Add functionnal version of bron and carbosh algorith for clique finding
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<td><span class="summary-sig"><a href="obitools.oligo-module.html#wordIterator" class="summary-sig-name">wordIterator</a>(<span class="summary-sig-arg">size</span>,
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<span class="summary-sig-arg">_prefix</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>)</span><br />
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Iterate thought the list of all DNA word of size `size`.</td>
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<td align="right" valign="top">
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<span class="codelink"><a href="obitools.oligo-pysrc.html#wordIterator">source code</a></span>
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<span class="summary-type">iterator</span>
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
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<tr>
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<td><span class="summary-sig"><a href="obitools.oligo-module.html#wordSelector" class="summary-sig-name">wordSelector</a>(<span class="summary-sig-arg">words</span>,
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<span class="summary-sig-arg">accept</span>=<span class="summary-sig-default">None</span>,
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<span class="summary-sig-arg">reject</span>=<span class="summary-sig-default">None</span>)</span><br />
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Filter over a DNA word iterator.</td>
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<td align="right" valign="top">
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<span class="codelink"><a href="obitools.oligo-pysrc.html#wordSelector">source code</a></span>
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<span class="summary-type">int</span>
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<td><span class="summary-sig"><a href="obitools.oligo-module.html#wordDist" class="summary-sig-name">wordDist</a>(<span class="summary-sig-arg">w1</span>,
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<span class="summary-sig-arg">w2</span>)</span><br />
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estimate Hamming distance between two words of the same size.</td>
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<td align="right" valign="top">
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<span class="codelink"><a href="obitools.oligo-pysrc.html#wordDist">source code</a></span>
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<a name="_dna"></a><span class="summary-name">_dna</span> = <code title="'acgt'"><code class="variable-quote">'</code><code class="variable-string">acgt</code><code class="variable-quote">'</code></code>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">wordIterator</span>(<span class="sig-arg">size</span>,
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<span class="sig-arg">_prefix</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>)</span>
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</h3>
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</td><td align="right" valign="top"
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><span class="codelink"><a href="obitools.oligo-pysrc.html#wordIterator">source code</a></span>
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</td>
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</table>
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Iterate thought the list of all DNA word of size `size`.
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<dl class="fields">
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<dt>Parameters:</dt>
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<dd><ul class="nomargin-top">
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<li><strong class="pname"><code>size</code></strong> (int) - size of the DNA word</li>
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<li><strong class="pname"><code>_prefix</code></strong> (<p>string</p>
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@return an iterator on DNA word (str)) - internal parameter used for recursion purpose</li>
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</ul></dd>
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<dt>Returns: iterator</dt>
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</dl>
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</td></tr></table>
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</div>
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<a name="wordSelector"></a>
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<div>
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<table class="details" border="1" cellpadding="3"
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cellspacing="0" width="100%" bgcolor="white">
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">wordSelector</span>(<span class="sig-arg">words</span>,
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<span class="sig-arg">accept</span>=<span class="sig-default">None</span>,
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<span class="sig-arg">reject</span>=<span class="sig-default">None</span>)</span>
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</h3>
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</td><td align="right" valign="top"
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><span class="codelink"><a href="obitools.oligo-pysrc.html#wordSelector">source code</a></span>
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</td>
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</table>
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Filter over a DNA word iterator.
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<dl class="fields">
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<dt>Parameters:</dt>
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<dd><ul class="nomargin-top">
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<li><strong class="pname"><code>words</code></strong> (an iterator) - an iterable object other a list of DNA words</li>
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<li><strong class="pname"><code>accept</code></strong> (list) - a list of predicat. Eeach predicat is a function accepting one
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str parametter and returning a boolean value.</li>
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<li><strong class="pname"><code>reject</code></strong> (<p>list</p>
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@return an iterator on DNA word (str)) - a list of predicat. Eeach predicat is a function accepting one
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str parametter and returning a boolean value.</li>
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</ul></dd>
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<dt>Returns: iterator</dt>
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</dl>
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</td></tr></table>
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</div>
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<a name="wordDist"></a>
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<div>
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<table class="details" border="1" cellpadding="3"
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cellspacing="0" width="100%" bgcolor="white">
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
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<tr valign="top"><td>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">wordDist</span>(<span class="sig-arg">w1</span>,
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<span class="sig-arg">w2</span>)</span>
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</h3>
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</td><td align="right" valign="top"
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><span class="codelink"><a href="obitools.oligo-pysrc.html#wordDist">source code</a></span>
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</td>
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</table>
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estimate Hamming distance between two words of the same size.
