site,Variable Bio.Restriction.Restriction.Acc16I.site=Bio.Restriction.Restriction.Acc16I-class.html#site,Variable Bio.Restriction.Restriction.Acc36I.site=Bio.Restriction.Restriction.Acc36I-class.html#site,Variable Bio.Restriction.Restriction.Acc65I.site=Bio.Restriction.Restriction.Acc65I-class.html#site,Variable Bio.Restriction.Restriction.AccB1I.site=Bio.Restriction.Restriction.AccB1I-class.html#site,Variable Bio.Restriction.Restriction.AccB7I.site=Bio.Restriction.Restriction.AccB7I-class.html#site,Variable Bio.Restriction.Restriction.AccBSI.site=Bio.Restriction.Restriction.AccBSI-class.html#site,Variable Bio.Restriction.Restriction.AccI.site=Bio.Restriction.Restriction.AccI-class.html#site,Variable Bio.Restriction.Restriction.AccII.site=Bio.Restriction.Restriction.AccII-class.html#site,Variable Bio.Restriction.Restriction.AccIII.site=Bio.Restriction.Restriction.AccIII-class.html#site,Variable Bio.Restriction.Restriction.AceIII.site=Bio.Restriction.Restriction.AceIII-class.html#site,Variable Bio.Restriction.Restriction.AciI.site=Bio.Restriction.Restriction.AciI-class.html#site,Variable Bio.Restriction.Restriction.AclI.site=Bio.Restriction.Restriction.AclI-class.html#site,Variable Bio.Restriction.Restriction.AclWI.site=Bio.Restriction.Restriction.AclWI-class.html#site,Variable Bio.Restriction.Restriction.AcoI.site=Bio.Restriction.Restriction.AcoI-class.html#site,Variable Bio.Restriction.Restriction.AcsI.site=Bio.Restriction.Restriction.AcsI-class.html#site,Variable Bio.Restriction.Restriction.AcuI.site=Bio.Restriction.Restriction.AcuI-class.html#site,Variable Bio.Restriction.Restriction.AcvI.site=Bio.Restriction.Restriction.AcvI-class.html#site,Variable Bio.Restriction.Restriction.AcyI.site=Bio.Restriction.Restriction.AcyI-class.html#site,Variable Bio.Restriction.Restriction.AdeI.site=Bio.Restriction.Restriction.AdeI-class.html#site,Variable Bio.Restriction.Restriction.AfaI.site=Bio.Restriction.Restriction.AfaI-class.html#site,Variable Bio.Restriction.Restriction.AfeI.site=Bio.Restriction.Restriction.AfeI-class.html#site,Variable Bio.Restriction.Restriction.AfiI.site=Bio.Restriction.Restriction.AfiI-class.html#site,Variable Bio.Restriction.Restriction.AflII.site=Bio.Restriction.Restriction.AflII-class.html#site,Variable Bio.Restriction.Restriction.AflIII.site=Bio.Restriction.Restriction.AflIII-class.html#site,Variable Bio.Restriction.Restriction.AgeI.site=Bio.Restriction.Restriction.AgeI-class.html#site,Variable Bio.Restriction.Restriction.AgsI.site=Bio.Restriction.Restriction.AgsI-class.html#site,Variable Bio.Restriction.Restriction.AhaIII.site=Bio.Restriction.Restriction.AhaIII-class.html#site,Variable Bio.Restriction.Restriction.AhdI.site=Bio.Restriction.Restriction.AhdI-class.html#site,Variable Bio.Restriction.Restriction.AhlI.site=Bio.Restriction.Restriction.AhlI-class.html#site,Variable Bio.Restriction.Restriction.AjiI.site=Bio.Restriction.Restriction.AjiI-class.html#site,Variable Bio.Restriction.Restriction.AjnI.site=Bio.Restriction.Restriction.AjnI-class.html#site,Variable Bio.Restriction.Restriction.AjuI.site=Bio.Restriction.Restriction.AjuI-class.html#site,Variable Bio.Restriction.Restriction.AleI.site=Bio.Restriction.Restriction.AleI-class.html#site,Variable Bio.Restriction.Restriction.AlfI.site=Bio.Restriction.Restriction.AlfI-class.html#site,Variable Bio.Restriction.Restriction.AloI.site=Bio.Restriction.Restriction.AloI-class.html#site,Variable Bio.Restriction.Restriction.AluBI.site=Bio.Restriction.Restriction.AluBI-class.html#site,Variable Bio.Restriction.Restriction.AluI.site=Bio.Restriction.Restriction.AluI-class.html#site,Variable Bio.Restriction.Restriction.Alw21I.site=Bio.Restriction.Restriction.Alw21I-class.html#site,Variable Bio.Restriction.Restriction.Alw26I.site=Bio.Restriction.Restriction.Alw26I-class.html#site,Variable Bio.Restriction.Restriction.Alw44I.site=Bio.Restriction.Restriction.Alw44I-class.html#site,Variable Bio.Restriction.Restriction.AlwFI.site=Bio.Restriction.Restriction.AlwFI-class.html#site,Variable Bio.Restriction.Restriction.AlwI.site=Bio.Restriction.Restriction.AlwI-class.html#site,Variable Bio.Restriction.Restriction.AlwNI.site=Bio.Restriction.Restriction.AlwNI-class.html#site,Variable Bio.Restriction.Restriction.Ama87I.site=Bio.Restriction.Restriction.Ama87I-class.html#site,Variable Bio.Restriction.Restriction.Aor13HI.site=Bio.Restriction.Restriction.Aor13HI-class.html#site,Variable Bio.Restriction.Restriction.Aor51HI.site=Bio.Restriction.Restriction.Aor51HI-class.html#site,Variable Bio.Restriction.Restriction.ApaBI.site=Bio.Restriction.Restriction.ApaBI-class.html#site,Variable Bio.Restriction.Restriction.ApaI.site=Bio.Restriction.Restriction.ApaI-class.html#site,Variable Bio.Restriction.Restriction.ApaLI.site=Bio.Restriction.Restriction.ApaLI-class.html#site,Variable Bio.Restriction.Restriction.ApeKI.site=Bio.Restriction.Restriction.ApeKI-class.html#site,Variable Bio.Restriction.Restriction.ApoI.site=Bio.Restriction.Restriction.ApoI-class.html#site,Variable Bio.Restriction.Restriction.ApyPI.site=Bio.Restriction.Restriction.ApyPI-class.html#site,Variable Bio.Restriction.Restriction.AquII.site=Bio.Restriction.Restriction.AquII-class.html#site,Variable Bio.Restriction.Restriction.AquIII.site=Bio.Restriction.Restriction.AquIII-class.html#site,Variable Bio.Restriction.Restriction.AquIV.site=Bio.Restriction.Restriction.AquIV-class.html#site,Variable Bio.Restriction.Restriction.ArsI.site=Bio.Restriction.Restriction.ArsI-class.html#site,Variable Bio.Restriction.Restriction.AscI.site=Bio.Restriction.Restriction.AscI-class.html#site,Variable Bio.Restriction.Restriction.AseI.site=Bio.Restriction.Restriction.AseI-class.html#site,Variable Bio.Restriction.Restriction.Asi256I.site=Bio.Restriction.Restriction.Asi256I-class.html#site,Variable Bio.Restriction.Restriction.AsiGI.site=Bio.Restriction.Restriction.AsiGI-class.html#site,Variable Bio.Restriction.Restriction.AsiSI.site=Bio.Restriction.Restriction.AsiSI-class.html#site,Variable Bio.Restriction.Restriction.Asp700I.site=Bio.Restriction.Restriction.Asp700I-class.html#site,Variable Bio.Restriction.Restriction.Asp718I.site=Bio.Restriction.Restriction.Asp718I-class.html#site,Variable Bio.Restriction.Restriction.AspA2I.site=Bio.Restriction.Restriction.AspA2I-class.html#site,Variable Bio.Restriction.Restriction.AspCNI.site=Bio.Restriction.Restriction.AspCNI-class.html#site,Variable Bio.Restriction.Restriction.AspEI.site=Bio.Restriction.Restriction.AspEI-class.html#site,Variable Bio.Restriction.Restriction.AspI.site=Bio.Restriction.Restriction.AspI-class.html#site,Variable Bio.Restriction.Restriction.AspLEI.site=Bio.Restriction.Restriction.AspLEI-class.html#site,Variable Bio.Restriction.Restriction.AspS9I.site=Bio.Restriction.Restriction.AspS9I-class.html#site,Variable Bio.Restriction.Restriction.AssI.site=Bio.Restriction.Restriction.AssI-class.html#site,Variable Bio.Restriction.Restriction.AsuC2I.site=Bio.Restriction.Restriction.AsuC2I-class.html#site,Variable Bio.Restriction.Restriction.AsuHPI.site=Bio.Restriction.Restriction.AsuHPI-class.html#site,Variable Bio.Restriction.Restriction.AsuI.site=Bio.Restriction.Restriction.AsuI-class.html#site,Variable Bio.Restriction.Restriction.AsuII.site=Bio.Restriction.Restriction.AsuII-class.html#site,Variable Bio.Restriction.Restriction.AsuNHI.site=Bio.Restriction.Restriction.AsuNHI-class.html#site,Variable Bio.Restriction.Restriction.AvaI.site=Bio.Restriction.Restriction.AvaI-class.html#site,Variable Bio.Restriction.Restriction.AvaII.site=Bio.Restriction.Restriction.AvaII-class.html#site,Variable Bio.Restriction.Restriction.AvaIII.site=Bio.Restriction.Restriction.AvaIII-class.html#site,Variable Bio.Restriction.Restriction.AviII.site=Bio.Restriction.Restriction.AviII-class.html#site,Variable Bio.Restriction.Restriction.AvrII.site=Bio.Restriction.Restriction.AvrII-class.html#site,Variable Bio.Restriction.Restriction.AxyI.site=Bio.Restriction.Restriction.AxyI-class.html#site,Variable Bio.Restriction.Restriction.BaeGI.site=Bio.Restriction.Restriction.BaeGI-class.html#site,Variable Bio.Restriction.Restriction.BaeI.site=Bio.Restriction.Restriction.BaeI-class.html#site,Variable Bio.Restriction.Restriction.BalI.site=Bio.Restriction.Restriction.BalI-class.html#site,Variable Bio.Restriction.Restriction.BamHI.site=Bio.Restriction.Restriction.BamHI-class.html#site,Variable Bio.Restriction.Restriction.BanI.site=Bio.Restriction.Restriction.BanI-class.html#site,Variable Bio.Restriction.Restriction.BanII.site=Bio.Restriction.Restriction.BanII-class.html#site,Variable Bio.Restriction.Restriction.BanIII.site=Bio.Restriction.Restriction.BanIII-class.html#site,Variable Bio.Restriction.Restriction.BarI.site=Bio.Restriction.Restriction.BarI-class.html#site,Variable Bio.Restriction.Restriction.BasI.site=Bio.Restriction.Restriction.BasI-class.html#site,Variable Bio.Restriction.Restriction.BauI.site=Bio.Restriction.Restriction.BauI-class.html#site,Variable Bio.Restriction.Restriction.BbeI.site=Bio.Restriction.Restriction.BbeI-class.html#site,Variable Bio.Restriction.Restriction.Bbr7I.site=Bio.Restriction.Restriction.Bbr7I-class.html#site,Variable Bio.Restriction.Restriction.BbrPI.site=Bio.Restriction.Restriction.BbrPI-class.html#site,Variable Bio.Restriction.Restriction.BbsI.site=Bio.Restriction.Restriction.BbsI-class.html#site,Variable Bio.Restriction.Restriction.BbuI.site=Bio.Restriction.Restriction.BbuI-class.html#site,Variable Bio.Restriction.Restriction.Bbv12I.site=Bio.Restriction.Restriction.Bbv12I-class.html#site,Variable Bio.Restriction.Restriction.BbvCI.site=Bio.Restriction.Restriction.BbvCI-class.html#site,Variable Bio.Restriction.Restriction.BbvI.site=Bio.Restriction.Restriction.BbvI-class.html#site,Variable Bio.Restriction.Restriction.BbvII.site=Bio.Restriction.Restriction.BbvII-class.html#site,Variable Bio.Restriction.Restriction.BccI.site=Bio.Restriction.Restriction.BccI-class.html#site,Variable Bio.Restriction.Restriction.Bce83I.site=Bio.Restriction.Restriction.Bce83I-class.html#site,Variable Bio.Restriction.Restriction.BceAI.site=Bio.Restriction.Restriction.BceAI-class.html#site,Variable Bio.Restriction.Restriction.BcefI.site=Bio.Restriction.Restriction.BcefI-class.html#site,Variable Bio.Restriction.Restriction.BcgI.site=Bio.Restriction.Restriction.BcgI-class.html#site,Variable Bio.Restriction.Restriction.BciVI.site=Bio.Restriction.Restriction.BciVI-class.html#site,Variable Bio.Restriction.Restriction.BclI.site=Bio.Restriction.Restriction.BclI-class.html#site,Variable Bio.Restriction.Restriction.BcnI.site=Bio.Restriction.Restriction.BcnI-class.html#site,Variable Bio.Restriction.Restriction.BcuI.site=Bio.Restriction.Restriction.BcuI-class.html#site,Variable Bio.Restriction.Restriction.BdaI.site=Bio.Restriction.Restriction.BdaI-class.html#site,Variable Bio.Restriction.Restriction.BetI.site=Bio.Restriction.Restriction.BetI-class.html#site,Variable Bio.Restriction.Restriction.BfaI.site=Bio.Restriction.Restriction.BfaI-class.html#site,Variable Bio.Restriction.Restriction.BfiI.site=Bio.Restriction.Restriction.BfiI-class.html#site,Variable Bio.Restriction.Restriction.BfmI.site=Bio.Restriction.Restriction.BfmI-class.html#site,Variable Bio.Restriction.Restriction.BfoI.site=Bio.Restriction.Restriction.BfoI-class.html#site,Variable Bio.Restriction.Restriction.BfrI.site=Bio.Restriction.Restriction.BfrI-class.html#site,Variable Bio.Restriction.Restriction.BfuAI.site=Bio.Restriction.Restriction.BfuAI-class.html#site,Variable Bio.Restriction.Restriction.BfuCI.site=Bio.Restriction.Restriction.BfuCI-class.html#site,Variable Bio.Restriction.Restriction.BfuI.site=Bio.Restriction.Restriction.BfuI-class.html#site,Variable Bio.Restriction.Restriction.BglI.site=Bio.Restriction.Restriction.BglI-class.html#site,Variable Bio.Restriction.Restriction.BglII.site=Bio.Restriction.Restriction.BglII-class.html#site,Variable Bio.Restriction.Restriction.BinI.site=Bio.Restriction.Restriction.BinI-class.html#site,Variable Bio.Restriction.Restriction.BisI.site=Bio.Restriction.Restriction.BisI-class.html#site,Variable Bio.Restriction.Restriction.BlnI.site=Bio.Restriction.Restriction.BlnI-class.html#site,Variable Bio.Restriction.Restriction.BlpI.site=Bio.Restriction.Restriction.BlpI-class.html#site,Variable Bio.Restriction.Restriction.BlsI.site=Bio.Restriction.Restriction.BlsI-class.html#site,Variable Bio.Restriction.Restriction.BmcAI.site=Bio.Restriction.Restriction.BmcAI-class.html#site,Variable Bio.Restriction.Restriction.Bme1390I.site=Bio.Restriction.Restriction.Bme1390I-class.html#site,Variable