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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.SeqUtils-module.html">Package SeqUtils</a> ::
Module CheckSum
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<h1 class="epydoc">Source Code for <a href="Bio.SeqUtils.CheckSum-module.html">Module Bio.SeqUtils.CheckSum</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># crc32, crc64, gcg, and seguid</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># crc64 is adapted from BioPerl</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-keyword">from</tt> <tt class="py-name">binascii</tt> <tt class="py-keyword">import</tt> <tt id="link-0" class="py-name" targets="Function Bio.SeqUtils.CheckSum.crc32()=Bio.SeqUtils.CheckSum-module.html#crc32"><a title="Bio.SeqUtils.CheckSum.crc32" class="py-name" href="#" onclick="return doclink('link-0', 'crc32', 'link-0');">crc32</a></tt> <tt class="py-keyword">as</tt> <tt class="py-name">_crc32</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"> </tt>
<a name="crc32"></a><div id="crc32-def"><a name="L6"></a><tt class="py-lineno"> 6</tt> <a class="py-toggle" href="#" id="crc32-toggle" onclick="return toggle('crc32');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils.CheckSum-module.html#crc32">crc32</a><tt class="py-op">(</tt><tt class="py-param">seq</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="crc32-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="crc32-expanded"><a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns the crc32 checksum for a sequence (string or Seq object)"""</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"> <tt class="py-keyword">try</tt> <tt class="py-op">:</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"> <tt class="py-comment">#Assume its a Seq object</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt class="py-name">_crc32</tt><tt class="py-op">(</tt><tt id="link-1" class="py-name" targets="Method Bio.GFF.Feature.seq()=Bio.GFF.Feature-class.html#seq,Method Bio.GFF.FeatureAggregate.seq()=Bio.GFF.FeatureAggregate-class.html#seq,Variable BioSQL.BioSeq.DBSeqRecord.seq=BioSQL.BioSeq.DBSeqRecord-class.html#seq"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-1', 'seq', 'link-1');">seq</a></tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Method Bio.Crystal.Crystal.tostring()=Bio.Crystal.Crystal-class.html#tostring,Method Bio.EUtils.POM.ElementNode.tostring()=Bio.EUtils.POM.ElementNode-class.html#tostring,Method Bio.Prosite.Pattern.Prosite.tostring()=Bio.Prosite.Pattern.Prosite-class.html#tostring,Method Bio.Seq.MutableSeq.tostring()=Bio.Seq.MutableSeq-class.html#tostring,Method Bio.Seq.Seq.tostring()=Bio.Seq.Seq-class.html#tostring,Method BioSQL.BioSeq.DBSeq.tostring()=BioSQL.BioSeq.DBSeq-class.html#tostring"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-2', 'tostring', 'link-2');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">AttributeError</tt> <tt class="py-op">:</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"> <tt class="py-comment">#Assume its a string</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt class="py-name">_crc32</tt><tt class="py-op">(</tt><tt id="link-3" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-3', 'seq', 'link-1');">seq</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"> </tt>
<a name="_init_table_h"></a><div id="_init_table_h-def"><a name="L15"></a><tt class="py-lineno"> 15</tt> <a class="py-toggle" href="#" id="_init_table_h-toggle" onclick="return toggle('_init_table_h');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils.CheckSum-module.html#_init_table_h">_init_table_h</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_init_table_h-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_init_table_h-expanded"><a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"> <tt id="link-4" class="py-name" targets="Variable Bio.SeqUtils.CheckSum._table_h=Bio.SeqUtils.CheckSum-module.html#_table_h"><a title="Bio.SeqUtils.CheckSum._table_h" class="py-name" href="#" onclick="return doclink('link-4', '_table_h', 'link-4');">_table_h</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-5" 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-5', 'i', 'link-5');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">256</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"> <tt class="py-name">l</tt> <tt class="py-op">=</tt> <tt id="link-6" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-6', 'i', 'link-5');">i</a></tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"> <tt class="py-name">part_h</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">j</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">8</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"> <tt class="py-name">rflag</tt> <tt class="py-op">=</tt> <tt class="py-name">l</tt> <tt class="py-op">&</tt> <tt class="py-number">1</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"> <tt class="py-name">l</tt> <tt class="py-op">>>=</tt> <tt