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Module dnal
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<h1 class="epydoc">Source Code for <a href="Bio.Wise.dnal-module.html">Module Bio.Wise.dnal</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment">#!/usr/bin/env python</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"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Bio.Wise contains modules for running and processing the output of</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># some of the models in the Wise2 package by Ewan Birney available from:</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># ftp://ftp.ebi.ac.uk/pub/software/unix/wise2/</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># http://www.ebi.ac.uk/Wise2/</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># </tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Bio.Wise.psw is for protein Smith-Waterman alignments</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Bio.Wise.dnal is for Smith-Waterman DNA alignments</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">__future__</tt> <tt class="py-keyword">import</tt> <tt class="py-name">division</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-name">__version__</tt> <tt class="py-op">=</tt> <tt class="py-string">"$Revision: 1.11 $"</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">commands</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">itertools</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">os</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">re</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</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-keyword">import</tt> <tt id="link-1" class="py-name" targets="Package Bio.Wise=Bio.Wise-module.html"><a title="Bio.Wise" class="py-name" href="#" onclick="return doclink('link-1', 'Wise', 'link-1');">Wise</a></tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt id="link-2" class="py-name" targets="Variable Bio.Wise.dnal._SCORE_MATCH=Bio.Wise.dnal-module.html#_SCORE_MATCH"><a title="Bio.Wise.dnal._SCORE_MATCH" class="py-name" href="#" onclick="return doclink('link-2', '_SCORE_MATCH', 'link-2');">_SCORE_MATCH</a></tt> <tt class="py-op">=</tt> <tt class="py-number">4</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt id="link-3" class="py-name" targets="Variable Bio.Wise.dnal._SCORE_MISMATCH=Bio.Wise.dnal-module.html#_SCORE_MISMATCH"><a title="Bio.Wise.dnal._SCORE_MISMATCH" class="py-name" href="#" onclick="return doclink('link-3', '_SCORE_MISMATCH', 'link-3');">_SCORE_MISMATCH</a></tt> <tt class="py-op">=</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt id="link-4" class="py-name" targets="Variable Bio.Wise.dnal._SCORE_GAP_START=Bio.Wise.dnal-module.html#_SCORE_GAP_START"><a title="Bio.Wise.dnal._SCORE_GAP_START" class="py-name" href="#" onclick="return doclink('link-4', '_SCORE_GAP_START', 'link-4');">_SCORE_GAP_START</a></tt> <tt class="py-op">=</tt> <tt class="py-op">-</tt><tt class="py-number">5</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt id="link-5" class="py-name" targets="Variable Bio.Wise.dnal._SCORE_GAP_EXTENSION=Bio.Wise.dnal-module.html#_SCORE_GAP_EXTENSION"><a title="Bio.Wise.dnal._SCORE_GAP_EXTENSION" class="py-name" href="#" onclick="return doclink('link-5', '_SCORE_GAP_EXTENSION', 'link-5');">_SCORE_GAP_EXTENSION</a></tt> <tt class="py-op">=</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt id="link-6" class="py-name" targets="Variable Bio.Wise.dnal._CMDLINE_DNAL=Bio.Wise.dnal-module.html#_CMDLINE_DNAL"><a title="Bio.Wise.dnal._CMDLINE_DNAL" class="py-name" href="#" onclick="return doclink('link-6', '_CMDLINE_DNAL', 'link-6');">_CMDLINE_DNAL</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-string">"dnal"</tt><tt class="py-op">,</tt> <tt class="py-string">"-alb"</tt><tt class="py-op">,</tt> <tt class="py-string">"-nopretty"</tt><tt class="py-op">]</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"> </tt>
<a name="_build_dnal_cmdline"></a><div id="_build_dnal_cmdline-def"><a name="L32"></a><tt class="py-lineno"> 32</tt> <a class="py-toggle" href="#" id="_build_dnal_cmdline-toggle" onclick="return toggle('_build_dnal_cmdline');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Wise.dnal-module.html#_build_dnal_cmdline">_build_dnal_cmdline</a><tt class="py-op">(</tt><tt class="py-param">match</tt><tt class="py-op">,</tt> <tt class="py-param">mismatch</tt><tt class="py-op">,</tt> <tt class="py-param">gap</tt><tt class="py-op">,</tt> <tt class="py-param">extension</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_build_dnal_cmdline-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_build_dnal_cmdline-expanded"><a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> <tt class="py-name">res</tt> <tt class="py-op">=</tt> <tt id="link-7" class="py-name"><a title="Bio.Wise.dnal._CMDLINE_DNAL" class="py-name" href="#" onclick="return doclink('link-7', '_CMDLINE_DNAL', 'link-6');">_CMDLINE_DNAL</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">.