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<dl class="fields">
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<dt>Parameters:</dt>
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<dd><ul class="nomargin-top">
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<li><strong class="pname"><code>w1</code></strong> (str) - the first word</li>
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<li><strong class="pname"><code>w2</code></strong> (str) - the second word</li>
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</ul></dd>
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<dt>Returns: int</dt>
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<dd>the count of difference between the two words</dd>
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</dl>
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<h1 class="epydoc">Source Code for <a href="obitools.oligo-module.html">Package obitools.oligo</a></h1>
|
|
||||||
<pre class="py-src">
|
|
||||||
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">itertools</tt> <tt class="py-keyword">import</tt> <tt class="py-name">imap</tt> </tt>
|
|
||||||
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"> </tt>
|
|
||||||
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"> </tt>
|
|
||||||
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt id="link-0" class="py-name" targets="Variable obitools.oligo._dna=obitools.oligo-module.html#_dna"><a title="obitools.oligo._dna" class="py-name" href="#" onclick="return doclink('link-0', '_dna', 'link-0');">_dna</a></tt><tt class="py-op">=</tt><tt class="py-string">'acgt'</tt> </tt>
|
|
||||||
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"> </tt>
|
|
||||||
<a name="wordIterator"></a><div id="wordIterator-def"><a name="L6"></a><tt class="py-lineno"> 6</tt> <a class="py-toggle" href="#" id="wordIterator-toggle" onclick="return toggle('wordIterator');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.oligo-module.html#wordIterator">wordIterator</a><tt class="py-op">(</tt><tt class="py-param">size</tt><tt class="py-op">,</tt><tt class="py-param">_prefix</tt><tt class="py-op">=</tt><tt class="py-string">''</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
||||||
</div><div id="wordIterator-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="wordIterator-expanded"><a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
|
|
||||||
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring"> Iterate thought the list of all DNA word of</tt> </tt>
|
|
||||||
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring"> size `size`.</tt> </tt>
|
|
||||||
<a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
|
|
||||||
<a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"><tt class="py-docstring"> @param size: size of the DNA word</tt> </tt>
|
|
||||||
<a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"><tt class="py-docstring"> @type size: int</tt> </tt>
|
|
||||||
<a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"><tt class="py-docstring"> @param _prefix: internal parameter used for recursion purpose</tt> </tt>
|
|
||||||
<a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"><tt class="py-docstring"> @type _prefix: string</tt> </tt>
|
|
||||||
<a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
|
|
||||||
<a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"><tt class="py-docstring"> @return an iterator on DNA word (str)</tt> </tt>
|
|
||||||
<a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: iterator</tt> </tt>
|
|
||||||
<a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
|
|
||||||
<a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">size</tt><tt class="py-op">:</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">l</tt> <tt class="py-keyword">in</tt> <tt id="link-1" class="py-name"><a title="obitools.oligo._dna" class="py-name" href="#" onclick="return doclink('link-1', '_dna', 'link-0');">_dna</a></tt><tt class="py-op">:</tt> </tt>
|
|
||||||
<a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">w</tt> <tt class="py-keyword">in</tt> <tt id="link-2" class="py-name" targets="Function obitools.oligo.wordIterator()=obitools.oligo-module.html#wordIterator"><a title="obitools.oligo.wordIterator" class="py-name" href="#" onclick="return doclink('link-2', 'wordIterator', 'link-2');">wordIterator</a></tt><tt class="py-op">(</tt><tt class="py-name">size</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">_prefix</tt><tt class="py-op">+</tt><tt class="py-name">l</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
||||||
<a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-name">w</tt> </tt>
|
|
||||||
<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
|
|
||||||
<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-name">_prefix</tt> </tt>
|
|
||||||
</div><a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"> </tt>
|
|
||||||
<a name="wordSelector"></a><div id="wordSelector-def"><a name="L26"></a><tt class="py-lineno">26</tt> <a class="py-toggle" href="#" id="wordSelector-toggle" onclick="return toggle('wordSelector');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.oligo-module.html#wordSelector">wordSelector</a><tt class="py-op">(</tt><tt class="py-param">words</tt><tt class="py-op">,</tt><tt class="py-param">accept</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-param">reject</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
||||||
</div><div id="wordSelector-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="wordSelector-expanded"><a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
|
|
||||||
<a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"><tt class="py-docstring"> Filter over a DNA word iterator.</tt> </tt>
|
|
||||||
<a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
|
|
||||||
<a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"><tt class="py-docstring"> @param words: an iterable object other a list of DNA words</tt> </tt>
|
|
||||||
<a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"><tt class="py-docstring"> @type words: an iterator</tt> </tt>
|
|
||||||
<a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"><tt class="py-docstring"> @param accept: a list of predicat. Eeach predicat is a function</tt> </tt>
|
|
||||||