Bio.Restriction.Restriction.Bme18I.site=Bio.Restriction.Restriction.Bme18I-class.html#site,Variable Bio.Restriction.Restriction.BmeRI.site=Bio.Restriction.Restriction.BmeRI-class.html#site,Variable Bio.Restriction.Restriction.BmeT110I.site=Bio.Restriction.Restriction.BmeT110I-class.html#site,Variable Bio.Restriction.Restriction.BmgBI.site=Bio.Restriction.Restriction.BmgBI-class.html#site,Variable Bio.Restriction.Restriction.BmgI.site=Bio.Restriction.Restriction.BmgI-class.html#site,Variable Bio.Restriction.Restriction.BmgT120I.site=Bio.Restriction.Restriction.BmgT120I-class.html#site,Variable Bio.Restriction.Restriction.BmiI.site=Bio.Restriction.Restriction.BmiI-class.html#site,Variable Bio.Restriction.Restriction.BmrFI.site=Bio.Restriction.Restriction.BmrFI-class.html#site,Variable Bio.Restriction.Restriction.BmrI.site=Bio.Restriction.Restriction.BmrI-class.html#site,Variable Bio.Restriction.Restriction.BmsI.site=Bio.Restriction.Restriction.BmsI-class.html#site,Variable Bio.Restriction.Restriction.BmtI.site=Bio.Restriction.Restriction.BmtI-class.html#site,Variable Bio.Restriction.Restriction.BmuI.site=Bio.Restriction.Restriction.BmuI-class.html#site,Variable Bio.Restriction.Restriction.BoxI.site=Bio.Restriction.Restriction.BoxI-class.html#site,Variable Bio.Restriction.Restriction.BpiI.site=Bio.Restriction.Restriction.BpiI-class.html#site,Variable Bio.Restriction.Restriction.BplI.site=Bio.Restriction.Restriction.BplI-class.html#site,Variable Bio.Restriction.Restriction.BpmI.site=Bio.Restriction.Restriction.BpmI-class.html#site,Variable Bio.Restriction.Restriction.Bpu10I.site=Bio.Restriction.Restriction.Bpu10I-class.html#site,Variable Bio.Restriction.Restriction.Bpu1102I.site=Bio.Restriction.Restriction.Bpu1102I-class.html#site,Variable Bio.Restriction.Restriction.Bpu14I.site=Bio.Restriction.Restriction.Bpu14I-class.html#site,Variable Bio.Restriction.Restriction.BpuAI.site=Bio.Restriction.Restriction.BpuAI-class.html#site,Variable Bio.Restriction.Restriction.BpuEI.site=Bio.Restriction.Restriction.BpuEI-class.html#site,Variable Bio.Restriction.Restriction.BpuMI.site=Bio.Restriction.Restriction.BpuMI-class.html#site,Variable Bio.Restriction.Restriction.BpvUI.site=Bio.Restriction.Restriction.BpvUI-class.html#site,Variable Bio.Restriction.Restriction.Bsa29I.site=Bio.Restriction.Restriction.Bsa29I-class.html#site,Variable Bio.Restriction.Restriction.BsaAI.site=Bio.Restriction.Restriction.BsaAI-class.html#site,Variable Bio.Restriction.Restriction.BsaBI.site=Bio.Restriction.Restriction.BsaBI-class.html#site,Variable Bio.Restriction.Restriction.BsaHI.site=Bio.Restriction.Restriction.BsaHI-class.html#site,Variable Bio.Restriction.Restriction.BsaI.site=Bio.Restriction.Restriction.BsaI-class.html#site,Variable Bio.Restriction.Restriction.BsaJI.site=Bio.Restriction.Restriction.BsaJI-class.html#site,Variable Bio.Restriction.Restriction.BsaMI.site=Bio.Restriction.Restriction.BsaMI-class.html#site,Variable Bio.Restriction.Restriction.BsaWI.site=Bio.Restriction.Restriction.BsaWI-class.html#site,Variable Bio.Restriction.Restriction.BsaXI.site=Bio.Restriction.Restriction.BsaXI-class.html#site,Variable Bio.Restriction.Restriction.BsbI.site=Bio.Restriction.Restriction.BsbI-class.html#site,Variable Bio.Restriction.Restriction.Bsc4I.site=Bio.Restriction.Restriction.Bsc4I-class.html#site,Variable Bio.Restriction.Restriction.BscAI.site=Bio.Restriction.Restriction.BscAI-class.html#site,Variable Bio.Restriction.Restriction.BscGI.site=Bio.Restriction.Restriction.BscGI-class.html#site,Variable Bio.Restriction.Restriction.Bse118I.site=Bio.Restriction.Restriction.Bse118I-class.html#site,Variable Bio.Restriction.Restriction.Bse1I.site=Bio.Restriction.Restriction.Bse1I-class.html#site,Variable Bio.Restriction.Restriction.Bse21I.site=Bio.Restriction.Restriction.Bse21I-class.html#site,Variable Bio.Restriction.Restriction.Bse3DI.site=Bio.Restriction.Restriction.Bse3DI-class.html#site,Variable Bio.Restriction.Restriction.Bse8I.site=Bio.Restriction.Restriction.Bse8I-class.html#site,Variable Bio.Restriction.Restriction.BseAI.site=Bio.Restriction.Restriction.BseAI-class.html#site,Variable Bio.Restriction.Restriction.BseBI.site=Bio.Restriction.Restriction.BseBI-class.html#site,Variable Bio.Restriction.Restriction.BseCI.site=Bio.Restriction.Restriction.BseCI-class.html#site,Variable Bio.Restriction.Restriction.BseDI.site=Bio.Restriction.Restriction.BseDI-class.html#site,Variable Bio.Restriction.Restriction.BseGI.site=Bio.Restriction.Restriction.BseGI-class.html#site,Variable Bio.Restriction.Restriction.BseJI.site=Bio.Restriction.Restriction.BseJI-class.html#site,Variable Bio.Restriction.Restriction.BseLI.site=Bio.Restriction.Restriction.BseLI-class.html#site,Variable Bio.Restriction.Restriction.BseMI.site=Bio.Restriction.Restriction.BseMI-class.html#site,Variable Bio.Restriction.Restriction.BseMII.site=Bio.Restriction.Restriction.BseMII-class.html#site,Variable Bio.Restriction.Restriction.BseNI.site=Bio.Restriction.Restriction.BseNI-class.html#site,Variable Bio.Restriction.Restriction.BsePI.site=Bio.Restriction.Restriction.BsePI-class.html#site,Variable Bio.Restriction.Restriction.BseRI.site=Bio.Restriction.Restriction.BseRI-class.html#site,Variable Bio.Restriction.Restriction.BseSI.site=Bio.Restriction.Restriction.BseSI-class.html#site,Variable Bio.Restriction.Restriction.BseX3I.site=Bio.Restriction.Restriction.BseX3I-class.html#site,Variable Bio.Restriction.Restriction.BseXI.site=Bio.Restriction.Restriction.BseXI-class.html#site,Variable Bio.Restriction.Restriction.BseYI.site=Bio.Restriction.Restriction.BseYI-class.html#site,Variable Bio.Restriction.Restriction.BsgI.site=Bio.Restriction.Restriction.BsgI-class.html#site,Variable Bio.Restriction.Restriction.Bsh1236I.site=Bio.Restriction.Restriction.Bsh1236I-class.html#site,Variable Bio.Restriction.Restriction.Bsh1285I.site=Bio.Restriction.Restriction.Bsh1285I-class.html#site,Variable Bio.Restriction.Restriction.BshFI.site=Bio.Restriction.Restriction.BshFI-class.html#site,Variable Bio.Restriction.Restriction.BshNI.site=Bio.Restriction.Restriction.BshNI-class.html#site,Variable Bio.Restriction.Restriction.BshTI.site=Bio.Restriction.Restriction.BshTI-class.html#site,Variable Bio.Restriction.Restriction.BshVI.site=Bio.Restriction.Restriction.BshVI-class.html#site,Variable Bio.Restriction.Restriction.BsiEI.site=Bio.Restriction.Restriction.BsiEI-class.html#site,Variable Bio.Restriction.Restriction.BsiHKAI.site=Bio.Restriction.Restriction.BsiHKAI-class.html#site,Variable Bio.Restriction.Restriction.BsiHKCI.site=Bio.Restriction.Restriction.BsiHKCI-class.html#site,Variable Bio.Restriction.Restriction.BsiI.site=Bio.Restriction.Restriction.BsiI-class.html#site,Variable Bio.Restriction.Restriction.BsiSI.site=Bio.Restriction.Restriction.BsiSI-class.html#site,Variable Bio.Restriction.Restriction.BsiWI.site=Bio.Restriction.Restriction.BsiWI-class.html#site,Variable Bio.Restriction.Restriction.BsiYI.site=Bio.Restriction.Restriction.BsiYI-class.html#site,Variable Bio.Restriction.Restriction.BslFI.site=Bio.Restriction.Restriction.BslFI-class.html#site,Variable Bio.Restriction.Restriction.BslI.site=Bio.Restriction.Restriction.BslI-class.html#site,Variable Bio.Restriction.Restriction.BsmAI.site=Bio.Restriction.Restriction.BsmAI-class.html#site,Variable Bio.Restriction.Restriction.BsmBI.site=Bio.Restriction.Restriction.BsmBI-class.html#site,Variable Bio.Restriction.Restriction.BsmFI.site=Bio.Restriction.Restriction.BsmFI-class.html#site,Variable Bio.Restriction.Restriction.BsmI.site=Bio.Restriction.Restriction.BsmI-class.html#site,Variable Bio.Restriction.Restriction.BsnI.site=Bio.Restriction.Restriction.BsnI-class.html#site,Variable Bio.Restriction.Restriction.Bso31I.site=Bio.Restriction.Restriction.Bso31I-class.html#site,Variable Bio.Restriction.Restriction.BsoBI.site=Bio.Restriction.Restriction.BsoBI-class.html#site,Variable Bio.Restriction.Restriction.Bsp119I.site=Bio.Restriction.Restriction.Bsp119I-class.html#site,Variable Bio.Restriction.Restriction.Bsp120I.site=Bio.Restriction.Restriction.Bsp120I-class.html#site,Variable Bio.Restriction.Restriction.Bsp1286I.site=Bio.Restriction.Restriction.Bsp1286I-class.html#site,Variable Bio.Restriction.Restriction.Bsp13I.site=Bio.Restriction.Restriction.Bsp13I-class.html#site,Variable Bio.Restriction.Restriction.Bsp1407I.site=Bio.Restriction.Restriction.Bsp1407I-class.html#site,Variable Bio.Restriction.Restriction.Bsp143I.site=Bio.Restriction.Restriction.Bsp143I-class.html#site,Variable Bio.Restriction.Restriction.Bsp1720I.site=Bio.Restriction.Restriction.Bsp1720I-class.html#site,Variable Bio.Restriction.Restriction.Bsp19I.site=Bio.Restriction.Restriction.Bsp19I-class.html#site,Variable Bio.Restriction.Restriction.Bsp24I.site=Bio.Restriction.Restriction.Bsp24I-class.html#site,Variable Bio.Restriction.Restriction.Bsp68I.site=Bio.Restriction.Restriction.Bsp68I-class.html#site,Variable Bio.Restriction.Restriction.BspACI.site=Bio.Restriction.Restriction.BspACI-class.html#site,Variable Bio.Restriction.Restriction.BspCNI.site=Bio.Restriction.Restriction.BspCNI-class.html#site,Variable Bio.Restriction.Restriction.BspD6I.site=Bio.Restriction.Restriction.BspD6I-class.html#site,Variable Bio.Restriction.Restriction.BspDI.site=Bio.Restriction.Restriction.BspDI-class.html#site,Variable Bio.Restriction.Restriction.BspEI.site=Bio.Restriction.Restriction.BspEI-class.html#site,Variable Bio.Restriction.Restriction.BspFNI.site=Bio.Restriction.Restriction.BspFNI-class.html#site,Variable Bio.Restriction.Restriction.BspGI.site=Bio.Restriction.Restriction.BspGI-class.html#site,Variable Bio.Restriction.Restriction.BspHI.site=Bio.Restriction.Restriction.BspHI-class.html#site,Variable Bio.Restriction.Restriction.BspLI.site=Bio.Restriction.Restriction.BspLI-class.html#site,Variable Bio.Restriction.Restriction.BspLU11I.site=Bio.Restriction.Restriction.BspLU11I-class.html#site,Variable Bio.Restriction.Restriction.BspMI.site=Bio.Restriction.Restriction.BspMI-class.html#site,Variable Bio.Restriction.Restriction.BspMII.site=Bio.Restriction.Restriction.BspMII-class.html#site,Variable Bio.Restriction.Restriction.BspNCI.site=Bio.Restriction.Restriction.BspNCI-class.html#site,Variable Bio.Restriction.Restriction.BspOI.site=Bio.Restriction.Restriction.BspOI-class.html#site,Variable Bio.Restriction.Restriction.BspPI.site=Bio.Restriction.Restriction.BspPI-class.html#site,Variable Bio.Restriction.Restriction.BspQI.site=Bio.Restriction.Restriction.BspQI-class.html#site,Variable Bio.Restriction.Restriction.BspT104I.site=Bio.Restriction.Restriction.BspT104I-class.html#site,Variable Bio.Restriction.Restriction.BspT107I.site=Bio.Restriction.Restriction.BspT107I-class.html#site,Variable Bio.Restriction.Restriction.BspTI.site=Bio.Restriction.Restriction.BspTI-class.html#site,Variable Bio.Restriction.Restriction.BspTNI.site=Bio.Restriction.Restriction.BspTNI-class.html#site,Variable Bio.Restriction.Restriction.BspXI.site=Bio.Restriction.Restriction.BspXI-class.html#site,Variable Bio.Restriction.Restriction.BsrBI.site=Bio.Restriction.Restriction.BsrBI-class.html#site,Variable Bio.Restriction.Restriction.BsrDI.site=Bio.Restriction.Restriction.BsrDI-class.html#site,Variable Bio.Restriction.Restriction.BsrFI.site=Bio.Restriction.Restriction.BsrFI-class.html#site,Variable Bio.Restriction.Restriction.BsrGI.site=Bio.Restriction.Restriction.BsrGI-class.html#site,Variable Bio.Restriction.Restriction.BsrI.site=Bio.Restriction.Restriction.BsrI-class.html#site,Variable Bio.Restriction.Restriction.BsrSI.site=Bio.Restriction.Restriction.BsrSI-class.html#site,Variable Bio.Restriction.Restriction.BssAI.site=Bio.Restriction.Restriction.BssAI-class.html#site,Variable Bio.Restriction.Restriction.BssECI.site=Bio.Restriction.Restriction.BssECI-class.html#site,Variable Bio.Restriction.Restriction.BssHII.site=Bio.Restriction.Restriction.BssHII-class.html#site,Variable Bio.Restriction.Restriction.BssKI.site=Bio.Restriction.Restriction.BssKI-class.html#site,Variable Bio.Restriction.Restriction.BssMI.site=Bio.Restriction.Restriction.BssMI-class.html#site,Variable Bio.Restriction.Restriction.BssNAI.site=Bio.Restriction.Restriction.BssNAI-class.html#site,Variable Bio.Restriction.Restriction.BssNI.site=Bio.Restriction.Restriction.BssNI-class.html#site,Variable Bio.Restriction.Restriction.BssSI.site=Bio.Restriction.Restriction.BssSI-class.html#site,Variable Bio.Restriction.Restriction.BssT1I.site=Bio.Restriction.Restriction.BssT1I-class.html#site,Variable