</tt><tt id="link-8" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.extend()=Bio.EUtils.POM.ElementNode-class.html#extend,Method Bio.SCOP.Raf.SeqMap.extend()=Bio.SCOP.Raf.SeqMap-class.html#extend,Method Bio.Seq.MutableSeq.extend()=Bio.Seq.MutableSeq-class.html#extend"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-8', 'extend', 'link-8');">extend</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-match"</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-9" class="py-name" targets="Method Bio.Parsers.spark.GenericASTMatcher.match()=Bio.Parsers.spark.GenericASTMatcher-class.html#match,Method Bio.Prosite.Pattern.Prosite.match()=Bio.Prosite.Pattern.Prosite-class.html#match,Function Bio.triefind.match()=Bio.triefind-module.html#match,Method Martel.msre_parse.Tokenizer.match()=Martel.msre_parse.Tokenizer-class.html#match"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-9', 'match', 'link-9');">match</a></tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">.</tt><tt id="link-10" class="py-name"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-10', 'extend', 'link-8');">extend</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-mis"</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">mismatch</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">.</tt><tt id="link-11" class="py-name"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-11', 'extend', 'link-8');">extend</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-gap"</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-op">-</tt><tt class="py-name">gap</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-comment"># negative: convert score to penalty</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">.</tt><tt id="link-12" class="py-name"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-12', 'extend', 'link-8');">extend</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-ext"</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-op">-</tt><tt class="py-name">extension</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-comment"># negative: convert score to penalty</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">res</tt> </tt>
</div><a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"><tt id="link-13" class="py-name" targets="Variable Bio.Wise.dnal._CMDLINE_FGREP_COUNT=Bio.Wise.dnal-module.html#_CMDLINE_FGREP_COUNT"><a title="Bio.Wise.dnal._CMDLINE_FGREP_COUNT" class="py-name" href="#" onclick="return doclink('link-13', '_CMDLINE_FGREP_COUNT', 'link-13');">_CMDLINE_FGREP_COUNT</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"fgrep -c '%s' %s"</tt> </tt>
<a name="_fgrep_count"></a><div id="_fgrep_count-def"><a name="L42"></a><tt class="py-lineno"> 42</tt> <a class="py-toggle" href="#" id="_fgrep_count-toggle" onclick="return toggle('_fgrep_count');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Wise.dnal-module.html#_fgrep_count">_fgrep_count</a><tt class="py-op">(</tt><tt class="py-param">pattern</tt><tt class="py-op">,</tt> <tt class="py-param">file</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_fgrep_count-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_fgrep_count-expanded"><a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">commands</tt><tt class="py-op">.</tt><tt class="py-name">getoutput</tt><tt class="py-op">(</tt><tt id="link-14" class="py-name"><a title="Bio.Wise.dnal._CMDLINE_FGREP_COUNT" class="py-name" href="#" onclick="return doclink('link-14', '_CMDLINE_FGREP_COUNT', 'link-13');">_CMDLINE_FGREP_COUNT</a></tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-15" class="py-name" targets="Method Bio.Prosite._RecordConsumer.pattern()=Bio.Prosite._RecordConsumer-class.html#pattern"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-15', 'pattern', 'link-15');">pattern</a></tt><tt class="py-op">,</tt> <tt class="py-name">file</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt id="link-16" class="py-name" targets="Variable Bio.Wise.dnal._re_alb_line2coords=Bio.Wise.dnal-module.html#_re_alb_line2coords"><a title="Bio.Wise.dnal._re_alb_line2coords" class="py-name" href="#" onclick="return doclink('link-16', '_re_alb_line2coords', 'link-16');">_re_alb_line2coords</a></tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name" targets="Function Bio.Prosite.Pattern.compile()=Bio.Prosite.Pattern-module.html#compile"><a title="Bio.Prosite.Pattern.compile" class="py-name" href="#" onclick="return doclink('link-17', 'compile', 'link-17');">compile</a></tt><tt class="py-op">(</tt><tt class="py-string">r"^\[([^:]+):[^\[]+\[([^:]+):"</tt><tt class="py-op">)</tt> </tt>