<a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"><tt class="py-docstring"> accepting one str parametter and returning a boolean</tt> </tt>
|
|
||||||
<a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"><tt class="py-docstring"> value.</tt> </tt>
|
|
||||||
<a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"><tt class="py-docstring"> @type accept: list</tt> </tt>
|
|
||||||
<a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"><tt class="py-docstring"> @param reject: a list of predicat. Eeach predicat is a function</tt> </tt>
|
|
||||||
<a name="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"><tt class="py-docstring"> accepting one str parametter and returning a boolean</tt> </tt>
|
|
||||||
<a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"><tt class="py-docstring"> value.</tt> </tt>
|
|
||||||
<a name="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"><tt class="py-docstring"> @type reject: list</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"> @return an iterator on DNA word (str)</tt> </tt>
|
|
||||||
<a name="L42"></a><tt class="py-lineno">42</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: iterator</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-keyword">if</tt> <tt class="py-name">accept</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
|
|
||||||
<a name="L45"></a><tt class="py-lineno">45</tt> <tt class="py-line"> <tt class="py-name">accept</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
|
|
||||||
<a name="L46"></a><tt class="py-lineno">46</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">reject</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
|
|
||||||
<a name="L47"></a><tt class="py-lineno">47</tt> <tt class="py-line"> <tt class="py-name">reject</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</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">w</tt> <tt class="py-keyword">in</tt> <tt class="py-name">words</tt><tt class="py-op">:</tt> </tt>
|
|
||||||
<a name="L49"></a><tt class="py-lineno">49</tt> <tt class="py-line"> <tt class="py-name">accepted</tt> <tt class="py-op">=</tt> <tt class="py-name">reduce</tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">y</tt><tt class="py-op">:</tt> <tt class="py-name">bool</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt> <tt class="py-keyword">and</tt> <tt class="py-name">bool</tt><tt class="py-op">(</tt><tt class="py-name">y</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
|
|
||||||
<a name="L50"></a><tt class="py-lineno">50</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">p</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">p</tt> <tt class="py-keyword">in</tt> <tt class="py-name">accept</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
|
|
||||||
<a name="L51"></a><tt class="py-lineno">51</tt> <tt class="py-line"> <tt class="py-name">True</tt><tt class="py-op">)</tt> </tt>
|
|
||||||
<a name="L52"></a><tt class="py-lineno">52</tt> <tt class="py-line"> <tt class="py-name">rejected</tt> <tt class="py-op">=</tt> <tt class="py-name">reduce</tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">y</tt><tt class="py-op">:</tt><tt class="py-name">bool</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> <tt class="py-name">bool</tt><tt class="py-op">(</tt><tt class="py-name">y</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
|
|
||||||
<a name="L53"></a><tt class="py-lineno">53</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">p</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">p</tt> <tt class="py-keyword">in</tt> <tt class="py-name">reject</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
|
|
||||||
<a name="L54"></a><tt class="py-lineno">54</tt> <tt class="py-line"> <tt class="py-name">False</tt><tt class="py-op">)</tt> </tt>
|
|
||||||
<a name="L55"></a><tt class="py-lineno">55</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">accepted</tt> <tt class="py-keyword">and</tt> <tt class="py-keyword">not</tt> <tt class="py-name">rejected</tt><tt class="py-op">:</tt> </tt>
|
|
||||||
<a name="L56"></a><tt class="py-lineno">56</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-name">w</tt> </tt>
|
|
||||||
</div><a name="L57"></a><tt class="py-lineno">57</tt> <tt class="py-line"> </tt>
|
|
||||||
<a name="wordDist"></a><div id="wordDist-def"><a name="L58"></a><tt class="py-lineno">58</tt> <a class="py-toggle" href="#" id="wordDist-toggle" onclick="return toggle('wordDist');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.oligo-module.html#wordDist">wordDist</a><tt class="py-op">(</tt><tt class="py-param">w1</tt><tt class="py-op">,</tt><tt class="py-param">w2</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
||||||
</div><div id="wordDist-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="wordDist-expanded"><a name="L59"></a><tt class="py-lineno">59</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
|
|
||||||
<a name="L60"></a><tt class="py-lineno">60</tt> <tt class="py-line"><tt class="py-docstring"> estimate Hamming distance between two words of the same size.</tt> </tt>
|
|
||||||
<a name="L61"></a><tt class="py-lineno">61</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
|
|
||||||
<a name="L62"></a><tt class="py-lineno">62</tt> <tt class="py-line"><tt class="py-docstring"> @param w1: the first word</tt> </tt>
|
|
||||||
<a name="L63"></a><tt class="py-lineno">63</tt> <tt class="py-line"><tt class="py-docstring"> @type w1: str</tt> </tt>
|
|
||||||
<a name="L64"></a><tt class="py-lineno">64</tt> <tt class="py-line"><tt class="py-docstring"> @param w2: the second word</tt> </tt>
|
|
||||||
<a name="L65"></a><tt class="py-lineno">65</tt> <tt class="py-line"><tt class="py-docstring"> @type w2: str</tt> </tt>
|
|
||||||
<a name="L66"></a><tt class="py-lineno">66</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
|
|
||||||
<a name="L67"></a><tt class="py-lineno">67</tt> <tt class="py-line"><tt class="py-docstring"> @return: the count of difference between the two words</tt> </tt>
|
|
||||||
<a name="L68"></a><tt class="py-lineno">68</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: int</tt> </tt>
|
|
||||||
<a name="L69"></a><tt class="py-lineno">69</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
|
|
||||||