class="py-number">1</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">part_h</tt> <tt class="py-op">&</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> <tt class="py-name">l</tt> <tt class="py-op">|=</tt> <tt class="py-op">(</tt><tt class="py-number">1L</tt> <tt class="py-op"><<</tt> <tt class="py-number">31</tt><tt class="py-op">)</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"> <tt class="py-name">part_h</tt> <tt class="py-op">>>=</tt> <tt class="py-number">1L</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">rflag</tt><tt class="py-op">:</tt> <tt class="py-name">part_h</tt> <tt class="py-op">^=</tt> <tt class="py-number">0xd8000000L</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"> <tt id="link-7" class="py-name"><a title="Bio.SeqUtils.CheckSum._table_h" class="py-name" href="#" onclick="return doclink('link-7', '_table_h', 'link-4');">_table_h</a></tt><tt class="py-op">.</tt><tt id="link-8" class="py-name" targets="Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-class.html#append,Method Bio.EUtils.POM.ElementNode.append()=Bio.EUtils.POM.ElementNode-class.html#append,Method Bio.EUtils.sourcegen.SourceFile.append()=Bio.EUtils.sourcegen.SourceFile-class.html#append,Method Bio.SCOP.Raf.SeqMap.append()=Bio.SCOP.Raf.SeqMap-class.html#append,Method Bio.Seq.MutableSeq.append()=Bio.Seq.MutableSeq-class.html#append,Method Bio.Wise.psw.Alignment.append()=Bio.Wise.psw.Alignment-class.html#append,Method Bio.Wise.psw.AlignmentColumn.append()=Bio.Wise.psw.AlignmentColumn-class.html#append,Method Martel.msre_parse.SubPattern.append()=Martel.msre_parse.SubPattern-class.html#append"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-8', 'append', 'link-8');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">part_h</tt><tt class="py-op">)</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-9" class="py-name"><a title="Bio.SeqUtils.CheckSum._table_h" class="py-name" href="#" onclick="return doclink('link-9', '_table_h', 'link-4');">_table_h</a></tt> </tt>
</div><a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-comment"># Initialisation</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-10" class="py-name"><a title="Bio.SeqUtils.CheckSum._table_h" class="py-name" href="#" onclick="return doclink('link-10', '_table_h', 'link-4');">_table_h</a></tt> <tt class="py-op">=</tt> <tt id="link-11" class="py-name" targets="Function Bio.SeqUtils.CheckSum._init_table_h()=Bio.SeqUtils.CheckSum-module.html#_init_table_h"><a title="Bio.SeqUtils.CheckSum._init_table_h" class="py-name" href="#" onclick="return doclink('link-11', '_init_table_h', 'link-11');">_init_table_h</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"> </tt>
<a name="crc64"></a><div id="crc64-def"><a name="L32"></a><tt class="py-lineno"> 32</tt> <a class="py-toggle" href="#" id="crc64-toggle" onclick="return toggle('crc64');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils.CheckSum-module.html#crc64">crc64</a><tt class="py-op">(</tt><tt class="py-param">s</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="crc64-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="crc64-expanded"><a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns the crc64 checksum for a sequence (string or Seq object)"""</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"> <tt class="py-name">crcl</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> <tt class="py-name">crch</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">c</tt> <tt class="py-keyword">in</tt> <tt id="link-12" class="py-name" targets="Variable Martel.test.test_swissprot38.s=Martel.test.test_swissprot38-module.html#s"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-12', 's', 'link-12');">s</a></tt><tt class="py-op">:</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt class="py-name">shr</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">crch</tt> <tt class="py-op">&</tt> <tt class="py-number">0xFF</tt><tt class="py-op">)</tt> <tt class="py-op"><<</tt> <tt class="py-number">24</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt class="py-name">temp1h</tt> <tt class="py-op">=</tt> <tt class="py-name">crch</tt> <tt class="py-op">>></tt> <tt class="py-number">8</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt class="py-name">temp1l</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">crcl</tt> <tt class="py-op">>></tt> <tt class="py-number">8</tt><tt class="py-op">)</tt> <tt class="py-op">|</tt> <tt class="py-name">shr</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> <tt class="py-name">idx</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">crcl</tt> <tt class="py-op">^</tt> <tt class="py-name">ord</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">&</tt> <tt class="py-number">0xFF</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-name">crch</tt> <tt class="py-op">=</tt> <tt class="py-name">temp1h</tt> <tt class="py-op">^</tt> <tt id="link-13" class="py-name"><a title="Bio.SeqUtils.CheckSum._table_h" class="py-name" href="#" onclick="return doclink('link-13', '_table_h', 'link-4');">_table_h</a></tt><tt class="py-op">[</tt><tt class="py-name">idx</tt><tt class="py-op">]</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt class="py-name">crcl</tt> <tt class="py-op">=</tt> <tt class="py-name">temp1l</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"CRC-%08X%08X"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">crch</tt><tt class="py-op">,</tt> <tt class="py-name">crcl</tt><tt class="py-op">)</tt> </tt>