<a name="_alb_line2coords"></a><div id="_alb_line2coords-def"><a name="L46"></a><tt class="py-lineno"> 46</tt> <a class="py-toggle" href="#" id="_alb_line2coords-toggle" onclick="return toggle('_alb_line2coords');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Wise.dnal-module.html#_alb_line2coords">_alb_line2coords</a><tt class="py-op">(</tt><tt class="py-param">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_alb_line2coords-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_alb_line2coords-expanded"><a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">coord</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-number">1</tt> <tt class="py-comment"># one-based -> zero-based</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">coord</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt class="py-keyword">in</tt> <tt id="link-18" class="py-name"><a title="Bio.Wise.dnal._re_alb_line2coords" class="py-name" href="#" onclick="return doclink('link-18', '_re_alb_line2coords', 'link-16');">_re_alb_line2coords</a></tt><tt class="py-op">.</tt><tt id="link-19" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-19', 'match', 'link-9');">match</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name" targets="Method Bio.Prosite.Pattern.PrositeMatch.groups()=Bio.Prosite.Pattern.PrositeMatch-class.html#groups"><a title="Bio.Prosite.Pattern.PrositeMatch.groups" class="py-name" href="#" onclick="return doclink('link-20', 'groups', 'link-20');">groups</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
</div><a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> </tt>
<a name="_get_coords"></a><div id="_get_coords-def"><a name="L51"></a><tt class="py-lineno"> 51</tt> <a class="py-toggle" href="#" id="_get_coords-toggle" onclick="return toggle('_get_coords');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Wise.dnal-module.html#_get_coords">_get_coords</a><tt class="py-op">(</tt><tt class="py-param">filename</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_get_coords-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_get_coords-expanded"><a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> <tt class="py-name">alb</tt> <tt class="py-op">=</tt> <tt class="py-name">file</tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-name">start_line</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-name">end_line</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt class="py-name">alb</tt><tt class="py-op">:</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">"["</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">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">start_line</tt><tt class="py-op">:</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-name">start_line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt> <tt class="py-comment"># rstrip not needed</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-name">end_line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">end_line</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> <tt class="py-comment"># sequence is too short</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">zip</tt><tt class="py-op">(</tt><tt class="py-op">*</tt><tt id="link-21" class="py-name" targets="Method Bio.GFF.FeatureAggregate.map()=Bio.GFF.FeatureAggregate-class.html#map"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-21', 'map', 'link-21');">map</a></tt><tt class="py-op">(</tt><tt id="link-22" class="py-name" targets="Function Bio.Wise.dnal._alb_line2coords()=Bio.Wise.dnal-module.html#_alb_line2coords"><a title="Bio.Wise.dnal._alb_line2coords" class="py-name" href="#" onclick="return doclink('link-22', '_alb_line2coords', 'link-22');">_alb_line2coords</a></tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-name">start_line</tt><tt class="py-op">,</tt> <tt class="py-name">end_line</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-comment"># returns [(start0, end0), (start1, end1)]</tt> </tt>
</div><a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> </tt>
<a name="_any"></a><div id="_any-def"><a name="L69"></a><tt class="py-lineno"> 69</tt> <a class="py-toggle" href="#" id="_any-toggle" onclick="return toggle('_any');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Wise.dnal-module.html#_any">_any</a><tt class="py-op">(</tt><tt class="py-param">seq</tt><tt class="py-op">,</tt> <tt class="py-param">pred</tt><tt class="py-op">=</tt><tt class="py-name">bool</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_any-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_any-expanded"><a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-docstring">"Returns True if pred(x) is True at least one element in the iterable"</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-23" class="py-name" targets="Variable Bio.EUtils.POM.True=Bio.EUtils.POM-module.html#True"><a title="Bio.EUtils.POM.True" class="py-name" href="#" onclick="return doclink('link-23', 'True', 'link-23');">True</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">itertools</tt><tt class="py-op">.</tt><tt class="py-name">imap</tt><tt class="py-op">(</tt><tt class="py-name">pred</tt><tt class="py-op">,</tt> <tt id="link-24" 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-24', 'seq', 'link-24');">seq</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> </tt>