<a name="L70"></a><tt class="py-lineno">70</tt> <tt class="py-line"> <tt class="py-name">dist</tt> <tt class="py-op">=</tt> <tt class="py-name">reduce</tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">y</tt><tt class="py-op">:</tt><tt class="py-name">x</tt><tt class="py-op">+</tt><tt class="py-name">y</tt><tt class="py-op">,</tt> </tt>
|
|
||||||
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<a href="obitools-module.html">Package obitools</a> ::
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<a href="obitools.oligo-module.html">Package oligo</a> ::
|
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Module options
|
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||||||
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<!-- ==================== MODULE DESCRIPTION ==================== -->
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<h1 class="epydoc">Module options</h1><span class="codelink"><a href="obitools.oligo.options-pysrc.html">source code</a></span><br /><br />
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|
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|
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||||||
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|
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||||||
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||||||
<td><span class="summary-sig"><a name="addOligoOptions"></a><span class="summary-sig-name">addOligoOptions</span>(<span class="summary-sig-arg">optionManager</span>)</span></td>
|
|
||||||
<td align="right" valign="top">
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||||||
<span class="codelink"><a href="obitools.oligo.options-pysrc.html#addOligoOptions">source code</a></span>
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||||||
<td><span class="summary-sig"><a name="dnaWordIterator"></a><span class="summary-sig-name">dnaWordIterator</span>(<span class="summary-sig-arg">options</span>)</span></td>
|
|
||||||
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|
|
||||||
<span class="codelink"><a href="obitools.oligo.options-pysrc.html#dnaWordIterator">source code</a></span>
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<a href="obitools-module.html">Package obitools</a> ::
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|
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||||||
<table cellpadding="0" cellspacing="0">
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<!-- hide/show private -->
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|
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onclick="toggle_private();">hide private</a>]</span></td></tr>
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||||||
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>[<a href="frames.html" target="_top">frames</a
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target="_top">no frames</a>]</span></td></tr>
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||||||
</table>
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|
||||||
<h1 class="epydoc">Source Code for <a href="obitools.oligo.options-module.html">Module obitools.oligo.options</a></h1>
|
|
||||||
<pre class="py-src">
|
|
||||||
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">logging</tt> <tt class="py-keyword">import</tt> <tt class="py-name">debug</tt><tt class="py-op">,</tt><tt class="py-name">root</tt><tt class="py-op">,</tt><tt class="py-name">DEBUG</tt> </tt>
|
|
||||||
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"> </tt>
|
|
||||||
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"> </tt>
|
|
||||||
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"> </tt>
|
|
||||||
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package obitools=obitools-module.html"><a title="obitools" class="py-name" href="#" onclick="return doclink('link-0', 'obitools', 'link-0');">obitools</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Package obitools.oligo=obitools.oligo-module.html"><a title="obitools.oligo" class="py-name" href="#" onclick="return doclink('link-1', 'oligo', 'link-1');">oligo</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name" targets="Function obitools.oligo.wordSelector()=obitools.oligo-module.html#wordSelector"><a title="obitools.oligo.wordSelector" class="py-name" href="#" onclick="return doclink('link-2', 'wordSelector', 'link-2');">wordSelector</a></tt><tt class="py-op">,</tt><tt id="link-3" class="py-name" targets="Function obitools.oligo.wordIterator()=obitools.oligo-module.html#wordIterator"><a title="obitools.oligo.wordIterator" class="py-name" href="#" onclick="return doclink('link-3', 'wordIterator', 'link-3');">wordIterator</a></tt> </tt>
|
|
||||||
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-4" class="py-name"><a title="obitools" class="py-name" href="#" onclick="return doclink('link-4', 'obitools', 'link-0');">obitools</a></tt><tt class="py-op">.</tt><tt id="link-5" class="py-name"><a title="obitools.oligo" class="py-name" href="#" onclick="return doclink('link-5', 'oligo', 'link-1');">oligo</a></tt> <tt class="py-keyword">import</tt> <tt id="link-6" class="py-name" targets="Module obitools.oligo.predicat=obitools.oligo.predicat-module.html"><a title="obitools.oligo.predicat" class="py-name" href="#" onclick="return doclink('link-6', 'predicat', 'link-6');">predicat</a></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>
|
|
||||||
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"> </tt>
|
|
||||||
<a name="_acceptedOptionCallback"></a><div id="_acceptedOptionCallback-def"><a name="L10"></a><tt class="py-lineno"> 10</tt> <a class="py-toggle" href="#" id="_acceptedOptionCallback-toggle" onclick="return toggle('_acceptedOptionCallback');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.oligo.options-module.html#_acceptedOptionCallback">_acceptedOptionCallback</a><tt class="py-op">(</tt><tt class="py-param">options</tt><tt class="py-op">,</tt><tt class="py-param">opt</tt><tt class="py-op">,</tt><tt class="py-param">value</tt><tt class="py-op">,</tt><tt class="py-param">parser</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
||||||
</div><div id="_acceptedOptionCallback-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_acceptedOptionCallback-expanded"><a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">hasattr</tt><tt class="py-op">(</tt><tt class="py-name">parser</tt><tt class="py-op">.</tt><tt class="py-name">values</tt><tt class="py-op">,</tt> <tt class="py-string">'acceptedOligo'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