Bio.Restriction.Restriction.Bst1107I.site=Bio.Restriction.Restriction.Bst1107I-class.html#site,Variable Bio.Restriction.Restriction.Bst2BI.site=Bio.Restriction.Restriction.Bst2BI-class.html#site,Variable Bio.Restriction.Restriction.Bst2UI.site=Bio.Restriction.Restriction.Bst2UI-class.html#site,Variable Bio.Restriction.Restriction.Bst4CI.site=Bio.Restriction.Restriction.Bst4CI-class.html#site,Variable Bio.Restriction.Restriction.Bst6I.site=Bio.Restriction.Restriction.Bst6I-class.html#site,Variable Bio.Restriction.Restriction.Bst98I.site=Bio.Restriction.Restriction.Bst98I-class.html#site,Variable Bio.Restriction.Restriction.BstACI.site=Bio.Restriction.Restriction.BstACI-class.html#site,Variable Bio.Restriction.Restriction.BstAFI.site=Bio.Restriction.Restriction.BstAFI-class.html#site,Variable Bio.Restriction.Restriction.BstAPI.site=Bio.Restriction.Restriction.BstAPI-class.html#site,Variable Bio.Restriction.Restriction.BstAUI.site=Bio.Restriction.Restriction.BstAUI-class.html#site,Variable Bio.Restriction.Restriction.BstBAI.site=Bio.Restriction.Restriction.BstBAI-class.html#site,Variable Bio.Restriction.Restriction.BstBI.site=Bio.Restriction.Restriction.BstBI-class.html#site,Variable Bio.Restriction.Restriction.BstC8I.site=Bio.Restriction.Restriction.BstC8I-class.html#site,Variable Bio.Restriction.Restriction.BstDEI.site=Bio.Restriction.Restriction.BstDEI-class.html#site,Variable Bio.Restriction.Restriction.BstDSI.site=Bio.Restriction.Restriction.BstDSI-class.html#site,Variable Bio.Restriction.Restriction.BstEII.site=Bio.Restriction.Restriction.BstEII-class.html#site,Variable Bio.Restriction.Restriction.BstENI.site=Bio.Restriction.Restriction.BstENI-class.html#site,Variable Bio.Restriction.Restriction.BstF5I.site=Bio.Restriction.Restriction.BstF5I-class.html#site,Variable Bio.Restriction.Restriction.BstFNI.site=Bio.Restriction.Restriction.BstFNI-class.html#site,Variable Bio.Restriction.Restriction.BstH2I.site=Bio.Restriction.Restriction.BstH2I-class.html#site,Variable Bio.Restriction.Restriction.BstHHI.site=Bio.Restriction.Restriction.BstHHI-class.html#site,Variable Bio.Restriction.Restriction.BstKTI.site=Bio.Restriction.Restriction.BstKTI-class.html#site,Variable Bio.Restriction.Restriction.BstMAI.site=Bio.Restriction.Restriction.BstMAI-class.html#site,Variable Bio.Restriction.Restriction.BstMBI.site=Bio.Restriction.Restriction.BstMBI-class.html#site,Variable Bio.Restriction.Restriction.BstMCI.site=Bio.Restriction.Restriction.BstMCI-class.html#site,Variable Bio.Restriction.Restriction.BstMWI.site=Bio.Restriction.Restriction.BstMWI-class.html#site,Variable Bio.Restriction.Restriction.BstNI.site=Bio.Restriction.Restriction.BstNI-class.html#site,Variable Bio.Restriction.Restriction.BstNSI.site=Bio.Restriction.Restriction.BstNSI-class.html#site,Variable Bio.Restriction.Restriction.BstOI.site=Bio.Restriction.Restriction.BstOI-class.html#site,Variable Bio.Restriction.Restriction.BstPAI.site=Bio.Restriction.Restriction.BstPAI-class.html#site,Variable Bio.Restriction.Restriction.BstPI.site=Bio.Restriction.Restriction.BstPI-class.html#site,Variable Bio.Restriction.Restriction.BstSCI.site=Bio.Restriction.Restriction.BstSCI-class.html#site,Variable Bio.Restriction.Restriction.BstSFI.site=Bio.Restriction.Restriction.BstSFI-class.html#site,Variable Bio.Restriction.Restriction.BstSLI.site=Bio.Restriction.Restriction.BstSLI-class.html#site,Variable Bio.Restriction.Restriction.BstSNI.site=Bio.Restriction.Restriction.BstSNI-class.html#site,Variable Bio.Restriction.Restriction.BstUI.site=Bio.Restriction.Restriction.BstUI-class.html#site,Variable Bio.Restriction.Restriction.BstV1I.site=Bio.Restriction.Restriction.BstV1I-class.html#site,Variable Bio.Restriction.Restriction.BstV2I.site=Bio.Restriction.Restriction.BstV2I-class.html#site,Variable Bio.Restriction.Restriction.BstX2I.site=Bio.Restriction.Restriction.BstX2I-class.html#site,Variable Bio.Restriction.Restriction.BstXI.site=Bio.Restriction.Restriction.BstXI-class.html#site,Variable Bio.Restriction.Restriction.BstYI.site=Bio.Restriction.Restriction.BstYI-class.html#site,Variable Bio.Restriction.Restriction.BstZ17I.site=Bio.Restriction.Restriction.BstZ17I-class.html#site,Variable Bio.Restriction.Restriction.BstZI.site=Bio.Restriction.Restriction.BstZI-class.html#site,Variable Bio.Restriction.Restriction.Bsu15I.site=Bio.Restriction.Restriction.Bsu15I-class.html#site,Variable Bio.Restriction.Restriction.Bsu36I.site=Bio.Restriction.Restriction.Bsu36I-class.html#site,Variable Bio.Restriction.Restriction.BsuRI.site=Bio.Restriction.Restriction.BsuRI-class.html#site,Variable Bio.Restriction.Restriction.BsuTUI.site=Bio.Restriction.Restriction.BsuTUI-class.html#site,Variable Bio.Restriction.Restriction.BtgI.site=Bio.Restriction.Restriction.BtgI-class.html#site,Variable Bio.Restriction.Restriction.BtgZI.site=Bio.Restriction.Restriction.BtgZI-class.html#site,Variable Bio.Restriction.Restriction.BthCI.site=Bio.Restriction.Restriction.BthCI-class.html#site,Variable Bio.Restriction.Restriction.BtrI.site=Bio.Restriction.Restriction.BtrI-class.html#site,Variable Bio.Restriction.Restriction.BtsCI.site=Bio.Restriction.Restriction.BtsCI-class.html#site,Variable Bio.Restriction.Restriction.BtsI.site=Bio.Restriction.Restriction.BtsI-class.html#site,Variable Bio.Restriction.Restriction.BtuMI.site=Bio.Restriction.Restriction.BtuMI-class.html#site,Variable Bio.Restriction.Restriction.BveI.site=Bio.Restriction.Restriction.BveI-class.html#site,Variable Bio.Restriction.Restriction.Cac8I.site=Bio.Restriction.Restriction.Cac8I-class.html#site,Variable Bio.Restriction.Restriction.CaiI.site=Bio.Restriction.Restriction.CaiI-class.html#site,Variable Bio.Restriction.Restriction.CauII.site=Bio.Restriction.Restriction.CauII-class.html#site,Variable Bio.Restriction.Restriction.CciI.site=Bio.Restriction.Restriction.CciI-class.html#site,Variable Bio.Restriction.Restriction.CciNI.site=Bio.Restriction.Restriction.CciNI-class.html#site,Variable Bio.Restriction.Restriction.CdiI.site=Bio.Restriction.Restriction.CdiI-class.html#site,Variable Bio.Restriction.Restriction.CdpI.site=Bio.Restriction.Restriction.CdpI-class.html#site,Variable Bio.Restriction.Restriction.CelII.site=Bio.Restriction.Restriction.CelII-class.html#site,Variable Bio.Restriction.Restriction.CfoI.site=Bio.Restriction.Restriction.CfoI-class.html#site,Variable Bio.Restriction.Restriction.Cfr10I.site=Bio.Restriction.Restriction.Cfr10I-class.html#site,Variable Bio.Restriction.Restriction.Cfr13I.site=Bio.Restriction.Restriction.Cfr13I-class.html#site,Variable Bio.Restriction.Restriction.Cfr42I.site=Bio.Restriction.Restriction.Cfr42I-class.html#site,Variable Bio.Restriction.Restriction.Cfr9I.site=Bio.Restriction.Restriction.Cfr9I-class.html#site,Variable Bio.Restriction.Restriction.CfrI.site=Bio.Restriction.Restriction.CfrI-class.html#site,Variable Bio.Restriction.Restriction.ChaI.site=Bio.Restriction.Restriction.ChaI-class.html#site,Variable Bio.Restriction.Restriction.CjeI.site=Bio.Restriction.Restriction.CjeI-class.html#site,Variable Bio.Restriction.Restriction.CjeNII.site=Bio.Restriction.Restriction.CjeNII-class.html#site,Variable Bio.Restriction.Restriction.CjePI.site=Bio.Restriction.Restriction.CjePI-class.html#site,Variable Bio.Restriction.Restriction.CjuI.site=Bio.Restriction.Restriction.CjuI-class.html#site,Variable Bio.Restriction.Restriction.CjuII.site=Bio.Restriction.Restriction.CjuII-class.html#site,Variable Bio.Restriction.Restriction.ClaI.site=Bio.Restriction.Restriction.ClaI-class.html#site,Variable Bio.Restriction.Restriction.CpoI.site=Bio.Restriction.Restriction.CpoI-class.html#site,Variable Bio.Restriction.Restriction.CseI.site=Bio.Restriction.Restriction.CseI-class.html#site,Variable Bio.Restriction.Restriction.CsiI.site=Bio.Restriction.Restriction.CsiI-class.html#site,Variable Bio.Restriction.Restriction.Csp45I.site=Bio.Restriction.Restriction.Csp45I-class.html#site,Variable Bio.Restriction.Restriction.Csp6I.site=Bio.Restriction.Restriction.Csp6I-class.html#site,Variable Bio.Restriction.Restriction.CspAI.site=Bio.Restriction.Restriction.CspAI-class.html#site,Variable Bio.Restriction.Restriction.CspCI.site=Bio.Restriction.Restriction.CspCI-class.html#site,Variable Bio.Restriction.Restriction.CspI.site=Bio.Restriction.Restriction.CspI-class.html#site,Variable Bio.Restriction.Restriction.CstMI.site=Bio.Restriction.Restriction.CstMI-class.html#site,Variable Bio.Restriction.Restriction.CviAII.site=Bio.Restriction.Restriction.CviAII-class.html#site,Variable Bio.Restriction.Restriction.CviJI.site=Bio.Restriction.Restriction.CviJI-class.html#site,Variable Bio.Restriction.Restriction.CviKI_1.site=Bio.Restriction.Restriction.CviKI_1-class.html#site,Variable Bio.Restriction.Restriction.CviQI.site=Bio.Restriction.Restriction.CviQI-class.html#site,Variable Bio.Restriction.Restriction.CviRI.site=Bio.Restriction.Restriction.CviRI-class.html#site,Variable Bio.Restriction.Restriction.DdeI.site=Bio.Restriction.Restriction.DdeI-class.html#site,Variable Bio.Restriction.Restriction.DinI.site=Bio.Restriction.Restriction.DinI-class.html#site,Variable Bio.Restriction.Restriction.DpnI.site=Bio.Restriction.Restriction.DpnI-class.html#site,Variable Bio.Restriction.Restriction.DpnII.site=Bio.Restriction.Restriction.DpnII-class.html#site,Variable Bio.Restriction.Restriction.DraI.site=Bio.Restriction.Restriction.DraI-class.html#site,Variable Bio.Restriction.Restriction.DraII.site=Bio.Restriction.Restriction.DraII-class.html#site,Variable Bio.Restriction.Restriction.DraIII.site=Bio.Restriction.Restriction.DraIII-class.html#site,Variable Bio.Restriction.Restriction.DraRI.site=Bio.Restriction.Restriction.DraRI-class.html#site,Variable Bio.Restriction.Restriction.DrdI.site=Bio.Restriction.Restriction.DrdI-class.html#site,Variable Bio.Restriction.Restriction.DrdII.site=Bio.Restriction.Restriction.DrdII-class.html#site,Variable Bio.Restriction.Restriction.DrdIV.site=Bio.Restriction.Restriction.DrdIV-class.html#site,Variable Bio.Restriction.Restriction.DriI.site=Bio.Restriction.Restriction.DriI-class.html#site,Variable Bio.Restriction.Restriction.DsaI.site=Bio.Restriction.Restriction.DsaI-class.html#site,Variable Bio.Restriction.Restriction.DseDI.site=Bio.Restriction.Restriction.DseDI-class.html#site,Variable Bio.Restriction.Restriction.EaeI.site=Bio.Restriction.Restriction.EaeI-class.html#site,Variable Bio.Restriction.Restriction.EagI.site=Bio.Restriction.Restriction.EagI-class.html#site,Variable Bio.Restriction.Restriction.Eam1104I.site=Bio.Restriction.Restriction.Eam1104I-class.html#site,Variable Bio.Restriction.Restriction.Eam1105I.site=Bio.Restriction.Restriction.Eam1105I-class.html#site,Variable Bio.Restriction.Restriction.EarI.site=Bio.Restriction.Restriction.EarI-class.html#site,Variable Bio.Restriction.Restriction.EciI.site=Bio.Restriction.Restriction.EciI-class.html#site,Variable Bio.Restriction.Restriction.Ecl136II.site=Bio.Restriction.Restriction.Ecl136II-class.html#site,Variable Bio.Restriction.Restriction.EclXI.site=Bio.Restriction.Restriction.EclXI-class.html#site,Variable Bio.Restriction.Restriction.Eco105I.site=Bio.Restriction.Restriction.Eco105I-class.html#site,Variable Bio.Restriction.Restriction.Eco130I.site=Bio.Restriction.Restriction.Eco130I-class.html#site,Variable Bio.Restriction.Restriction.Eco147I.site=Bio.Restriction.Restriction.Eco147I-class.html#site,Variable Bio.Restriction.Restriction.Eco24I.site=Bio.Restriction.Restriction.Eco24I-class.html#site,Variable Bio.Restriction.Restriction.Eco31I.site=Bio.Restriction.Restriction.Eco31I-class.html#site,Variable Bio.Restriction.Restriction.Eco32I.site=Bio.Restriction.Restriction.Eco32I-class.html#site,Variable Bio.Restriction.Restriction.Eco47I.site=Bio.Restriction.Restriction.Eco47I-class.html#site,Variable Bio.Restriction.Restriction.Eco47III.site=Bio.Restriction.Restriction.Eco47III-class.html#site,Variable Bio.Restriction.Restriction.Eco52I.site=Bio.Restriction.Restriction.Eco52I-class.html#site,Variable Bio.Restriction.Restriction.Eco53kI.site=Bio.Restriction.Restriction.Eco53kI-class.html#site,Variable Bio.Restriction.Restriction.Eco57I.site=Bio.Restriction.Restriction.Eco57I-class.html#site,Variable Bio.Restriction.Restriction.Eco57MI.site=Bio.Restriction.Restriction.Eco57MI-class.html#site,Variable Bio.Restriction.Restriction.Eco72I.site=Bio.Restriction.Restriction.Eco72I-class.html#site,Variable Bio.Restriction.Restriction.Eco81I.site=Bio.Restriction.Restriction.Eco81I-class.html#site,Variable