<a name="Statistics"></a><div id="Statistics-def"><a name="L73"></a><tt class="py-lineno"> 73</tt> <a class="py-toggle" href="#" id="Statistics-toggle" onclick="return toggle('Statistics');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Wise.dnal.Statistics-class.html">Statistics</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Statistics-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Statistics-expanded"><a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"><tt class="py-docstring"> Calculate statistics from an ALB report</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="Statistics.__init__"></a><div id="Statistics.__init__-def"><a name="L77"></a><tt class="py-lineno"> 77</tt> <a class="py-toggle" href="#" id="Statistics.__init__-toggle" onclick="return toggle('Statistics.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Wise.dnal.Statistics-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">filename</tt><tt class="py-op">,</tt> <tt class="py-param">match</tt><tt class="py-op">,</tt> <tt class="py-param">mismatch</tt><tt class="py-op">,</tt> <tt class="py-param">gap</tt><tt class="py-op">,</tt> <tt class="py-param">extension</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Statistics.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Statistics.__init__-expanded"><a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">matches</tt> <tt class="py-op">=</tt> <tt id="link-25" class="py-name" targets="Function Bio.Wise.dnal._fgrep_count()=Bio.Wise.dnal-module.html#_fgrep_count"><a title="Bio.Wise.dnal._fgrep_count" class="py-name" href="#" onclick="return doclink('link-25', '_fgrep_count', 'link-25');">_fgrep_count</a></tt><tt class="py-op">(</tt><tt class="py-string">'"SEQUENCE" %s'</tt> <tt class="py-op">%</tt> <tt id="link-26" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-26', 'match', 'link-9');">match</a></tt><tt class="py-op">,</tt> <tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mismatches</tt> <tt class="py-op">=</tt> <tt id="link-27" class="py-name"><a title="Bio.Wise.dnal._fgrep_count" class="py-name" href="#" onclick="return doclink('link-27', '_fgrep_count', 'link-25');">_fgrep_count</a></tt><tt class="py-op">(</tt><tt class="py-string">'"SEQUENCE" %s'</tt> <tt class="py-op">%</tt> <tt class="py-name">mismatch</tt><tt class="py-op">,</tt> <tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">gaps</tt> <tt class="py-op">=</tt> <tt id="link-28" class="py-name"><a title="Bio.Wise.dnal._fgrep_count" class="py-name" href="#" onclick="return doclink('link-28', '_fgrep_count', 'link-25');">_fgrep_count</a></tt><tt class="py-op">(</tt><tt class="py-string">'"INSERT" %s'</tt> <tt class="py-op">%</tt> <tt class="py-name">gap</tt><tt class="py-op">,</tt> <tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">gap</tt> <tt class="py-op">==</tt> <tt class="py-name">extension</tt><tt class="py-op">:</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">extensions</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">extensions</tt> <tt class="py-op">=</tt> <tt id="link-29" class="py-name"><a title="Bio.Wise.dnal._fgrep_count" class="py-name" href="#" onclick="return doclink('link-29', '_fgrep_count', 'link-25');">_fgrep_count</a></tt><tt class="py-op">(</tt><tt class="py-string">'"INSERT" %s'</tt> <tt class="py-op">%</tt> <tt class="py-name">extension</tt><tt class="py-op">,</tt> <tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-30" class="py-name" targets="Method Bio.Blast.NCBIStandalone._HSPConsumer.score()=Bio.Blast.NCBIStandalone._HSPConsumer-class.html#score,Variable Bio.expressions.blast.ncbiblast.score=Bio.expressions.blast.ncbiblast-module.html#score"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-30', 'score', 'link-30');">score</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-31" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-31', 'match', 'link-9');">match</a></tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">matches</tt> <tt class="py-op">+</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-name">mismatch</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mismatches</tt> <tt class="py-op">+</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-name">gap</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">gaps</tt> <tt