||||||
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"> <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt class="py-name">values</tt><tt class="py-op">.</tt><tt class="py-name">acceptedOligo</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
|
|
||||||
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"> <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt class="py-name">values</tt><tt class="py-op">.</tt><tt class="py-name">acceptedOligo</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name" targets="Method obitools.align.Alignement.append()=obitools.align.Alignement-class.html#append"><a title="obitools.align.Alignement.append" class="py-name" href="#" onclick="return doclink('link-7', 'append', 'link-7');">append</a></tt><tt class="py-op">(</tt><tt id="link-8" class="py-name"><a title="obitools.oligo.predicat" class="py-name" href="#" onclick="return doclink('link-8', 'predicat', 'link-6');">predicat</a></tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Function obitools.oligo.predicat.rePredicatGenerator()=obitools.oligo.predicat-module.html#rePredicatGenerator"><a title="obitools.oligo.predicat.rePredicatGenerator" class="py-name" href="#" onclick="return doclink('link-9', 'rePredicatGenerator', 'link-9');">rePredicatGenerator</a></tt><tt class="py-op">(</tt><tt class="py-name">value</tt><tt class="py-op">)</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="_rejectedOptionCallback"></a><div id="_rejectedOptionCallback-def"><a name="L15"></a><tt class="py-lineno"> 15</tt> <a class="py-toggle" href="#" id="_rejectedOptionCallback-toggle" onclick="return toggle('_rejectedOptionCallback');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.oligo.options-module.html#_rejectedOptionCallback">_rejectedOptionCallback</a><tt class="py-op">(</tt><tt class="py-param">options</tt><tt class="py-op">,</tt><tt class="py-param">opt</tt><tt class="py-op">,</tt><tt class="py-param">value</tt><tt class="py-op">,</tt><tt class="py-param">parser</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
||||||
</div><div id="_rejectedOptionCallback-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_rejectedOptionCallback-expanded"><a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"> <tt class="py-name">debug</tt><tt class="py-op">(</tt><tt class="py-name">value</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">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">hasattr</tt><tt class="py-op">(</tt><tt class="py-name">parser</tt><tt class="py-op">.</tt><tt class="py-name">values</tt><tt class="py-op">,</tt> <tt class="py-string">'rejectedOligo'</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">parser</tt><tt class="py-op">.</tt><tt class="py-name">values</tt><tt class="py-op">.</tt><tt class="py-name">rejectedOligo</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
|
|
||||||
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"> <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt class="py-name">values</tt><tt class="py-op">.</tt><tt class="py-name">rejectedOligo</tt><tt class="py-op">.</tt><tt id="link-10" class="py-name"><a title="obitools.align.Alignement.append" class="py-name" href="#" onclick="return doclink('link-10', 'append', 'link-7');">append</a></tt><tt class="py-op">(</tt><tt id="link-11" class="py-name"><a title="obitools.oligo.predicat" class="py-name" href="#" onclick="return doclink('link-11', 'predicat', 'link-6');">predicat</a></tt><tt class="py-op">.</tt><tt id="link-12" class="py-name"><a title="obitools.oligo.predicat.rePredicatGenerator" class="py-name" href="#" onclick="return doclink('link-12', 'rePredicatGenerator', 'link-9');">rePredicatGenerator</a></tt><tt class="py-op">(</tt><tt class="py-name">value</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
|
|
||||||
</div><a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"> </tt>
|
|
||||||
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"> </tt>
|
|
||||||
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"> </tt>
|
|
||||||
<a name="addOligoOptions"></a><div id="addOligoOptions-def"><a name="L23"></a><tt class="py-lineno"> 23</tt> <a class="py-toggle" href="#" id="addOligoOptions-toggle" onclick="return toggle('addOligoOptions');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.oligo.options-module.html#addOligoOptions">addOligoOptions</a><tt class="py-op">(</tt><tt class="py-param">optionManager</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
||||||
</div><div id="addOligoOptions-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="addOligoOptions-expanded"><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 class="py-name">optionManager</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt><tt class="py-string">'-s'</tt><tt class="py-op">,</tt><tt class="py-string">'--oligo-size'</tt><tt class="py-op">,</tt> </tt>
|
|
||||||
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"> <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store"</tt><tt class="py-op">,</tt> <tt class="py-name">dest</tt><tt class="py-op">=</tt><tt class="py-string">"oligoSize"</tt><tt class="py-op">,</tt> </tt>
|
|
||||||
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"> <tt class="py-name">metavar</tt><tt class="py-op">=</tt><tt class="py-string">"<###>"</tt><tt class="py-op">,</tt> </tt>
|
|
||||||
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"> <tt class="py-name">type</tt><tt class="py-op">=</tt><tt class="py-string">"int"</tt><tt class="py-op">,</tt> </tt>
|
|
||||||
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"> <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"Size of oligonucleotide to generate"</tt><tt class="py-op">)</tt> </tt>
|
|
||||||
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"> </tt>
|
|
||||||
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"> <tt class="py-name">optionManager</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt><tt class="py-string">'-f'</tt><tt class="py-op">,</tt><tt class="py-string">'--family-size'</tt><tt class="py-op">,</tt> </tt>
|
|
||||||