</div><a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> </tt>
<a name="gcg"></a><div id="gcg-def"><a name="L47"></a><tt class="py-lineno"> 47</tt> <a class="py-toggle" href="#" id="gcg-toggle" onclick="return toggle('gcg');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils.CheckSum-module.html#gcg">gcg</a><tt class="py-op">(</tt><tt class="py-param">seq</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="gcg-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="gcg-expanded"><a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns the GCG checksum (int) for a sequence (string or Seq object)</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-docstring"> Given a nucleotide or amino-acid secuence (or any string),</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"><tt class="py-docstring"> returns the GCG checksum (int). Checksum used by GCG program.</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"><tt class="py-docstring"> seq type = str.</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"><tt class="py-docstring"> Based on BioPerl GCG_checksum. Adapted by Sebastian Bassi</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"><tt class="py-docstring"> with the help of John Lenton, Pablo Ziliani, and Gabriel Genellina.</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"><tt class="py-docstring"> All sequences are converted to uppercase """</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt id="link-14" class="py-name" targets="Method Bio.Crystal.Chain.index()=Bio.Crystal.Chain-class.html#index,Method Bio.EUtils.POM.ElementNode.index()=Bio.EUtils.POM.ElementNode-class.html#index,Method Bio.SCOP.Raf.SeqMap.index()=Bio.SCOP.Raf.SeqMap-class.html#index,Method Bio.Seq.MutableSeq.index()=Bio.Seq.MutableSeq-class.html#index"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-14', 'index', 'link-14');">index</a></tt> <tt class="py-op">=</tt> <tt class="py-name">checksum</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-15" class="py-name" targets="Variable Bio.GenBank.LocationParser.Integer.type=Bio.GenBank.LocationParser.Integer-class.html#type,Variable Bio.GenBank.LocationParser.Symbol.type=Bio.GenBank.LocationParser.Symbol-class.html#type,Variable Bio.GenBank.LocationParser.UnsignedInteger.type=Bio.GenBank.LocationParser.UnsignedInteger-class.html#type"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-15', 'type', 'link-15');">type</a></tt><tt class="py-op">(</tt><tt id="link-16" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-16', 'seq', 'link-1');">seq</a></tt><tt class="py-op">)</tt><tt class="py-op">!=</tt><tt id="link-17" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-17', 'type', 'link-15');">type</a></tt><tt class="py-op">(</tt><tt class="py-string">"aa"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt id="link-18" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-18', 'seq', 'link-1');">seq</a></tt><tt class="py-op">=</tt><tt id="link-19" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-19', 'seq', 'link-1');">seq</a></tt><tt class="py-op">.</tt><tt id="link-20" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-20', 'tostring', 'link-2');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">char</tt> <tt class="py-keyword">in</tt> <tt id="link-21" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-21', 'seq', 'link-1');">seq</a></tt><tt class="py-op">:</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt id="link-22" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-22', 'index', 'link-14');">index</a></tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-name">checksum</tt> <tt class="py-op">+=</tt> <tt id="link-23" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-23', 'index', 'link-14');">index</a></tt> <tt class="py-op">*</tt> <tt class="py-name">ord</tt><tt class="py-op">(</tt><tt class="py-name">char</tt><tt class="py-op">.</tt><tt class="py-name">upper</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-24" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-24', 'index', 'link-14');">index</a></tt> <tt class="py-op">==</tt> <tt class="py-number">57</tt><tt class="py-op">:</tt> <tt id="link-25" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-25', 'index', 'link-14');">index</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">checksum</tt> <tt class="py-op">%</tt> <tt class="py-number">10000</tt> </tt>
</div><a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> </tt>