class="py-op">+</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-name">extension</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">extensions</tt><tt class="py-op">)</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-32" class="py-name" targets="Function Bio.Wise.dnal._any()=Bio.Wise.dnal-module.html#_any"><a title="Bio.Wise.dnal._any" class="py-name" href="#" onclick="return doclink('link-32', '_any', 'link-32');">_any</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">matches</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mismatches</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">gaps</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">extensions</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">coords</tt> <tt class="py-op">=</tt> <tt id="link-33" class="py-name" targets="Function Bio.Wise.dnal._get_coords()=Bio.Wise.dnal-module.html#_get_coords"><a title="Bio.Wise.dnal._get_coords" class="py-name" href="#" onclick="return doclink('link-33', '_get_coords', 'link-33');">_get_coords</a></tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">coords</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
</div><a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> </tt>
<a name="Statistics.identity_fraction"></a><div id="Statistics.identity_fraction-def"><a name="L97"></a><tt class="py-lineno"> 97</tt> <a class="py-toggle" href="#" id="Statistics.identity_fraction-toggle" onclick="return toggle('Statistics.identity_fraction');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Wise.dnal.Statistics-class.html#identity_fraction">identity_fraction</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Statistics.identity_fraction-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Statistics.identity_fraction-expanded"><a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">matches</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">matches</tt><tt class="py-op">+</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mismatches</tt><tt class="py-op">)</tt> </tt>
</div><a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt id="link-34" class="py-name" targets="Variable Bio.Wise.dnal.Statistics.header=Bio.Wise.dnal.Statistics-class.html#header,Variable Bio.expressions.blast.ncbiblast.header=Bio.expressions.blast.ncbiblast-module.html#header,Variable Bio.expressions.blast.wublast.header=Bio.expressions.blast.wublast-module.html#header,Variable Bio.expressions.blocks.header=Bio.expressions.blocks-module.html#header,Variable Bio.expressions.genbank.header=Bio.expressions.genbank-module.html#header,Variable Bio.expressions.hmmpfam.header=Bio.expressions.hmmpfam-module.html#header"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-34', 'header', 'link-34');">header</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"identity_fraction\tmatches\tmismatches\tgaps\textensions"</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> </tt>
<a name="Statistics.__str__"></a><div id="Statistics.__str__-def"><a name="L102"></a><tt class="py-lineno">102</tt> <a class="py-toggle" href="#" id="Statistics.__str__-toggle" onclick="return toggle('Statistics.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Wise.dnal.Statistics-class.html#__str__">__str__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Statistics.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Statistics.__str__-expanded"><a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"\t"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-35" class="py-name" targets="Variable Bio.MarkovModel.x=Bio.MarkovModel-module.html#x,Variable Bio.Statistics.lowess.x=Bio.Statistics.lowess-module.html#x"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-35', 'x', 'link-35');">x</a></tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt id="link-36" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-36', 'x', 'link-35');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name" targets="Method Bio.Wise.dnal.Statistics.identity_fraction()=Bio.Wise.dnal.Statistics-class.html#identity_fraction"><a title="Bio.Wise.dnal.Statistics.identity_fraction" class="py-name" href="#" onclick="return doclink('link-37', 'identity_fraction', 'link-37');">identity_fraction</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">matches</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mismatches</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">gaps</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">extensions</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> </tt>