Bio.Restriction.Restriction.Eco88I.site=Bio.Restriction.Restriction.Eco88I-class.html#site,Variable Bio.Restriction.Restriction.Eco91I.site=Bio.Restriction.Restriction.Eco91I-class.html#site,Variable Bio.Restriction.Restriction.EcoHI.site=Bio.Restriction.Restriction.EcoHI-class.html#site,Variable Bio.Restriction.Restriction.EcoICRI.site=Bio.Restriction.Restriction.EcoICRI-class.html#site,Variable Bio.Restriction.Restriction.EcoNI.site=Bio.Restriction.Restriction.EcoNI-class.html#site,Variable Bio.Restriction.Restriction.EcoO109I.site=Bio.Restriction.Restriction.EcoO109I-class.html#site,Variable Bio.Restriction.Restriction.EcoO65I.site=Bio.Restriction.Restriction.EcoO65I-class.html#site,Variable Bio.Restriction.Restriction.EcoRI.site=Bio.Restriction.Restriction.EcoRI-class.html#site,Variable Bio.Restriction.Restriction.EcoRII.site=Bio.Restriction.Restriction.EcoRII-class.html#site,Variable Bio.Restriction.Restriction.EcoRV.site=Bio.Restriction.Restriction.EcoRV-class.html#site,Variable Bio.Restriction.Restriction.EcoT14I.site=Bio.Restriction.Restriction.EcoT14I-class.html#site,Variable Bio.Restriction.Restriction.EcoT22I.site=Bio.Restriction.Restriction.EcoT22I-class.html#site,Variable Bio.Restriction.Restriction.EcoT38I.site=Bio.Restriction.Restriction.EcoT38I-class.html#site,Variable Bio.Restriction.Restriction.EgeI.site=Bio.Restriction.Restriction.EgeI-class.html#site,Variable Bio.Restriction.Restriction.EheI.site=Bio.Restriction.Restriction.EheI-class.html#site,Variable Bio.Restriction.Restriction.ErhI.site=Bio.Restriction.Restriction.ErhI-class.html#site,Variable Bio.Restriction.Restriction.EsaBC3I.site=Bio.Restriction.Restriction.EsaBC3I-class.html#site,Variable Bio.Restriction.Restriction.EsaSSI.site=Bio.Restriction.Restriction.EsaSSI-class.html#site,Variable Bio.Restriction.Restriction.Esp3I.site=Bio.Restriction.Restriction.Esp3I-class.html#site,Variable Bio.Restriction.Restriction.EspI.site=Bio.Restriction.Restriction.EspI-class.html#site,Variable Bio.Restriction.Restriction.FaeI.site=Bio.Restriction.Restriction.FaeI-class.html#site,Variable Bio.Restriction.Restriction.FaiI.site=Bio.Restriction.Restriction.FaiI-class.html#site,Variable Bio.Restriction.Restriction.FalI.site=Bio.Restriction.Restriction.FalI-class.html#site,Variable Bio.Restriction.Restriction.FaqI.site=Bio.Restriction.Restriction.FaqI-class.html#site,Variable Bio.Restriction.Restriction.FatI.site=Bio.Restriction.Restriction.FatI-class.html#site,Variable Bio.Restriction.Restriction.FauI.site=Bio.Restriction.Restriction.FauI-class.html#site,Variable Bio.Restriction.Restriction.FauNDI.site=Bio.Restriction.Restriction.FauNDI-class.html#site,Variable Bio.Restriction.Restriction.FbaI.site=Bio.Restriction.Restriction.FbaI-class.html#site,Variable Bio.Restriction.Restriction.FblI.site=Bio.Restriction.Restriction.FblI-class.html#site,Variable Bio.Restriction.Restriction.FinI.site=Bio.Restriction.Restriction.FinI-class.html#site,Variable Bio.Restriction.Restriction.FmuI.site=Bio.Restriction.Restriction.FmuI-class.html#site,Variable Bio.Restriction.Restriction.Fnu4HI.site=Bio.Restriction.Restriction.Fnu4HI-class.html#site,Variable Bio.Restriction.Restriction.FnuDII.site=Bio.Restriction.Restriction.FnuDII-class.html#site,Variable Bio.Restriction.Restriction.FokI.site=Bio.Restriction.Restriction.FokI-class.html#site,Variable Bio.Restriction.Restriction.FriOI.site=Bio.Restriction.Restriction.FriOI-class.html#site,Variable Bio.Restriction.Restriction.FseI.site=Bio.Restriction.Restriction.FseI-class.html#site,Variable Bio.Restriction.Restriction.Fsp4HI.site=Bio.Restriction.Restriction.Fsp4HI-class.html#site,Variable Bio.Restriction.Restriction.FspAI.site=Bio.Restriction.Restriction.FspAI-class.html#site,Variable Bio.Restriction.Restriction.FspBI.site=Bio.Restriction.Restriction.FspBI-class.html#site,Variable Bio.Restriction.Restriction.FspI.site=Bio.Restriction.Restriction.FspI-class.html#site,Variable Bio.Restriction.Restriction.GdiII.site=Bio.Restriction.Restriction.GdiII-class.html#site,Variable Bio.Restriction.Restriction.GlaI.site=Bio.Restriction.Restriction.GlaI-class.html#site,Variable Bio.Restriction.Restriction.GluI.site=Bio.Restriction.Restriction.GluI-class.html#site,Variable Bio.Restriction.Restriction.GsaI.site=Bio.Restriction.Restriction.GsaI-class.html#site,Variable Bio.Restriction.Restriction.GsuI.site=Bio.Restriction.Restriction.GsuI-class.html#site,Variable Bio.Restriction.Restriction.HaeI.site=Bio.Restriction.Restriction.HaeI-class.html#site,Variable Bio.Restriction.Restriction.HaeII.site=Bio.Restriction.Restriction.HaeII-class.html#site,Variable Bio.Restriction.Restriction.HaeIII.site=Bio.Restriction.Restriction.HaeIII-class.html#site,Variable Bio.Restriction.Restriction.HapII.site=Bio.Restriction.Restriction.HapII-class.html#site,Variable Bio.Restriction.Restriction.HgaI.site=Bio.Restriction.Restriction.HgaI-class.html#site,Variable Bio.Restriction.Restriction.HgiAI.site=Bio.Restriction.Restriction.HgiAI-class.html#site,Variable Bio.Restriction.Restriction.HgiCI.site=Bio.Restriction.Restriction.HgiCI-class.html#site,Variable Bio.Restriction.Restriction.HgiEII.site=Bio.Restriction.Restriction.HgiEII-class.html#site,Variable Bio.Restriction.Restriction.HgiJII.site=Bio.Restriction.Restriction.HgiJII-class.html#site,Variable Bio.Restriction.Restriction.HhaI.site=Bio.Restriction.Restriction.HhaI-class.html#site,Variable Bio.Restriction.Restriction.Hin1I.site=Bio.Restriction.Restriction.Hin1I-class.html#site,Variable Bio.Restriction.Restriction.Hin1II.site=Bio.Restriction.Restriction.Hin1II-class.html#site,Variable Bio.Restriction.Restriction.Hin4I.site=Bio.Restriction.Restriction.Hin4I-class.html#site,Variable Bio.Restriction.Restriction.Hin4II.site=Bio.Restriction.Restriction.Hin4II-class.html#site,Variable Bio.Restriction.Restriction.Hin6I.site=Bio.Restriction.Restriction.Hin6I-class.html#site,Variable Bio.Restriction.Restriction.HinP1I.site=Bio.Restriction.Restriction.HinP1I-class.html#site,Variable Bio.Restriction.Restriction.HincII.site=Bio.Restriction.Restriction.HincII-class.html#site,Variable Bio.Restriction.Restriction.HindII.site=Bio.Restriction.Restriction.HindII-class.html#site,Variable Bio.Restriction.Restriction.HindIII.site=Bio.Restriction.Restriction.HindIII-class.html#site,Variable Bio.Restriction.Restriction.HinfI.site=Bio.Restriction.Restriction.HinfI-class.html#site,Variable Bio.Restriction.Restriction.HpaI.site=Bio.Restriction.Restriction.HpaI-class.html#site,Variable Bio.Restriction.Restriction.HpaII.site=Bio.Restriction.Restriction.HpaII-class.html#site,Variable Bio.Restriction.Restriction.HphI.site=Bio.Restriction.Restriction.HphI-class.html#site,Variable Bio.Restriction.Restriction.Hpy166II.site=Bio.Restriction.Restriction.Hpy166II-class.html#site,Variable Bio.Restriction.Restriction.Hpy178III.site=Bio.Restriction.Restriction.Hpy178III-class.html#site,Variable Bio.Restriction.Restriction.Hpy188I.site=Bio.Restriction.Restriction.Hpy188I-class.html#site,Variable Bio.Restriction.Restriction.Hpy188III.site=Bio.Restriction.Restriction.Hpy188III-class.html#site,Variable Bio.Restriction.Restriction.Hpy8I.site=Bio.Restriction.Restriction.Hpy8I-class.html#site,Variable Bio.Restriction.Restriction.Hpy99I.site=Bio.Restriction.Restriction.Hpy99I-class.html#site,Variable Bio.Restriction.Restriction.HpyAV.site=Bio.Restriction.Restriction.HpyAV-class.html#site,Variable Bio.Restriction.Restriction.HpyCH4III.site=Bio.Restriction.Restriction.HpyCH4III-class.html#site,Variable Bio.Restriction.Restriction.HpyCH4IV.site=Bio.Restriction.Restriction.HpyCH4IV-class.html#site,Variable Bio.Restriction.Restriction.HpyCH4V.site=Bio.Restriction.Restriction.HpyCH4V-class.html#site,Variable Bio.Restriction.Restriction.HpyF10VI.site=Bio.Restriction.Restriction.HpyF10VI-class.html#site,Variable Bio.Restriction.Restriction.HpyF3I.site=Bio.Restriction.Restriction.HpyF3I-class.html#site,Variable Bio.Restriction.Restriction.Hsp92I.site=Bio.Restriction.Restriction.Hsp92I-class.html#site,Variable Bio.Restriction.Restriction.Hsp92II.site=Bio.Restriction.Restriction.Hsp92II-class.html#site,Variable Bio.Restriction.Restriction.HspAI.site=Bio.Restriction.Restriction.HspAI-class.html#site,Variable Bio.Restriction.Restriction.ItaI.site=Bio.Restriction.Restriction.ItaI-class.html#site,Variable Bio.Restriction.Restriction.KasI.site=Bio.Restriction.Restriction.KasI-class.html#site,Variable Bio.Restriction.Restriction.KflI.site=Bio.Restriction.Restriction.KflI-class.html#site,Variable Bio.Restriction.Restriction.Kpn2I.site=Bio.Restriction.Restriction.Kpn2I-class.html#site,Variable Bio.Restriction.Restriction.KpnI.site=Bio.Restriction.Restriction.KpnI-class.html#site,Variable Bio.Restriction.Restriction.Ksp22I.site=Bio.Restriction.Restriction.Ksp22I-class.html#site,Variable Bio.Restriction.Restriction.Ksp632I.site=Bio.Restriction.Restriction.Ksp632I-class.html#site,Variable Bio.Restriction.Restriction.KspAI.site=Bio.Restriction.Restriction.KspAI-class.html#site,Variable Bio.Restriction.Restriction.KspI.site=Bio.Restriction.Restriction.KspI-class.html#site,Variable Bio.Restriction.Restriction.Kzo9I.site=Bio.Restriction.Restriction.Kzo9I-class.html#site,Variable Bio.Restriction.Restriction.LguI.site=Bio.Restriction.Restriction.LguI-class.html#site,Variable Bio.Restriction.Restriction.LpnI.site=Bio.Restriction.Restriction.LpnI-class.html#site,Variable Bio.Restriction.Restriction.Lsp1109I.site=Bio.Restriction.Restriction.Lsp1109I-class.html#site,Variable Bio.Restriction.Restriction.LweI.site=Bio.Restriction.Restriction.LweI-class.html#site,Variable Bio.Restriction.Restriction.MabI.site=Bio.Restriction.Restriction.MabI-class.html#site,Variable Bio.Restriction.Restriction.MaeI.site=Bio.Restriction.Restriction.MaeI-class.html#site,Variable Bio.Restriction.Restriction.MaeII.site=Bio.Restriction.Restriction.MaeII-class.html#site,Variable Bio.Restriction.Restriction.MaeIII.site=Bio.Restriction.Restriction.MaeIII-class.html#site,Variable Bio.Restriction.Restriction.MalI.site=Bio.Restriction.Restriction.MalI-class.html#site,Variable Bio.Restriction.Restriction.MaqI.site=Bio.Restriction.Restriction.MaqI-class.html#site,Variable Bio.Restriction.Restriction.MauBI.site=Bio.Restriction.Restriction.MauBI-class.html#site,Variable Bio.Restriction.Restriction.MbiI.site=Bio.Restriction.Restriction.MbiI-class.html#site,Variable Bio.Restriction.Restriction.MboI.site=Bio.Restriction.Restriction.MboI-class.html#site,Variable Bio.Restriction.Restriction.MboII.site=Bio.Restriction.Restriction.MboII-class.html#site,Variable Bio.Restriction.Restriction.McaTI.site=Bio.Restriction.Restriction.McaTI-class.html#site,Variable Bio.Restriction.Restriction.McrI.site=Bio.Restriction.Restriction.McrI-class.html#site,Variable Bio.Restriction.Restriction.MfeI.site=Bio.Restriction.Restriction.MfeI-class.html#site,Variable Bio.Restriction.Restriction.MflI.site=Bio.Restriction.Restriction.MflI-class.html#site,Variable Bio.Restriction.Restriction.MhlI.site=Bio.Restriction.Restriction.MhlI-class.html#site,Variable Bio.Restriction.Restriction.MjaIV.site=Bio.Restriction.Restriction.MjaIV-class.html#site,Variable Bio.Restriction.Restriction.MlsI.site=Bio.Restriction.Restriction.MlsI-class.html#site,Variable Bio.Restriction.Restriction.MluI.site=Bio.Restriction.Restriction.MluI-class.html#site,Variable Bio.Restriction.Restriction.MluNI.site=Bio.Restriction.Restriction.MluNI-class.html#site,Variable Bio.Restriction.Restriction.Mly113I.site=Bio.Restriction.Restriction.Mly113I-class.html#site,Variable Bio.Restriction.Restriction.MlyI.site=Bio.Restriction.Restriction.MlyI-class.html#site,Variable Bio.Restriction.Restriction.MmeI.site=Bio.Restriction.Restriction.MmeI-class.html#site,Variable Bio.Restriction.Restriction.MnlI.site=Bio.Restriction.Restriction.MnlI-class.html#site,Variable Bio.Restriction.Restriction.Mph1103I.site=Bio.Restriction.Restriction.Mph1103I-class.html#site,Variable Bio.Restriction.Restriction.MreI.site=Bio.Restriction.Restriction.MreI-class.html#site,Variable Bio.Restriction.Restriction.MroI.site=Bio.Restriction.Restriction.MroI-class.html#site,Variable Bio.Restriction.Restriction.MroNI.site=Bio.Restriction.Restriction.MroNI-class.html#site,Variable Bio.Restriction.Restriction.MroXI.site=Bio.Restriction.Restriction.MroXI-class.html#site,Variable Bio.Restriction.Restriction.MscI.site=Bio.Restriction.Restriction.MscI-class.html#site,Variable Bio.Restriction.Restriction.MseI.site=Bio.Restriction.Restriction.MseI-class.html#site,Variable