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store"</tt><tt class="py-op">,</tt> <tt class="py-name">dest</tt><tt class="py-op">=</tt><tt class="py-string">"familySize"</tt><tt class="py-op">,</tt> </tt>
|
|
||||||
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> <tt class="py-name">metavar</tt><tt class="py-op">=</tt><tt class="py-string">"<###>"</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">type</tt><tt class="py-op">=</tt><tt class="py-string">"int"</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">help</tt><tt class="py-op">=</tt><tt class="py-string">"Size of oligonucleotide family to generate"</tt><tt class="py-op">)</tt> </tt>
|
|
||||||
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> </tt>
|
|
||||||
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt class="py-name">optionManager</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt><tt class="py-string">'-d'</tt><tt class="py-op">,</tt><tt class="py-string">'--distance'</tt><tt class="py-op">,</tt> </tt>
|
|
||||||
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store"</tt><tt class="py-op">,</tt> <tt class="py-name">dest</tt><tt class="py-op">=</tt><tt class="py-string">"oligoDist"</tt><tt class="py-op">,</tt> </tt>
|
|
||||||
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt class="py-name">metavar</tt><tt class="py-op">=</tt><tt class="py-string">"<###>"</tt><tt class="py-op">,</tt> </tt>
|
|
||||||
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> <tt class="py-name">type</tt><tt class="py-op">=</tt><tt class="py-string">"int"</tt><tt class="py-op">,</tt> </tt>
|
|
||||||
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-name">default</tt><tt class="py-op">=</tt><tt class="py-number">1</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">help</tt><tt class="py-op">=</tt><tt class="py-string">"minimal distance between two oligonucleotides"</tt><tt class="py-op">)</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-name">optionManager</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt><tt class="py-string">'-g'</tt><tt class="py-op">,</tt><tt class="py-string">'--gc-max'</tt><tt class="py-op">,</tt> </tt>
|
|
||||||
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store"</tt><tt class="py-op">,</tt> <tt class="py-name">dest</tt><tt class="py-op">=</tt><tt class="py-string">"gcMax"</tt><tt class="py-op">,</tt> </tt>
|
|
||||||
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt class="py-name">metavar</tt><tt class="py-op">=</tt><tt class="py-string">"<###>"</tt><tt class="py-op">,</tt> </tt>
|
|
||||||
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-name">type</tt><tt class="py-op">=</tt><tt class="py-string">"int"</tt><tt class="py-op">,</tt> </tt>
|
|
||||||
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-name">default</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> </tt>
|
|
||||||
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"maximum count of G or C nucleotide acceptable in a word"</tt><tt class="py-op">)</tt> </tt>
|
|
||||||
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> </tt>
|
|
||||||
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt class="py-name">optionManager</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt><tt class="py-string">'-a'</tt><tt class="py-op">,</tt><tt class="py-string">'--accepted'</tt><tt class="py-op">,</tt> </tt>
|
|
||||||
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"callback"</tt><tt class="py-op">,</tt> <tt class="py-name">callback</tt><tt class="py-op">=</tt><tt id="link-13" class="py-name" targets="Function obitools.oligo.options._acceptedOptionCallback()=obitools.oligo.options-module.html#_acceptedOptionCallback"><a title="obitools.oligo.options._acceptedOptionCallback" class="py-name" href="#" onclick="return doclink('link-13', '_acceptedOptionCallback', 'link-13');">_acceptedOptionCallback</a></tt><tt class="py-op">,</tt> </tt>
|
|
||||||
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-name">metavar</tt><tt class="py-op">=</tt><tt class="py-string">"<regular pattern>"</tt><tt class="py-op">,</tt> </tt>
|
|
||||||
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-name">type</tt><tt class="py-op">=</tt><tt class="py-string">"str"</tt><tt class="py-op">,</tt> </tt>
|
|
||||||
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"pattern of accepted oligonucleotide"</tt><tt class="py-op">)</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-name">optionManager</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt><tt class="py-string">'-r'</tt><tt class="py-op">,</tt><tt class="py-string">'--rejected'</tt><tt class="py-op">,</tt> </tt>
|
|
||||||
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"callback"</tt><tt class="py-op">,</tt> <tt class="py-name">callback</tt><tt class="py-op">=</tt><tt id="link-14" class="py-name" targets="Function obitools.oligo.options._rejectedOptionCallback()=obitools.oligo.options-module.html#_rejectedOptionCallback"><a title="obitools.oligo.options._rejectedOptionCallback" class="py-name" href="#" onclick="return doclink('link-14', '_rejectedOptionCallback', 'link-14');">_rejectedOptionCallback</a></tt><tt class="py-op">,</tt> </tt>
|
|
||||||
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-name">metavar</tt><tt class="py-op">=</tt><tt class="py-string">"<regular pattern>"</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">type</tt><tt class="py-op">=</tt><tt class="py-string">"str"</tt><tt class="py-op">,</tt> </tt>
|
|
||||||
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"pattern of rejected oligonucleotide"</tt><tt class="py-op">)</tt> </tt>
|
|
||||||
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> </tt>
|
|
||||||
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-name">optionManager</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt><tt class="py-string">'-p'</tt><tt class="py-op">,</tt><tt class="py-string">'--homopolymere'</tt><tt class="py-op">,</tt> </tt>
|
|
||||||
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store"</tt><tt class="py-op">,</tt> <tt class="py-name">dest</tt><tt class="py-op">=</tt><tt class="py-string">"homopolymere"</tt><tt class="py-op">,</tt> </tt>
|
|
||||||
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-name">metavar</tt><tt class="py-op">=</tt><tt class="py-string">"<###>"</tt><tt class="py-op">,</tt> </tt>