<a name="align"></a><div id="align-def"><a name="L105"></a><tt class="py-lineno">105</tt> <a class="py-toggle" href="#" id="align-toggle" onclick="return toggle('align');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Wise.dnal-module.html#align">align</a><tt class="py-op">(</tt><tt class="py-param">pair</tt><tt class="py-op">,</tt> <tt class="py-param">match</tt><tt class="py-op">=</tt><tt id="link-38" class="py-name"><a title="Bio.Wise.dnal._SCORE_MATCH" class="py-name" href="#" onclick="return doclink('link-38', '_SCORE_MATCH', 'link-2');">_SCORE_MATCH</a></tt><tt class="py-op">,</tt> <tt class="py-param">mismatch</tt><tt class="py-op">=</tt><tt id="link-39" class="py-name"><a title="Bio.Wise.dnal._SCORE_MISMATCH" class="py-name" href="#" onclick="return doclink('link-39', '_SCORE_MISMATCH', 'link-3');">_SCORE_MISMATCH</a></tt><tt class="py-op">,</tt> <tt class="py-param">gap</tt><tt class="py-op">=</tt><tt id="link-40" class="py-name"><a title="Bio.Wise.dnal._SCORE_GAP_START" class="py-name" href="#" onclick="return doclink('link-40', '_SCORE_GAP_START', 'link-4');">_SCORE_GAP_START</a></tt><tt class="py-op">,</tt> <tt class="py-param">extension</tt><tt class="py-op">=</tt><tt id="link-41" class="py-name"><a title="Bio.Wise.dnal._SCORE_GAP_EXTENSION" class="py-name" href="#" onclick="return doclink('link-41', '_SCORE_GAP_EXTENSION', 'link-5');">_SCORE_GAP_EXTENSION</a></tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-param">keywds</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="align-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="align-expanded"><a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-name">cmdline</tt> <tt class="py-op">=</tt> <tt id="link-42" class="py-name" targets="Function Bio.Wise.dnal._build_dnal_cmdline()=Bio.Wise.dnal-module.html#_build_dnal_cmdline"><a title="Bio.Wise.dnal._build_dnal_cmdline" class="py-name" href="#" onclick="return doclink('link-42', '_build_dnal_cmdline', 'link-42');">_build_dnal_cmdline</a></tt><tt class="py-op">(</tt><tt id="link-43" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-43', 'match', 'link-9');">match</a></tt><tt class="py-op">,</tt> <tt class="py-name">mismatch</tt><tt class="py-op">,</tt> <tt class="py-name">gap</tt><tt class="py-op">,</tt> <tt class="py-name">extension</tt><tt class="py-op">)</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-name">temp_file</tt> <tt class="py-op">=</tt> <tt id="link-44" class="py-name"><a title="Bio.Wise" class="py-name" href="#" onclick="return doclink('link-44', 'Wise', 'link-1');">Wise</a></tt><tt class="py-op">.</tt><tt id="link-45" class="py-name" targets="Method Bio.Blast.NCBIStandalone._HSPConsumer.align()=Bio.Blast.NCBIStandalone._HSPConsumer-class.html#align,Class Bio.FSSP.fssp_rec.align=Bio.FSSP.fssp_rec.align-class.html,Function Bio.Wise.align()=Bio.Wise-module.html#align,Function Bio.Wise.dnal.align()=Bio.Wise.dnal-module.html#align,Function Bio.Wise.psw.align()=Bio.Wise.psw-module.html#align,Variable Bio.pairwise2.align=Bio.pairwise2-module.html#align"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.align
Bio.FSSP.fssp_rec.align
Bio.Wise.align
Bio.Wise.dnal.align
Bio.Wise.psw.align
Bio.pairwise2.align" class="py-name" href="#" onclick="return doclink('link-45', 'align', 'link-45');">align</a></tt><tt class="py-op">(</tt><tt class="py-name">cmdline</tt><tt class="py-op">,</tt> <tt class="py-name">pair</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-name">keywds</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">try</tt><tt class="py-op">:</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-46" class="py-name" targets="Package Bio.Statistics=Bio.Statistics-module.html,Class Bio.Wise.dnal.Statistics=Bio.Wise.dnal.Statistics-class.html"><a title="Bio.Statistics
Bio.Wise.dnal.Statistics" class="py-name" href="#" onclick="return doclink('link-46', 'Statistics', 'link-46');">Statistics</a></tt><tt class="py-op">(</tt><tt class="py-name">temp_file</tt><tt class="py-op">.</tt><tt id="link-47" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.name=Bio.Encodings.IUPACEncoding-module.html#name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-47', 'name', 'link-47');">name</a></tt><tt class="py-op">,</tt> <tt id="link-48" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-48', 'match', 'link-9');">match</a></tt><tt class="py-op">,</tt> <tt class="py-name">mismatch</tt><tt class="py-op">,</tt> <tt class="py-name">gap</tt><tt class="py-op">,</tt> <tt class="py-name">extension</tt><tt class="py-op">)</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</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="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-name">keywds</tt><tt class="py-op">[</tt><tt class="py-string">'dry_run'</tt><tt class="py-op">]</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">KeyError</tt><tt class="py-op">:</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> </tt>
</div><a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> </tt>