Bio.Restriction.Restriction.MslI.site=Bio.Restriction.Restriction.MslI-class.html#site,Variable Bio.Restriction.Restriction.Msp20I.site=Bio.Restriction.Restriction.Msp20I-class.html#site,Variable Bio.Restriction.Restriction.MspA1I.site=Bio.Restriction.Restriction.MspA1I-class.html#site,Variable Bio.Restriction.Restriction.MspCI.site=Bio.Restriction.Restriction.MspCI-class.html#site,Variable Bio.Restriction.Restriction.MspI.site=Bio.Restriction.Restriction.MspI-class.html#site,Variable Bio.Restriction.Restriction.MspR9I.site=Bio.Restriction.Restriction.MspR9I-class.html#site,Variable Bio.Restriction.Restriction.MssI.site=Bio.Restriction.Restriction.MssI-class.html#site,Variable Bio.Restriction.Restriction.MstI.site=Bio.Restriction.Restriction.MstI-class.html#site,Variable Bio.Restriction.Restriction.MunI.site=Bio.Restriction.Restriction.MunI-class.html#site,Variable Bio.Restriction.Restriction.Mva1269I.site=Bio.Restriction.Restriction.Mva1269I-class.html#site,Variable Bio.Restriction.Restriction.MvaI.site=Bio.Restriction.Restriction.MvaI-class.html#site,Variable Bio.Restriction.Restriction.MvnI.site=Bio.Restriction.Restriction.MvnI-class.html#site,Variable Bio.Restriction.Restriction.MvrI.site=Bio.Restriction.Restriction.MvrI-class.html#site,Variable Bio.Restriction.Restriction.MwoI.site=Bio.Restriction.Restriction.MwoI-class.html#site,Variable Bio.Restriction.Restriction.NaeI.site=Bio.Restriction.Restriction.NaeI-class.html#site,Variable Bio.Restriction.Restriction.NarI.site=Bio.Restriction.Restriction.NarI-class.html#site,Variable Bio.Restriction.Restriction.NciI.site=Bio.Restriction.Restriction.NciI-class.html#site,Variable Bio.Restriction.Restriction.NcoI.site=Bio.Restriction.Restriction.NcoI-class.html#site,Variable Bio.Restriction.Restriction.NdeI.site=Bio.Restriction.Restriction.NdeI-class.html#site,Variable Bio.Restriction.Restriction.NdeII.site=Bio.Restriction.Restriction.NdeII-class.html#site,Variable Bio.Restriction.Restriction.NgoAVIII.site=Bio.Restriction.Restriction.NgoAVIII-class.html#site,Variable Bio.Restriction.Restriction.NgoMIV.site=Bio.Restriction.Restriction.NgoMIV-class.html#site,Variable Bio.Restriction.Restriction.NhaXI.site=Bio.Restriction.Restriction.NhaXI-class.html#site,Variable Bio.Restriction.Restriction.NheI.site=Bio.Restriction.Restriction.NheI-class.html#site,Variable Bio.Restriction.Restriction.NlaCI.site=Bio.Restriction.Restriction.NlaCI-class.html#site,Variable Bio.Restriction.Restriction.NlaIII.site=Bio.Restriction.Restriction.NlaIII-class.html#site,Variable Bio.Restriction.Restriction.NlaIV.site=Bio.Restriction.Restriction.NlaIV-class.html#site,Variable Bio.Restriction.Restriction.Nli3877I.site=Bio.Restriction.Restriction.Nli3877I-class.html#site,Variable Bio.Restriction.Restriction.NmeAIII.site=Bio.Restriction.Restriction.NmeAIII-class.html#site,Variable Bio.Restriction.Restriction.NmeDI.site=Bio.Restriction.Restriction.NmeDI-class.html#site,Variable Bio.Restriction.Restriction.NmuCI.site=Bio.Restriction.Restriction.NmuCI-class.html#site,Variable Bio.Restriction.Restriction.NotI.site=Bio.Restriction.Restriction.NotI-class.html#site,Variable Bio.Restriction.Restriction.NruI.site=Bio.Restriction.Restriction.NruI-class.html#site,Variable Bio.Restriction.Restriction.NsbI.site=Bio.Restriction.Restriction.NsbI-class.html#site,Variable Bio.Restriction.Restriction.NsiI.site=Bio.Restriction.Restriction.NsiI-class.html#site,Variable Bio.Restriction.Restriction.NspBII.site=Bio.Restriction.Restriction.NspBII-class.html#site,Variable Bio.Restriction.Restriction.NspI.site=Bio.Restriction.Restriction.NspI-class.html#site,Variable Bio.Restriction.Restriction.NspV.site=Bio.Restriction.Restriction.NspV-class.html#site,Variable Bio.Restriction.Restriction.OliI.site=Bio.Restriction.Restriction.OliI-class.html#site,Variable Bio.Restriction.Restriction.PabI.site=Bio.Restriction.Restriction.PabI-class.html#site,Variable Bio.Restriction.Restriction.PacI.site=Bio.Restriction.Restriction.PacI-class.html#site,Variable Bio.Restriction.Restriction.PaeI.site=Bio.Restriction.Restriction.PaeI-class.html#site,Variable Bio.Restriction.Restriction.PaeR7I.site=Bio.Restriction.Restriction.PaeR7I-class.html#site,Variable Bio.Restriction.Restriction.PagI.site=Bio.Restriction.Restriction.PagI-class.html#site,Variable Bio.Restriction.Restriction.PalAI.site=Bio.Restriction.Restriction.PalAI-class.html#site,Variable Bio.Restriction.Restriction.PasI.site=Bio.Restriction.Restriction.PasI-class.html#site,Variable Bio.Restriction.Restriction.PauI.site=Bio.Restriction.Restriction.PauI-class.html#site,Variable Bio.Restriction.Restriction.PceI.site=Bio.Restriction.Restriction.PceI-class.html#site,Variable Bio.Restriction.Restriction.PciI.site=Bio.Restriction.Restriction.PciI-class.html#site,Variable Bio.Restriction.Restriction.PciSI.site=Bio.Restriction.Restriction.PciSI-class.html#site,Variable Bio.Restriction.Restriction.PctI.site=Bio.Restriction.Restriction.PctI-class.html#site,Variable Bio.Restriction.Restriction.PdiI.site=Bio.Restriction.Restriction.PdiI-class.html#site,Variable Bio.Restriction.Restriction.PdmI.site=Bio.Restriction.Restriction.PdmI-class.html#site,Variable Bio.Restriction.Restriction.PfeI.site=Bio.Restriction.Restriction.PfeI-class.html#site,Variable Bio.Restriction.Restriction.Pfl1108I.site=Bio.Restriction.Restriction.Pfl1108I-class.html#site,Variable Bio.Restriction.Restriction.Pfl23II.site=Bio.Restriction.Restriction.Pfl23II-class.html#site,Variable Bio.Restriction.Restriction.PflFI.site=Bio.Restriction.Restriction.PflFI-class.html#site,Variable Bio.Restriction.Restriction.PflMI.site=Bio.Restriction.Restriction.PflMI-class.html#site,Variable Bio.Restriction.Restriction.PfoI.site=Bio.Restriction.Restriction.PfoI-class.html#site,Variable Bio.Restriction.Restriction.PhoI.site=Bio.Restriction.Restriction.PhoI-class.html#site,Variable Bio.Restriction.Restriction.PinAI.site=Bio.Restriction.Restriction.PinAI-class.html#site,Variable Bio.Restriction.Restriction.PlaDI.site=Bio.Restriction.Restriction.PlaDI-class.html#site,Variable Bio.Restriction.Restriction.Ple19I.site=Bio.Restriction.Restriction.Ple19I-class.html#site,Variable Bio.Restriction.Restriction.PleI.site=Bio.Restriction.Restriction.PleI-class.html#site,Variable Bio.Restriction.Restriction.PmaCI.site=Bio.Restriction.Restriction.PmaCI-class.html#site,Variable Bio.Restriction.Restriction.PmeI.site=Bio.Restriction.Restriction.PmeI-class.html#site,Variable Bio.Restriction.Restriction.PmlI.site=Bio.Restriction.Restriction.PmlI-class.html#site,Variable Bio.Restriction.Restriction.PpiI.site=Bio.Restriction.Restriction.PpiI-class.html#site,Variable Bio.Restriction.Restriction.PpsI.site=Bio.Restriction.Restriction.PpsI-class.html#site,Variable Bio.Restriction.Restriction.Ppu10I.site=Bio.Restriction.Restriction.Ppu10I-class.html#site,Variable 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Bio.Restriction.Restriction.Zsp2I.site" class="py-name" href="#" onclick="return doclink('link-27', 'site', 'link-27');">site</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt id="link-28" class="py-name"><a title="Bio.Restriction.Restriction.AanI.site
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<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-name">seq_record</tt><tt class="py-op">.</tt><tt id="link-29" class="py-name"><a title="Bio.SeqRecord.SeqRecord.letter_annotations" class="py-name" href="#" onclick="return doclink('link-29', 'letter_annotations', 'link-26');">letter_annotations</a></tt><tt class="py-op">[</tt><tt class="py-string">"peak_location"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> \ </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-op">[</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-30" class="py-name"><a title="Bio.Restriction.Restriction.AanI.site
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Bio.Restriction.Restriction.MspA1I.site
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Bio.Restriction.Restriction.MspI.site
Bio.Restriction.Restriction.MspR9I.site
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Bio.Restriction.Restriction.MstI.site
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Bio.Restriction.Restriction.PflMI.site
Bio.Restriction.Restriction.PfoI.site
Bio.Restriction.Restriction.PhoI.site
Bio.Restriction.Restriction.PinAI.site
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Bio.Restriction.Restriction.ScrFI.site
Bio.Restriction.Restriction.SdaI.site
Bio.Restriction.Restriction.SdeAI.site
Bio.Restriction.Restriction.SdeOSI.site
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Bio.Restriction.Restriction.SetI.site
Bio.Restriction.Restriction.SexAI.site
Bio.Restriction.Restriction.SfaAI.site
Bio.Restriction.Restriction.SfaNI.site
Bio.Restriction.Restriction.SfcI.site
Bio.Restriction.Restriction.SfeI.site
Bio.Restriction.Restriction.SfiI.site
Bio.Restriction.Restriction.SfoI.site
Bio.Restriction.Restriction.Sfr274I.site
Bio.Restriction.Restriction.Sfr303I.site
Bio.Restriction.Restriction.SfuI.site
Bio.Restriction.Restriction.SgfI.site
Bio.Restriction.Restriction.SgrAI.site
Bio.Restriction.Restriction.SgrBI.site
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Bio.Restriction.Restriction.SimI.site
Bio.Restriction.Restriction.SinI.site
Bio.Restriction.Restriction.SlaI.site
Bio.Restriction.Restriction.SmaI.site
Bio.Restriction.Restriction.SmiI.site
Bio.Restriction.Restriction.SmiMI.site
Bio.Restriction.Restriction.SmlI.site
Bio.Restriction.Restriction.SmoI.site
Bio.Restriction.Restriction.SmuI.site
Bio.Restriction.Restriction.SnaBI.site
Bio.Restriction.Restriction.SnaI.site
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Bio.Restriction.Restriction.SphI.site
Bio.Restriction.Restriction.SplI.site
Bio.Restriction.Restriction.SpoDI.site
Bio.Restriction.Restriction.SrfI.site
Bio.Restriction.Restriction.Sse232I.site
Bio.Restriction.Restriction.Sse8387I.site
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Bio.Restriction.Restriction.SseBI.site
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Bio.Restriction.Restriction.SspD5I.site
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Bio.Restriction.Restriction.Tru1I.site
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Bio.Restriction.Restriction.TsoI.site
Bio.Restriction.Restriction.Tsp45I.site
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Bio.Restriction.Restriction.Tsp509I.site
Bio.Restriction.Restriction.TspDTI.site
Bio.Restriction.Restriction.TspEI.site
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Bio.Restriction.Restriction.TspMI.site
Bio.Restriction.Restriction.TspRI.site
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Bio.Restriction.Restriction.TstI.site
Bio.Restriction.Restriction.TsuI.site
Bio.Restriction.Restriction.Tth111I.site
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Bio.Restriction.Restriction.UbaF11I.site
Bio.Restriction.Restriction.UbaF12I.site
Bio.Restriction.Restriction.UbaF13I.site
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Bio.Restriction.Restriction.Vha464I.site
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Bio.Restriction.Restriction.VpaK11AI.site
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Bio.Restriction.Restriction.XagI.site
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Bio.Restriction.Restriction.Zsp2I.site" class="py-name" href="#" onclick="return doclink('link-31', 'site', 'link-27');">site</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">phd_record</tt><tt class="py-op">.</tt><tt class="py-name">sites</tt><tt class="py-op">]</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">IndexError</tt><tt class="py-op">:</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-comment"># peak locations are not always there according to</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-comment"># David Gordon (the Consed author)</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-name">seq_record</tt> </tt>
</div><a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-comment">#All done</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> </tt>
<a name="PhdWriter"></a><div id="PhdWriter-def"><a name="L92"></a><tt class="py-lineno"> 92</tt> <a class="py-toggle" href="#" id="PhdWriter-toggle" onclick="return toggle('PhdWriter');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.SeqIO.PhdIO.PhdWriter-class.html">PhdWriter</a><tt class="py-op">(</tt><tt class="py-base-class">SequentialSequenceWriter</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PhdWriter-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="PhdWriter-expanded"><a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-docstring">"""Class to write Phd format files"""</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> </tt>