<a name="seguid"></a><div id="seguid-def"><a name="L65"></a><tt class="py-lineno"> 65</tt> <a class="py-toggle" href="#" id="seguid-toggle" onclick="return toggle('seguid');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils.CheckSum-module.html#seguid">seguid</a><tt class="py-op">(</tt><tt class="py-param">seq</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="seguid-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="seguid-expanded"><a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns the SEGUID (string) for a sequence (string or Seq object)</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"><tt class="py-docstring"> Given a nucleotide or amino-acid secuence (or any string),</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"><tt class="py-docstring"> returns the SEGUID string (A SEquence Globally Unique IDentifier).</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"><tt class="py-docstring"> seq type = str. </tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"><tt class="py-docstring"> For more information about SEGUID, see:</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"><tt class="py-docstring"> http://bioinformatics.anl.gov/seguid/</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"><tt class="py-docstring"> DOI: 10.1002/pmic.200600032 """</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-comment">#Python 2.5 sha1 is in hashlib</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">import</tt> <tt class="py-name">hashlib</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-name">m</tt> <tt class="py-op">=</tt> <tt class="py-name">hashlib</tt><tt class="py-op">.</tt><tt class="py-name">sha1</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-comment">#For older versions </tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">import</tt> <tt class="py-name">sha</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-name">m</tt> <tt class="py-op">=</tt> <tt class="py-name">sha</tt><tt class="py-op">.</tt><tt class="py-name">new</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">base64</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-26" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-26', 'type', 'link-15');">type</a></tt><tt class="py-op">(</tt><tt id="link-27" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-27', 'seq', 'link-1');">seq</a></tt><tt class="py-op">)</tt><tt class="py-op">!=</tt><tt id="link-28" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-28', 'type', 'link-15');">type</a></tt><tt class="py-op">(</tt><tt class="py-string">"aa"</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 id="link-29" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-29', 'seq', 'link-1');">seq</a></tt><tt class="py-op">=</tt><tt id="link-30" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-30', 'seq', 'link-1');">seq</a></tt><tt class="py-op">.</tt><tt id="link-31" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-31', 'tostring', 'link-2');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">upper</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt id="link-32" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-32', 'seq', 'link-1');">seq</a></tt><tt class="py-op">=</tt><tt id="link-33" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-33', 'seq', 'link-1');">seq</a></tt><tt class="py-op">.</tt><tt class="py-name">upper</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-name">m</tt><tt class="py-op">.</tt><tt id="link-34" class="py-name" targets="Method Bio.GenBank.NCBIDictionary.update()=Bio.GenBank.NCBIDictionary-class.html#update,Method Bio.Index._InMemoryIndex.update()=Bio.Index._InMemoryIndex-class.html#update,Method Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.update()=Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer-class.html#update,Method Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.update()=Bio.NeuralNetwork.BackPropagation.Layer.InputLayer-class.html#update,Method Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.update()=Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer-class.html#update,Method Bio.Prosite.ExPASyDictionary.update()=Bio.Prosite.ExPASyDictionary-class.html#update,Method Bio.Prosite.Prodoc.ExPASyDictionary.update()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#update,Method Bio.PubMed.Dictionary.update()=Bio.PubMed.Dictionary-class.html#update,Method Bio.Restriction._Update.Update.RebaseUpdate.update()=Bio.Restriction._Update.Update.RebaseUpdate-class.html#update,Method Bio.SwissProt.SProt.ExPASyDictionary.update()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#update"><a title="Bio.GenBank.NCBIDictionary.update
Bio.Index._InMemoryIndex.update
Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.update
Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.update
Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.update
Bio.Prosite.ExPASyDictionary.update
Bio.Prosite.Prodoc.ExPASyDictionary.update
Bio.PubMed.Dictionary.update