<a name="main"></a><div id="main-def"><a name="L117"></a><tt class="py-lineno">117</tt> <a class="py-toggle" href="#" id="main-toggle" onclick="return toggle('main');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Wise.dnal-module.html#main">main</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="main-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="main-expanded"><a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">sys</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-name">stats</tt> <tt class="py-op">=</tt> <tt id="link-49" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.align
Bio.FSSP.fssp_rec.align
Bio.Wise.align
Bio.Wise.dnal.align
Bio.Wise.psw.align
Bio.pairwise2.align" class="py-name" href="#" onclick="return doclink('link-49', 'align', 'link-45');">align</a></tt><tt class="py-op">(</tt><tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"\n"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</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">attr</tt><tt class="py-op">,</tt> <tt class="py-name">getattr</tt><tt class="py-op">(</tt><tt class="py-name">stats</tt><tt class="py-op">,</tt> <tt class="py-name">attr</tt><tt class="py-op">)</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">for</tt> <tt class="py-name">attr</tt> <tt class="py-keyword">in</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"matches"</tt><tt class="py-op">,</tt> <tt class="py-string">"mismatches"</tt><tt class="py-op">,</tt> <tt class="py-string">"gaps"</tt><tt class="py-op">,</tt> <tt class="py-string">"extensions"</tt><tt class="py-op">)</tt><tt class="py-op">]</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">print</tt> <tt class="py-string">"identity_fraction: %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">stats</tt><tt class="py-op">.</tt><tt id="link-50" class="py-name"><a title="Bio.Wise.dnal.Statistics.identity_fraction" class="py-name" href="#" onclick="return doclink('link-50', 'identity_fraction', 'link-37');">identity_fraction</a></tt><tt class="py-op">(</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">print</tt> <tt class="py-string">"coords: %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">coords</tt> </tt>
</div><a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> </tt>
<a name="_test"></a><div id="_test-def"><a name="L126"></a><tt class="py-lineno">126</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.Wise.dnal-module.html#_test">_test</a><tt class="py-op">(</tt><tt class="py-op">*</tt><tt class="py-param">args</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-param">keywds</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="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">doctest</tt><tt class="py-op">,</tt> <tt class="py-name">sys</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</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-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">modules</tt><tt class="py-op">[</tt><tt class="py-name">__name__</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-op">*</tt><tt class="py-name">args</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-name">keywds</tt><tt class="py-op">)</tt> </tt>
</div><a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> </tt>
<a name="L130"></a><tt class="py-lineno">130</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="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">__debug__</tt><tt class="py-op">:</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt id="link-51" class="py-name" targets="Function Bio.DocSQL._test()=Bio.DocSQL-module.html#_test,Function Bio.EUtils.MultiDict._test()=Bio.EUtils.MultiDict-module.html#_test,Function Bio.GFF._test()=Bio.GFF-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.DocSQL._test
Bio.EUtils.MultiDict._test
Bio.GFF._test
Bio.Wise._test
Bio.Wise.dnal._test
Bio.Wise.psw._test" class="py-name" href="#" onclick="return doclink('link-51', '_test', 'link-51');">_test</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt id="link-52" class="py-name" targets="Function Bio.EUtils.dtd2py.main()=Bio.EUtils.dtd2py-module.html#main,Function Bio.Mindy.main()=Bio.Mindy-module.html#main,Function Bio.Wise.dnal.main()=Bio.Wise.dnal-module.html#main,Function Bio.Wise.main()=Bio.Wise-module.html#main,Function Bio.Wise.psw.main()=Bio.Wise.psw-module.html#main,Function Bio.biblio.main()=Bio.biblio-module.html#main,Function Bio.expressions.blast.wublast.main()=Bio.expressions.blast.wublast-module.html#main,Function Martel.test.run_tests.main()=Martel.test.run_tests-module.html#main"><a title="Bio.EUtils.dtd2py.main
Bio.Mindy.main
Bio.Wise.dnal.main
Bio.Wise.main
Bio.Wise.psw.main
Bio.biblio.main
Bio.expressions.blast.wublast.main
Martel.test.run_tests.main" class="py-name" href="#" onclick="return doclink('link-52', 'main', 'link-52');">main</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> </tt><script type="text/javascript">
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