<a name="PhdWriter.__init__"></a><div id="PhdWriter.__init__-def"><a name="L95"></a><tt class="py-lineno"> 95</tt> <a class="py-toggle" href="#" id="PhdWriter.__init__-toggle" onclick="return toggle('PhdWriter.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqIO.PhdIO.PhdWriter-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">handle</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
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Bio.SwissProt.Reference.__init__
Bio.UniGene.Iterator.__init__
Bio.UniGene.ProtsimLine.__init__
Bio.UniGene.Record.__init__
Bio.UniGene.RecordParser.__init__
Bio.UniGene.STSLine.__init__
Bio.UniGene.SequenceLine.__init__
Bio.UniGene.UnigeneProtsimRecord.__init__
Bio.UniGene.UnigeneRecord.__init__
Bio.UniGene.UnigeneSTSRecord.__init__
Bio.UniGene.UnigeneSequenceRecord.__init__
Bio.UniGene._RecordConsumer.__init__
Bio.UniGene._Scanner.__init__
Bio.Wise.dnal.Statistics.__init__
Bio.Wise.psw.AlignmentColumn.__init__
Bio.Wise.psw.ColumnUnit.__init__
Bio.kNN.kNN.__init__
Bio.pairwise2.affine_penalty.__init__
Bio.pairwise2.dictionary_match.__init__
Bio.pairwise2.identity_match.__init__
BioSQL.BioSeq.DBSeq.__init__
BioSQL.BioSeq.DBSeqRecord.__init__
BioSQL.BioSeqDatabase.Adaptor.__init__
BioSQL.BioSeqDatabase.BioSeqDatabase.__init__
BioSQL.BioSeqDatabase.DBServer.__init__
BioSQL.DBUtils.Generic_dbutils.__init__
BioSQL.Loader.DatabaseLoader.__init__
BioSQL.Loader.DatabaseRemover.__init__" class="py-name" href="#" onclick="return doclink('link-33', '__init__', 'link-33');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt id="link-34" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-34', 'handle', 'link-15');">handle</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> </tt>
<a name="PhdWriter.write_record"></a><div id="PhdWriter.write_record-def"><a name="L98"></a><tt class="py-lineno"> 98</tt> <a class="py-toggle" href="#" id="PhdWriter.write_record-toggle" onclick="return toggle('PhdWriter.write_record');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqIO.PhdIO.PhdWriter-class.html#write_record">write_record</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">record</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PhdWriter.write_record-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PhdWriter.write_record-expanded"><a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-docstring">"""Write a single Phd record to the file."""</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-35" class="py-name"><a title="Bio.SeqRecord.SeqRecord.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-35', 'seq', 'link-19');">seq</a></tt><tt class="py-op">,</tt> <tt class="py-string">"No sequence present in SeqRecord"</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-comment"># This method returns the 'phred_quality' scores or converted</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-comment"># 'solexa_quality' scores if present, else raises a value error</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-name">phred_qualities</tt> <tt class="py-op">=</tt> <tt id="link-36" class="py-name"><a title="Bio.SeqIO.QualityIO" class="py-name" href="#" onclick="return doclink('link-36', 'QualityIO', 'link-12');">QualityIO</a></tt><tt class="py-op">.</tt><tt id="link-37" class="py-name" targets="Function Bio.SeqIO.QualityIO._get_phred_quality()=Bio.SeqIO.QualityIO-module.html#_get_phred_quality"><a title="Bio.SeqIO.QualityIO._get_phred_quality" class="py-name" href="#" onclick="return doclink('link-37', '_get_phred_quality', 'link-37');">_get_phred_quality</a></tt><tt class="py-op">(</tt><tt class="py-name">record</tt><tt class="py-op">)</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-name">peak_locations</tt> <tt class="py-op">=</tt> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-38" class="py-name"><a title="Bio.SeqRecord.SeqRecord.letter_annotations" class="py-name" href="#" onclick="return doclink('link-38', 'letter_annotations', 'link-26');">letter_annotations</a></tt><tt class="py-op">.</tt><tt id="link-39" class="py-name" targets="Method Bio.Crystal.Crystal.get()=Bio.Crystal.Crystal-class.html#get,Method Bio.Data.CodonTable.AmbiguousForwardTable.get()=Bio.Data.CodonTable.AmbiguousForwardTable-class.html#get,Method Bio.Restriction.Restriction.RestrictionBatch.get()=Bio.Restriction.Restriction.RestrictionBatch-class.html#get,Method Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get()=Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder-class.html#get,Method Bio.SeqIO._index.SeqFileRandomAccess.get()=Bio.SeqIO._index.SeqFileRandomAccess-class.html#get,Method Bio.SeqIO._index.SffRandomAccess.get()=Bio.SeqIO._index.SffRandomAccess-class.html#get,Method Bio.SeqIO._index.SffTrimedRandomAccess.get()=Bio.SeqIO._index.SffTrimedRandomAccess-class.html#get,Method Bio.SeqIO._index.UniprotRandomAccess.get()=Bio.SeqIO._index.UniprotRandomAccess-class.html#get,Method Bio.SeqIO._index._IndexedSeqFileDict.get()=Bio.SeqIO._index._IndexedSeqFileDict-class.html#get,Method Bio.SeqIO._index._SQLiteManySeqFilesDict.get()=Bio.SeqIO._index._SQLiteManySeqFilesDict-class.html#get"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqIO._index.SeqFileRandomAccess.get
Bio.SeqIO._index.SffRandomAccess.get
Bio.SeqIO._index.SffTrimedRandomAccess.get
Bio.SeqIO._index.UniprotRandomAccess.get
Bio.SeqIO._index._IndexedSeqFileDict.get
Bio.SeqIO._index._SQLiteManySeqFilesDict.get" class="py-name" href="#" onclick="return doclink('link-39', 'get', 'link-39');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">"peak_location"</tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-40" class="py-name"><a title="Bio.SeqRecord.SeqRecord.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-40', 'seq', 'link-19');">seq</a></tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">phred_qualities</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">"Number of "</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-string">"phd quality scores does not match length of sequence"</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">peak_locations</tt><tt class="py-op">:</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-41" class="py-name"><a title="Bio.SeqRecord.SeqRecord.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-41', 'seq', 'link-19');">seq</a></tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">peak_locations</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">"Number "</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-string">"of peak location scores does not match length of sequence"</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">None</tt> <tt class="py-keyword">in</tt> <tt class="py-name">phred_qualities</tt><tt class="py-op">:</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"A quality value of None was found"</tt><tt class="py-op">)</tt> </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">record</tt><tt class="py-op">.</tt><tt id="link-42" class="py-name"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description
Bio.Phylo.PhyloXMLIO.Writer.description" class="py-name" href="#" onclick="return doclink('link-42', 'description', 'link-24');">description</a></tt><tt class="py-op">.</tt><tt id="link-43" class="py-name" targets="Method Bio.Seq.Seq.startswith()=Bio.Seq.Seq-class.html#startswith"><a title="Bio.Seq.Seq.startswith" class="py-name" href="#" onclick="return doclink('link-43', 'startswith', 'link-43');">startswith</a></tt><tt class="py-op">(</tt><tt class="py-string">"%s "</tt> <tt class="py-op">%</tt> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-44" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Parser.id
Bio.Phylo.PhyloXMLIO.Writer.id" class="py-name" href="#" onclick="return doclink('link-44', 'id', 'link-20');">id</a></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 id="link-45" class="py-name" targets="Method Bio.Blast.NCBIStandalone._AlignmentConsumer.title()=Bio.Blast.NCBIStandalone._AlignmentConsumer-class.html#title,Method Bio.GenBank._FeatureConsumer.title()=Bio.GenBank._FeatureConsumer-class.html#title,Method Bio.GenBank._RecordConsumer.title()=Bio.GenBank._RecordConsumer-class.html#title"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title" class="py-name" href="#" onclick="return doclink('link-45', 'title', 'link-45');">title</a></tt> <tt class="py-op">=</tt> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-46" class="py-name"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description
Bio.Phylo.PhyloXMLIO.Writer.description" class="py-name" href="#" onclick="return doclink('link-46', 'description', 'link-24');">description</a></tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt id="link-47" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title" class="py-name" href="#" onclick="return doclink('link-47', 'title', 'link-45');">title</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"%s %s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-48" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Parser.id
Bio.Phylo.PhyloXMLIO.Writer.id" class="py-name" href="#" onclick="return doclink('link-48', 'id', 'link-20');">id</a></tt><tt class="py-op">,</tt> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-49" class="py-name"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description
Bio.Phylo.PhyloXMLIO.Writer.description" class="py-name" href="#" onclick="return doclink('link-49', 'description', 'link-24');">description</a></tt><tt class="py-op">)</tt> </tt>
<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 id="link-50" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-50', 'handle', 'link-15');">handle</a></tt><tt class="py-op">.</tt><tt id="link-51" class="py-name" targets="Function Bio.AlignIO.write()=Bio.AlignIO-module.html#write,Method Bio.Graphics.GenomeDiagram._Diagram.Diagram.write()=Bio.Graphics.GenomeDiagram._Diagram.Diagram-class.html#write,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.write()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#write,Method Bio.Phylo.NewickIO.Writer.write()=Bio.Phylo.NewickIO.Writer-class.html#write,Function Bio.Phylo.NewickIO.write()=Bio.Phylo.NewickIO-module.html#write,Function Bio.Phylo.NexusIO.write()=Bio.Phylo.NexusIO-module.html#write,Method Bio.Phylo.PhyloXMLIO.Writer.write()=Bio.Phylo.PhyloXMLIO.Writer-class.html#write,Function Bio.Phylo.PhyloXMLIO.write()=Bio.Phylo.PhyloXMLIO-module.html#write,Function Bio.Phylo._io.write()=Bio.Phylo._io-module.html#write,Function Bio.SeqIO.write()=Bio.SeqIO-module.html#write"><a title="Bio.AlignIO.write
Bio.Graphics.GenomeDiagram._Diagram.Diagram.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.Phylo.NewickIO.Writer.write
Bio.Phylo.NewickIO.write
Bio.Phylo.NexusIO.write
Bio.Phylo.PhyloXMLIO.Writer.write
Bio.Phylo.PhyloXMLIO.write
Bio.Phylo._io.write
Bio.SeqIO.write" class="py-name" href="#" onclick="return doclink('link-51', 'write', 'link-51');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"BEGIN_SEQUENCE %s\nBEGIN_COMMENT\n"</tt> \ </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-52" class="py-name" targets="Method Bio.AlignIO.Interfaces.AlignmentWriter.clean()=Bio.AlignIO.Interfaces.AlignmentWriter-class.html#clean,Method Bio.SeqIO.Interfaces.SequenceWriter.clean()=Bio.SeqIO.Interfaces.SequenceWriter-class.html#clean"><a title="Bio.AlignIO.Interfaces.AlignmentWriter.clean
Bio.SeqIO.Interfaces.SequenceWriter.clean" class="py-name" href="#" onclick="return doclink('link-52', 'clean', 'link-52');">clean</a></tt><tt class="py-op">(</tt><tt id="link-53" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title" class="py-name" href="#" onclick="return doclink('link-53', 'title', 'link-45');">title</a></tt><tt class="py-op">)</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">for</tt> <tt class="py-name">annot</tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">.</tt><tt id="link-54" class="py-name" targets="Method Bio.Seq.Seq.lower()=Bio.Seq.Seq-class.html#lower,Method Bio.Seq.UnknownSeq.lower()=Bio.Seq.UnknownSeq-class.html#lower,Method Bio.SeqRecord.SeqRecord.lower()=Bio.SeqRecord.SeqRecord-class.html#lower"><a title="Bio.Seq.Seq.lower