Bio.Restriction._Update.Update.RebaseUpdate.update
Bio.SwissProt.SProt.ExPASyDictionary.update" class="py-name" href="#" onclick="return doclink('link-34', 'update', 'link-34');">update</a></tt><tt class="py-op">(</tt><tt id="link-35" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-35', 'seq', 'link-1');">seq</a></tt><tt class="py-op">)</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-comment">#For Python 2.5</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt class="py-name">base64</tt><tt class="py-op">.</tt><tt class="py-name">b64encode</tt><tt class="py-op">(</tt><tt class="py-name">m</tt><tt class="py-op">.</tt><tt class="py-name">digest</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">rstrip</tt><tt class="py-op">(</tt><tt class="py-string">"="</tt><tt class="py-op">)</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-comment">#For older versions</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">import</tt> <tt class="py-name">os</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-comment">#Note: Using os.linesep doesn't work on Windows,</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#where os.linesep= "\r\n" but the encoded string</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#contains "\n" but not "\r\n"</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt class="py-name">base64</tt><tt class="py-op">.</tt><tt class="py-name">encodestring</tt><tt class="py-op">(</tt><tt class="py-name">m</tt><tt class="py-op">.</tt><tt class="py-name">digest</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">"\n"</tt><tt class="py-op">,</tt><tt class="py-string">""</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">rstrip</tt><tt class="py-op">(</tt><tt class="py-string">"="</tt><tt class="py-op">)</tt> </tt>
</div><a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</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="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"Quick self test"</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-name">str_light_chain_one</tt> <tt class="py-op">=</tt> <tt class="py-string">"QSALTQPASVSGSPGQSITISCTGTSSDVGSYNLVSWYQQHPGK"</tt> \ </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-op">+</tt> <tt class="py-string">"APKLMIYEGSKRPSGVSNRFSGSKSGNTASLTISGLQAEDEADY"</tt> \ </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-op">+</tt> <tt class="py-string">"YCSSYAGSSTLVFGGGTKLTVL"</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-name">str_light_chain_two</tt> <tt class="py-op">=</tt> <tt class="py-string">"QSALTQPASVSGSPGQSITISCTGTSSDVGSYNLVSWYQQHPGK"</tt> \ </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-op">+</tt> <tt class="py-string">"APKLMIYEGSKRPSGVSNRFSGSKSGNTASLTISGLQAEDEADY"</tt> \ </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-op">+</tt> <tt class="py-string">"YCCSYAGSSTWVFGGGTKLTVL"</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-36" class="py-name" targets="Function Bio.SeqUtils.CheckSum.crc64()=Bio.SeqUtils.CheckSum-module.html#crc64"><a title="Bio.SeqUtils.CheckSum.crc64" class="py-name" href="#" onclick="return doclink('link-36', 'crc64', 'link-36');">crc64</a></tt><tt class="py-op">(</tt><tt class="py-name">str_light_chain_one</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt id="link-37" class="py-name"><a title="Bio.SeqUtils.CheckSum.crc64" class="py-name" href="#" onclick="return doclink('link-37', 'crc64', 'link-36');">crc64</a></tt><tt class="py-op">(</tt><tt class="py-name">str_light_chain_two</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">assert</tt> <tt class="py-string">'CRC-44CAAD88706CC153'</tt> <tt class="py-op">==</tt> <tt id="link-38" class="py-name"><a title="Bio.SeqUtils.CheckSum.crc64" class="py-name" href="#" onclick="return doclink('link-38', 'crc64', 'link-36');">crc64</a></tt><tt class="py-op">(</tt><tt class="py-name">str_light_chain_one</tt><tt class="py-op">)</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-string">'BpBeDdcNUYNsdk46JoJdw7Pd3BI'</tt> <tt class="py-op">==</tt> <tt id="link-39" class="py-name" targets="Function Bio.SeqUtils.CheckSum.seguid()=Bio.SeqUtils.CheckSum-module.html#seguid"><a title="Bio.SeqUtils.CheckSum.seguid" class="py-name" href="#" onclick="return doclink('link-39', 'seguid', 'link-39');">seguid</a></tt><tt class="py-op">(</tt><tt class="py-name">str_light_chain_one</tt><tt class="py-op">)</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-string">'X5XEaayob1nZLOc7eVT9qyczarY'</tt> <tt class="py-op">==</tt> <tt id="link-40" class="py-name"><a title="Bio.SeqUtils.CheckSum.seguid" class="py-name" href="#" onclick="return doclink('link-40', 'seguid', 'link-39');">seguid</a></tt><tt class="py-op">(</tt><tt class="py-name">str_light_chain_two</tt><tt class="py-op">)</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"Done"</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> </tt><script type="text/javascript">
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