|
|
||||||
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-name">type</tt><tt class="py-op">=</tt><tt class="py-string">"int"</tt><tt class="py-op">,</tt> </tt>
|
|
||||||
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-name">default</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> </tt>
|
|
||||||
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"reject oligo with homopolymere longer than."</tt><tt class="py-op">)</tt> </tt>
|
|
||||||
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> </tt>
|
|
||||||
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-name">optionManager</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt><tt class="py-string">'-P'</tt><tt class="py-op">,</tt><tt class="py-string">'--homopolymere-min'</tt><tt class="py-op">,</tt> </tt>
|
|
||||||
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store"</tt><tt class="py-op">,</tt> <tt class="py-name">dest</tt><tt class="py-op">=</tt><tt class="py-string">"homopolymere_min"</tt><tt class="py-op">,</tt> </tt>
|
|
||||||
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-name">metavar</tt><tt class="py-op">=</tt><tt class="py-string">"<###>"</tt><tt class="py-op">,</tt> </tt>
|
|
||||||
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-name">type</tt><tt class="py-op">=</tt><tt class="py-string">"int"</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">default</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> </tt>
|
|
||||||
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"accept only oligo with homopolymere longer than."</tt><tt class="py-op">)</tt> </tt>
|
|
||||||
</div><a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> </tt>
|
|
||||||
<a name="dnaWordIterator"></a><div id="dnaWordIterator-def"><a name="L77"></a><tt class="py-lineno"> 77</tt> <a class="py-toggle" href="#" id="dnaWordIterator-toggle" onclick="return toggle('dnaWordIterator');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.oligo.options-module.html#dnaWordIterator">dnaWordIterator</a><tt class="py-op">(</tt><tt class="py-param">options</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
||||||
</div><div id="dnaWordIterator-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="dnaWordIterator-expanded"><a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> </tt>
|
|
||||||
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-15" class="py-name" targets="Module obitools.obischemas.options=obitools.obischemas.options-module.html,Module obitools.oligo.options=obitools.oligo.options-module.html,Package obitools.options=obitools.options-module.html"><a title="obitools.obischemas.options
|
|
||||||
obitools.oligo.options
|
|
||||||
obitools.options" class="py-name" href="#" onclick="return doclink('link-15', 'options', 'link-15');">options</a></tt><tt class="py-op">.</tt><tt class="py-name">oligoSize</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-string">"option -s or --oligo-size must be specified"</tt> </tt>
|
|
||||||
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-16" class="py-name"><a title="obitools.obischemas.options
|
|
||||||
obitools.oligo.options
|
|
||||||
obitools.options" class="py-name" href="#" onclick="return doclink('link-16', 'options', 'link-15');">options</a></tt><tt class="py-op">.</tt><tt class="py-name">familySize</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-string">"option -f or --family-size must be specified"</tt> </tt>
|
|
||||||
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-17" class="py-name"><a title="obitools.obischemas.options
|
|
||||||
obitools.oligo.options
|
|
||||||
obitools.options" class="py-name" href="#" onclick="return doclink('link-17', 'options', 'link-15');">options</a></tt><tt class="py-op">.</tt><tt class="py-name">oligoDist</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-string">"option -d or --distance must be specified"</tt> </tt>
|
|
||||||
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> </tt>
|
|
||||||
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-name">words</tt> <tt class="py-op">=</tt> <tt id="link-18" class="py-name"><a title="obitools.oligo.wordIterator" class="py-name" href="#" onclick="return doclink('link-18', 'wordIterator', 'link-3');">wordIterator</a></tt><tt class="py-op">(</tt><tt id="link-19" class="py-name"><a title="obitools.obischemas.options
|
|
||||||
obitools.oligo.options
|
|
||||||
obitools.options" class="py-name" href="#" onclick="return doclink('link-19', 'options', 'link-15');">options</a></tt><tt class="py-op">.</tt><tt class="py-name">oligoSize</tt><tt class="py-op">)</tt> </tt>
|
|
||||||
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-name">seed</tt> <tt class="py-op">=</tt> <tt class="py-string">'a'</tt> <tt class="py-op">*</tt> <tt id="link-20" class="py-name"><a title="obitools.obischemas.options
|
|
||||||
obitools.oligo.options
|
|
||||||
obitools.options" class="py-name" href="#" onclick="return doclink('link-20', 'options', 'link-15');">options</a></tt><tt class="py-op">.</tt><tt class="py-name">oligoSize</tt> </tt>
|
|
||||||
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> </tt>
|
|
||||||
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">hasattr</tt><tt class="py-op">(</tt><tt id="link-21" class="py-name"><a title="obitools.obischemas.options
|
|
||||||
obitools.oligo.options
|
|
||||||
obitools.options" class="py-name" href="#" onclick="return doclink('link-21', 'options', 'link-15');">options</a></tt><tt class="py-op">,</tt> <tt class="py-string">"acceptedOligo"</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 id="link-22" class="py-name"><a title="obitools.obischemas.options
|
|
||||||
obitools.oligo.options
|
|
||||||
obitools.options" class="py-name" href="#" onclick="return doclink('link-22', 'options', 'link-15');">options</a></tt><tt class="py-op">.</tt><tt class="py-name">acceptedOligo</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
|
|
||||||
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> </tt>
|
|
||||||
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">hasattr</tt><tt class="py-op">(</tt><tt id="link-23" class="py-name"><a title="obitools.obischemas.options
|
|
||||||
obitools.oligo.options
|
|
||||||