Bio.Seq.UnknownSeq.lower
Bio.SeqRecord.SeqRecord.lower" class="py-name" href="#" onclick="return doclink('link-54', 'lower', 'link-54');">lower</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">k</tt> <tt class="py-keyword">in</tt> <tt id="link-55" class="py-name"><a title="Bio.Sequencing.Phd" class="py-name" href="#" onclick="return doclink('link-55', 'Phd', 'link-5');">Phd</a></tt><tt class="py-op">.</tt><tt id="link-56" class="py-name" targets="Variable Bio.Sequencing.Phd.CKEYWORDS=Bio.Sequencing.Phd-module.html#CKEYWORDS"><a title="Bio.Sequencing.Phd.CKEYWORDS" class="py-name" href="#" onclick="return doclink('link-56', 'CKEYWORDS', 'link-56');">CKEYWORDS</a></tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt id="link-57" class="py-name" targets="Method Bio.Phylo.PhyloXMLIO.Writer.value()=Bio.Phylo.PhyloXMLIO.Writer-class.html#value"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-57', 'value', 'link-57');">value</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">annot</tt> <tt class="py-op">==</tt> <tt class="py-string">"trim"</tt><tt class="py-op">:</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-58" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-58', 'annotations', 'link-25');">annotations</a></tt><tt class="py-op">.</tt><tt id="link-59" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqIO._index.SeqFileRandomAccess.get
Bio.SeqIO._index.SffRandomAccess.get
Bio.SeqIO._index.SffTrimedRandomAccess.get
Bio.SeqIO._index.UniprotRandomAccess.get
Bio.SeqIO._index._IndexedSeqFileDict.get
Bio.SeqIO._index._SQLiteManySeqFilesDict.get" class="py-name" href="#" onclick="return doclink('link-59', 'get', 'link-39');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">"trim"</tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt id="link-60" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-60', 'value', 'link-57');">value</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"%s %s %.4f"</tt> <tt class="py-op">%</tt> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-61" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-61', 'annotations', 'link-25');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-string">"trim"</tt><tt class="py-op">]</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">annot</tt> <tt class="py-op">==</tt> <tt class="py-string">"trace_peak_area_ratio"</tt><tt class="py-op">:</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-62" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-62', 'annotations', 'link-25');">annotations</a></tt><tt class="py-op">.</tt><tt id="link-63" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqIO._index.SeqFileRandomAccess.get
Bio.SeqIO._index.SffRandomAccess.get
Bio.SeqIO._index.SffTrimedRandomAccess.get
Bio.SeqIO._index.UniprotRandomAccess.get
Bio.SeqIO._index._IndexedSeqFileDict.get
Bio.SeqIO._index._SQLiteManySeqFilesDict.get" class="py-name" href="#" onclick="return doclink('link-63', 'get', 'link-39');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">"trace_peak_area_ratio"</tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt id="link-64" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-64', 'value', 'link-57');">value</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"%.4f"</tt> <tt class="py-op">%</tt> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-65" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-65', 'annotations', 'link-25');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-string">"trace_peak_area_ratio"</tt><tt class="py-op">]</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt id="link-66" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-66', 'value', 'link-57');">value</a></tt> <tt class="py-op">=</tt> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-67" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-67', 'annotations', 'link-25');">annotations</a></tt><tt class="py-op">.</tt><tt id="link-68" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqIO._index.SeqFileRandomAccess.get
Bio.SeqIO._index.SffRandomAccess.get
Bio.SeqIO._index.SffTrimedRandomAccess.get
Bio.SeqIO._index.UniprotRandomAccess.get
Bio.SeqIO._index._IndexedSeqFileDict.get
Bio.SeqIO._index._SQLiteManySeqFilesDict.get" class="py-name" href="#" onclick="return doclink('link-68', 'get', 'link-39');">get</a></tt><tt class="py-op">(</tt><tt class="py-name">annot</tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-69" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-69', 'value', 'link-57');">value</a></tt> <tt class="py-keyword">or</tt> <tt id="link-70" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-70', 'value', 'link-57');">value</a></tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-71" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-71', 'handle', 'link-15');">handle</a></tt><tt class="py-op">.</tt><tt id="link-72" class="py-name"><a title="Bio.AlignIO.write
Bio.Graphics.GenomeDiagram._Diagram.Diagram.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.Phylo.NewickIO.Writer.write
Bio.Phylo.NewickIO.write
Bio.Phylo.NexusIO.write
Bio.Phylo.PhyloXMLIO.Writer.write
Bio.Phylo.PhyloXMLIO.write
Bio.Phylo._io.write
Bio.SeqIO.write" class="py-name" href="#" onclick="return doclink('link-72', 'write', 'link-51');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"%s: %s\n"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">annot</tt><tt class="py-op">.</tt><tt id="link-73" class="py-name" targets="Method Bio.Seq.Seq.upper()=Bio.Seq.Seq-class.html#upper,Method Bio.Seq.UnknownSeq.upper()=Bio.Seq.UnknownSeq-class.html#upper,Method Bio.SeqRecord.SeqRecord.upper()=Bio.SeqRecord.SeqRecord-class.html#upper"><a title="Bio.Seq.Seq.upper
Bio.Seq.UnknownSeq.upper
Bio.SeqRecord.SeqRecord.upper" class="py-name" href="#" onclick="return doclink('link-73', 'upper', 'link-73');">upper</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-74" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-74', 'value', 'link-57');">value</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-75" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-75', 'handle', 'link-15');">handle</a></tt><tt class="py-op">.</tt><tt id="link-76" class="py-name"><a title="Bio.AlignIO.write
Bio.Graphics.GenomeDiagram._Diagram.Diagram.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.Phylo.NewickIO.Writer.write
Bio.Phylo.NewickIO.write
Bio.Phylo.NexusIO.write
Bio.Phylo.PhyloXMLIO.Writer.write
Bio.Phylo.PhyloXMLIO.write
Bio.Phylo._io.write
Bio.SeqIO.write" class="py-name" href="#" onclick="return doclink('link-76', 'write', 'link-51');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"END_COMMENT\nBEGIN_DNA\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-77" 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-77', 'i', 'link-77');">i</a></tt><tt class="py-op">,</tt> <tt id="link-78" class="py-name"><a title="Bio.Restriction.Restriction.AanI.site
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Bio.Restriction.Restriction.PspEI.site
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Bio.Restriction.Restriction.SapI.site
Bio.Restriction.Restriction.SaqAI.site
Bio.Restriction.Restriction.SatI.site
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Bio.Restriction.Restriction.SbfI.site
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Bio.Restriction.Restriction.SciI.site
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Bio.Restriction.Restriction.SexAI.site
Bio.Restriction.Restriction.SfaAI.site
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Bio.Restriction.Restriction.SfiI.site
Bio.Restriction.Restriction.SfoI.site
Bio.Restriction.Restriction.Sfr274I.site
Bio.Restriction.Restriction.Sfr303I.site
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Bio.Restriction.Restriction.SgfI.site
Bio.Restriction.Restriction.SgrAI.site
Bio.Restriction.Restriction.SgrBI.site
Bio.Restriction.Restriction.SgrDI.site
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Bio.Restriction.Restriction.SinI.site
Bio.Restriction.Restriction.SlaI.site
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Bio.Restriction.Restriction.SmuI.site
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Bio.Restriction.Restriction.SphI.site
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Bio.Restriction.Restriction.SpoDI.site
Bio.Restriction.Restriction.SrfI.site
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Bio.Restriction.Restriction.Sse8387I.site
Bio.Restriction.Restriction.Sse8647I.site
Bio.Restriction.Restriction.Sse9I.site
Bio.Restriction.Restriction.SseBI.site
Bio.Restriction.Restriction.SsiI.site
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Bio.Restriction.Restriction.SspI.site
Bio.Restriction.Restriction.SstI.site
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Bio.Restriction.Restriction.StsI.site
Bio.Restriction.Restriction.StuI.site
Bio.Restriction.Restriction.StyD4I.site
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Bio.Restriction.Restriction.SwaI.site
Bio.Restriction.Restriction.TaaI.site
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Bio.Restriction.Restriction.TfiI.site
Bio.Restriction.Restriction.TliI.site
Bio.Restriction.Restriction.Tru1I.site
Bio.Restriction.Restriction.Tru9I.site
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Bio.Restriction.Restriction.TseI.site
Bio.Restriction.Restriction.TsoI.site
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Bio.Restriction.Restriction.Tsp4CI.site
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Bio.Restriction.Restriction.UbaF12I.site
Bio.Restriction.Restriction.UbaF13I.site
Bio.Restriction.Restriction.UbaF14I.site
Bio.Restriction.Restriction.UbaF9I.site
Bio.Restriction.Restriction.UbaPI.site
Bio.Restriction.Restriction.UnbI.site
Bio.Restriction.Restriction.Van91I.site
Bio.Restriction.Restriction.Vha464I.site
Bio.Restriction.Restriction.VneI.site
Bio.Restriction.Restriction.VpaK11AI.site
Bio.Restriction.Restriction.VpaK11BI.site
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Bio.Restriction.Restriction.XagI.site
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Bio.Restriction.Restriction.XbaI.site
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Bio.Restriction.Restriction.XhoI.site
Bio.Restriction.Restriction.XhoII.site
Bio.Restriction.Restriction.XmaCI.site
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Bio.Restriction.Restriction.XmiI.site
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Bio.Restriction.Restriction.ZraI.site
Bio.Restriction.Restriction.ZrmI.site
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BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-79', 'seq', 'link-19');">seq</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
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Bio.Graphics.GenomeDiagram._Diagram.Diagram.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.Phylo.NewickIO.Writer.write
Bio.Phylo.NewickIO.write
Bio.Phylo.NexusIO.write
Bio.Phylo.PhyloXMLIO.Writer.write
Bio.Phylo.PhyloXMLIO.write
Bio.Phylo._io.write
Bio.SeqIO.write" class="py-name" href="#" onclick="return doclink('link-81', 'write', 'link-51');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"%s %i %i\n"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt id="link-82" class="py-name"><a title="Bio.Restriction.Restriction.AanI.site
Bio.Restriction.Restriction.AarI.site
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Bio.Restriction.Restriction.PspGI.site
Bio.Restriction.Restriction.PspLI.site
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Bio.Restriction.Restriction.PspPRI.site
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Bio.Restriction.Restriction.PsrI.site
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Bio.Restriction.Restriction.PstI.site
Bio.Restriction.Restriction.PsuI.site
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Bio.Restriction.Restriction.PteI.site
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Bio.Restriction.Restriction.PvuII.site
Bio.Restriction.Restriction.RcaI.site
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Bio.Restriction.Restriction.RgaI.site
Bio.Restriction.Restriction.RigI.site
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Bio.Restriction.Restriction.RpaB5I.site
Bio.Restriction.Restriction.RruI.site
Bio.Restriction.Restriction.RsaI.site
Bio.Restriction.Restriction.RsaNI.site
Bio.Restriction.Restriction.RseI.site
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Bio.Restriction.Restriction.SacI.site
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Bio.Restriction.Restriction.SalI.site
Bio.Restriction.Restriction.SanDI.site
Bio.Restriction.Restriction.SapI.site
Bio.Restriction.Restriction.SaqAI.site
Bio.Restriction.Restriction.SatI.site
Bio.Restriction.Restriction.Sau3AI.site
Bio.Restriction.Restriction.Sau96I.site
Bio.Restriction.Restriction.SauI.site
Bio.Restriction.Restriction.SbfI.site
Bio.Restriction.Restriction.ScaI.site
Bio.Restriction.Restriction.SchI.site
Bio.Restriction.Restriction.SciI.site
Bio.Restriction.Restriction.ScrFI.site
Bio.Restriction.Restriction.SdaI.site
Bio.Restriction.Restriction.SdeAI.site
Bio.Restriction.Restriction.SdeOSI.site
Bio.Restriction.Restriction.SduI.site
Bio.Restriction.Restriction.SecI.site
Bio.Restriction.Restriction.SelI.site
Bio.Restriction.Restriction.SetI.site
Bio.Restriction.Restriction.SexAI.site
Bio.Restriction.Restriction.SfaAI.site
Bio.Restriction.Restriction.SfaNI.site
Bio.Restriction.Restriction.SfcI.site
Bio.Restriction.Restriction.SfeI.site
Bio.Restriction.Restriction.SfiI.site
Bio.Restriction.Restriction.SfoI.site
Bio.Restriction.Restriction.Sfr274I.site
Bio.Restriction.Restriction.Sfr303I.site
Bio.Restriction.Restriction.SfuI.site
Bio.Restriction.Restriction.SgfI.site
Bio.Restriction.Restriction.SgrAI.site
Bio.Restriction.Restriction.SgrBI.site
Bio.Restriction.Restriction.SgrDI.site
Bio.Restriction.Restriction.SgsI.site
Bio.Restriction.Restriction.SimI.site
Bio.Restriction.Restriction.SinI.site
Bio.Restriction.Restriction.SlaI.site
Bio.Restriction.Restriction.SmaI.site
Bio.Restriction.Restriction.SmiI.site
Bio.Restriction.Restriction.SmiMI.site
Bio.Restriction.Restriction.SmlI.site
Bio.Restriction.Restriction.SmoI.site
Bio.Restriction.Restriction.SmuI.site
Bio.Restriction.Restriction.SnaBI.site
Bio.Restriction.Restriction.SnaI.site
Bio.Restriction.Restriction.SpeI.site
Bio.Restriction.Restriction.SphI.site
Bio.Restriction.Restriction.SplI.site
Bio.Restriction.Restriction.SpoDI.site
Bio.Restriction.Restriction.SrfI.site
Bio.Restriction.Restriction.Sse232I.site
Bio.Restriction.Restriction.Sse8387I.site
Bio.Restriction.Restriction.Sse8647I.site
Bio.Restriction.Restriction.Sse9I.site
Bio.Restriction.Restriction.SseBI.site
Bio.Restriction.Restriction.SsiI.site
Bio.Restriction.Restriction.SspD5I.site
Bio.Restriction.Restriction.SspDI.site
Bio.Restriction.Restriction.SspI.site
Bio.Restriction.Restriction.SstI.site
Bio.Restriction.Restriction.SstII.site
Bio.Restriction.Restriction.Sth132I.site
Bio.Restriction.Restriction.Sth302II.site
Bio.Restriction.Restriction.StrI.site
Bio.Restriction.Restriction.StsI.site
Bio.Restriction.Restriction.StuI.site
Bio.Restriction.Restriction.StyD4I.site
Bio.Restriction.Restriction.StyI.site
Bio.Restriction.Restriction.SwaI.site
Bio.Restriction.Restriction.TaaI.site
Bio.Restriction.Restriction.TaiI.site
Bio.Restriction.Restriction.TaqI.site
Bio.Restriction.Restriction.TaqII.site
Bio.Restriction.Restriction.TatI.site
Bio.Restriction.Restriction.TauI.site
Bio.Restriction.Restriction.TfiI.site
Bio.Restriction.Restriction.TliI.site
Bio.Restriction.Restriction.Tru1I.site
Bio.Restriction.Restriction.Tru9I.site
Bio.Restriction.Restriction.TscAI.site
Bio.Restriction.Restriction.TseI.site
Bio.Restriction.Restriction.TsoI.site
Bio.Restriction.Restriction.Tsp45I.site
Bio.Restriction.Restriction.Tsp4CI.site
Bio.Restriction.Restriction.Tsp509I.site
Bio.Restriction.Restriction.TspDTI.site
Bio.Restriction.Restriction.TspEI.site
Bio.Restriction.Restriction.TspGWI.site
Bio.Restriction.Restriction.TspMI.site
Bio.Restriction.Restriction.TspRI.site
Bio.Restriction.Restriction.TssI.site
Bio.Restriction.Restriction.TstI.site
Bio.Restriction.Restriction.TsuI.site
Bio.Restriction.Restriction.Tth111I.site
Bio.Restriction.Restriction.Tth111II.site
Bio.Restriction.Restriction.UbaF11I.site
Bio.Restriction.Restriction.UbaF12I.site
Bio.Restriction.Restriction.UbaF13I.site
Bio.Restriction.Restriction.UbaF14I.site
Bio.Restriction.Restriction.UbaF9I.site
Bio.Restriction.Restriction.UbaPI.site
Bio.Restriction.Restriction.UnbI.site
Bio.Restriction.Restriction.Van91I.site
Bio.Restriction.Restriction.Vha464I.site
Bio.Restriction.Restriction.VneI.site
Bio.Restriction.Restriction.VpaK11AI.site
Bio.Restriction.Restriction.VpaK11BI.site
Bio.Restriction.Restriction.VspI.site
Bio.Restriction.Restriction.XagI.site
Bio.Restriction.Restriction.XapI.site
Bio.Restriction.Restriction.XbaI.site
Bio.Restriction.Restriction.XceI.site
Bio.Restriction.Restriction.XcmI.site
Bio.Restriction.Restriction.XhoI.site
Bio.Restriction.Restriction.XhoII.site
Bio.Restriction.Restriction.XmaCI.site
Bio.Restriction.Restriction.XmaI.site
Bio.Restriction.Restriction.XmaIII.site
Bio.Restriction.Restriction.XmaJI.site
Bio.Restriction.Restriction.XmiI.site
Bio.Restriction.Restriction.XmnI.site
Bio.Restriction.Restriction.XspI.site
Bio.Restriction.Restriction.ZraI.site
Bio.Restriction.Restriction.ZrmI.site
Bio.Restriction.Restriction.Zsp2I.site" class="py-name" href="#" onclick="return doclink('link-88', 'site', 'link-27');">site</a></tt><tt class="py-op">,</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt id="link-89" class="py-name"><a title="Bio.Blast.NCBIStandalone._BlastConsumer.round
Bio.Blast.NCBIStandalone._DescriptionConsumer.round" class="py-name" href="#" onclick="return doclink('link-89', 'round', 'link-83');">round</a></tt><tt class="py-op">(</tt><tt class="py-name">phred_qualities</tt><tt class="py-op">[</tt><tt id="link-90" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-90', 'i', 'link-77');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-91" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-91', 'handle', 'link-15');">handle</a></tt><tt class="py-op">.</tt><tt id="link-92" class="py-name"><a title="Bio.AlignIO.write
Bio.Graphics.GenomeDiagram._Diagram.Diagram.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.Phylo.NewickIO.Writer.write
Bio.Phylo.NewickIO.write
Bio.Phylo.NexusIO.write
Bio.Phylo.PhyloXMLIO.Writer.write
Bio.Phylo.PhyloXMLIO.write
Bio.Phylo._io.write
Bio.SeqIO.write" class="py-name" href="#" onclick="return doclink('link-92', 'write', 'link-51');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"END_DNA\nEND_SEQUENCE\n"</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> </tt>
<a name="_test"></a><div id="_test-def"><a name="L147"></a><tt class="py-lineno">147</tt> <a class="py-toggle" href="#" id="_test-toggle" onclick="return toggle('_test');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqIO.PhdIO-module.html#_test">_test</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_test-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_test-expanded"><a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt class="py-docstring">"""Run the Bio.SeqIO.PhdIO module's doctests.</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"><tt class="py-docstring"> This will try and locate the unit tests directory, and run the doctests</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"><tt class="py-docstring"> from there in order that the relative paths used in the examples work.</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">doctest</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">os</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">isdir</tt><tt class="py-op">(</tt><tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-string">".."</tt><tt class="py-op">,</tt> <tt class="py-string">".."</tt><tt class="py-op">,</tt> <tt class="py-string">"Tests"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"Runing doctests..."</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-name">cur_dir</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">abspath</tt><tt class="py-op">(</tt><tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">curdir</tt><tt class="py-op">)</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">chdir</tt><tt class="py-op">(</tt><tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-string">".."</tt><tt class="py-op">,</tt> <tt class="py-string">".."</tt><tt class="py-op">,</tt> <tt class="py-string">"Tests"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">isfile</tt><tt class="py-op">(</tt><tt class="py-string">"Phd/phd1"</tt><tt class="py-op">)</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-name">doctest</tt><tt class="py-op">.</tt><tt class="py-name">testmod</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">chdir</tt><tt class="py-op">(</tt><tt class="py-name">cur_dir</tt><tt class="py-op">)</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-keyword">del</tt> <tt class="py-name">cur_dir</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"Done"</tt> </tt>
</div><a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"><tt class="py-keyword">if</tt> <tt class="py-name">__name__</tt> <tt class="py-op">==</tt> <tt class="py-string">"__main__"</tt><tt class="py-op">:</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt id="link-93" class="py-name" targets="Function Bio.Align.Applications._Clustalw._test()=Bio.Align.Applications._Clustalw-module.html#_test,Function Bio.Align.Applications._Dialign._test()=Bio.Align.Applications._Dialign-module.html#_test,Function Bio.Align.Applications._Mafft._test()=Bio.Align.Applications._Mafft-module.html#_test,Function Bio.Align.Applications._Muscle._test()=Bio.Align.Applications._Muscle-module.html#_test,Function Bio.Align.Applications._Prank._test()=Bio.Align.Applications._Prank-module.html#_test,Function Bio.Align.Applications._Probcons._test()=Bio.Align.Applications._Probcons-module.html#_test,Function Bio.Align.Applications._TCoffee._test()=Bio.Align.Applications._TCoffee-module.html#_test,Function Bio.Align.Generic._test()=Bio.Align.Generic-module.html#_test,Function Bio.Align._test()=Bio.Align-module.html#_test,Function Bio.AlignIO.StockholmIO._test()=Bio.AlignIO.StockholmIO-module.html#_test,Function Bio.AlignIO._test()=Bio.AlignIO-module.html#_test,Function Bio.Application._test()=Bio.Application-module.html#_test,Function Bio.Blast.Applications._test()=Bio.Blast.Applications-module.html#_test,Function Bio.DocSQL._test()=Bio.DocSQL-module.html#_test,Function Bio.Emboss.Applications._test()=Bio.Emboss.Applications-module.html#_test,Function Bio.KEGG.Compound._test()=Bio.KEGG.Compound-module.html#_test,Function Bio.KEGG.Enzyme._test()=Bio.KEGG.Enzyme-module.html#_test,Function Bio.Motif._test()=Bio.Motif-module.html#_test,Function Bio.PDB.Selection._test()=Bio.PDB.Selection-module.html#_test,Function Bio.Seq._test()=Bio.Seq-module.html#_test,Function Bio.SeqFeature._test()=Bio.SeqFeature-module.html#_test,Function Bio.SeqIO.AceIO._test()=Bio.SeqIO.AceIO-module.html#_test,Function Bio.SeqIO.PhdIO._test()=Bio.SeqIO.PhdIO-module.html#_test,Function Bio.SeqIO.QualityIO._test()=Bio.SeqIO.QualityIO-module.html#_test,Function Bio.SeqIO._test()=Bio.SeqIO-module.html#_test,Function Bio.SeqRecord._test()=Bio.SeqRecord-module.html#_test,Function Bio.SeqUtils._test()=Bio.SeqUtils-module.html#_test,Function Bio.Sequencing.Applications._Novoalign._test()=Bio.Sequencing.Applications._Novoalign-module.html#_test,Function Bio.Statistics.lowess._test()=Bio.Statistics.lowess-module.html#_test,Function Bio.Wise._test()=Bio.Wise-module.html#_test,Function Bio.Wise.dnal._test()=Bio.Wise.dnal-module.html#_test,Function Bio.Wise.psw._test()=Bio.Wise.psw-module.html#_test"><a title="Bio.Align.Applications._Clustalw._test
Bio.Align.Applications._Dialign._test
Bio.Align.Applications._Mafft._test
Bio.Align.Applications._Muscle._test
Bio.Align.Applications._Prank._test
Bio.Align.Applications._Probcons._test
Bio.Align.Applications._TCoffee._test
Bio.Align.Generic._test
Bio.Align._test
Bio.AlignIO.StockholmIO._test
Bio.AlignIO._test
Bio.Application._test
Bio.Blast.Applications._test
Bio.DocSQL._test
Bio.Emboss.Applications._test
Bio.KEGG.Compound._test
Bio.KEGG.Enzyme._test
Bio.Motif._test
Bio.PDB.Selection._test
Bio.Seq._test
Bio.SeqFeature._test
Bio.SeqIO.AceIO._test
Bio.SeqIO.PhdIO._test
Bio.SeqIO.QualityIO._test
Bio.SeqIO._test
Bio.SeqRecord._test
Bio.SeqUtils._test
Bio.Sequencing.Applications._Novoalign._test
Bio.Statistics.lowess._test
Bio.Wise._test
Bio.Wise.dnal._test
Bio.Wise.psw._test" class="py-name" href="#" onclick="return doclink('link-93', '_test', 'link-93');">_test</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> </tt><script type="text/javascript">
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</pre>
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