obitools.options" class="py-name" href="#" onclick="return doclink('link-23', 'options', 'link-15');">options</a></tt><tt class="py-op">,</tt> <tt class="py-string">"rejectedOligo"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
||||||
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt id="link-24" class="py-name"><a title="obitools.obischemas.options
|
|
||||||
obitools.oligo.options
|
|
||||||
obitools.options" class="py-name" href="#" onclick="return doclink('link-24', 'options', 'link-15');">options</a></tt><tt class="py-op">.</tt><tt class="py-name">rejectedOligo</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
|
|
||||||
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> </tt>
|
|
||||||
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt id="link-25" class="py-name"><a title="obitools.obischemas.options
|
|
||||||
obitools.oligo.options
|
|
||||||
obitools.options" class="py-name" href="#" onclick="return doclink('link-25', 'options', 'link-15');">options</a></tt><tt class="py-op">.</tt><tt class="py-name">acceptedOligo</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name"><a title="obitools.align.Alignement.append" class="py-name" href="#" onclick="return doclink('link-26', 'append', 'link-7');">append</a></tt><tt class="py-op">(</tt><tt id="link-27" class="py-name"><a title="obitools.oligo.predicat" class="py-name" href="#" onclick="return doclink('link-27', 'predicat', 'link-6');">predicat</a></tt><tt class="py-op">.</tt><tt id="link-28" class="py-name" targets="Function obitools.oligo.predicat.distMinGenerator()=obitools.oligo.predicat-module.html#distMinGenerator"><a title="obitools.oligo.predicat.distMinGenerator" class="py-name" href="#" onclick="return doclink('link-28', 'distMinGenerator', 'link-28');">distMinGenerator</a></tt><tt class="py-op">(</tt><tt class="py-name">seed</tt><tt class="py-op">,</tt> <tt id="link-29" class="py-name"><a title="obitools.obischemas.options
|
|
||||||
obitools.oligo.options
|
|
||||||
obitools.options" class="py-name" href="#" onclick="return doclink('link-29', 'options', 'link-15');">options</a></tt><tt class="py-op">.</tt><tt class="py-name">oligoDist</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>
|
|
||||||
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-30" class="py-name"><a title="obitools.obischemas.options
|
|
||||||
obitools.oligo.options
|
|
||||||
obitools.options" class="py-name" href="#" onclick="return doclink('link-30', 'options', 'link-15');">options</a></tt><tt class="py-op">.</tt><tt class="py-name">homopolymere</tt><tt class="py-op">:</tt> </tt>
|
|
||||||
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt id="link-31" class="py-name"><a title="obitools.obischemas.options
|
|
||||||
obitools.oligo.options
|
|
||||||
obitools.options" class="py-name" href="#" onclick="return doclink('link-31', 'options', 'link-15');">options</a></tt><tt class="py-op">.</tt><tt class="py-name">rejectedOligo</tt><tt class="py-op">.</tt><tt id="link-32" class="py-name"><a title="obitools.align.Alignement.append" class="py-name" href="#" onclick="return doclink('link-32', 'append', 'link-7');">append</a></tt><tt class="py-op">(</tt><tt id="link-33" class="py-name"><a title="obitools.oligo.predicat" class="py-name" href="#" onclick="return doclink('link-33', 'predicat', 'link-6');">predicat</a></tt><tt class="py-op">.</tt><tt id="link-34" class="py-name" targets="Function obitools.oligo.predicat.homoPolymerGenerator()=obitools.oligo.predicat-module.html#homoPolymerGenerator"><a title="obitools.oligo.predicat.homoPolymerGenerator" class="py-name" href="#" onclick="return doclink('link-34', 'homoPolymerGenerator', 'link-34');">homoPolymerGenerator</a></tt><tt class="py-op">(</tt><tt id="link-35" class="py-name"><a title="obitools.obischemas.options
|
|
||||||
obitools.oligo.options
|
|
||||||
obitools.options" class="py-name" href="#" onclick="return doclink('link-35', 'options', 'link-15');">options</a></tt><tt class="py-op">.</tt><tt class="py-name">homopolymere</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
|
|
||||||
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> </tt>
|
|
||||||
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-36" class="py-name"><a title="obitools.obischemas.options
|
|
||||||
obitools.oligo.options
|
|
||||||
obitools.options" class="py-name" href="#" onclick="return doclink('link-36', 'options', 'link-15');">options</a></tt><tt class="py-op">.</tt><tt class="py-name">homopolymere_min</tt><tt class="py-op">:</tt> </tt>
|
|
||||||
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt id="link-37" class="py-name"><a title="obitools.obischemas.options
|
|
||||||
obitools.oligo.options
|
|
||||||
obitools.options" class="py-name" href="#" onclick="return doclink('link-37', 'options', 'link-15');">options</a></tt><tt class="py-op">.</tt><tt class="py-name">acceptedOligo</tt><tt class="py-op">.</tt><tt id="link-38" class="py-name"><a title="obitools.align.Alignement.append" class="py-name" href="#" onclick="return doclink('link-38', 'append', 'link-7');">append</a></tt><tt class="py-op">(</tt><tt id="link-39" class="py-name"><a title="obitools.oligo.predicat" class="py-name" href="#" onclick="return doclink('link-39', 'predicat', 'link-6');">predicat</a></tt><tt class="py-op">.</tt><tt id="link-40" class="py-name"><a title="obitools.oligo.predicat.homoPolymerGenerator" class="py-name" href="#" onclick="return doclink('link-40', 'homoPolymerGenerator', 'link-34');">homoPolymerGenerator</a></tt><tt class="py-op">(</tt><tt id="link-41" class="py-name"><a title="obitools.obischemas.options
|
|
||||||
obitools.oligo.options
|
|
||||||
obitools.options" class="py-name" href="#" onclick="return doclink('link-41', 'options', 'link-15');">options</a></tt><tt class="py-op">.</tt><tt class="py-name">homopolymere_min</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
|
|
||||||
<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 class="py-keyword">if</tt> <tt id="link-42" class="py-name"><a title="obitools.obischemas.options
|
|
||||||
obitools.oligo.options
|
|
||||||
obitools.options" class="py-name" href="#" onclick="return doclink('link-42', 'options', 'link-15');">options</a></tt><tt class="py-op">.</tt><tt class="py-name">gcMax</tt><tt class="py-op">:</tt> </tt>
|
|
||||||
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt id="link-43" class="py-name"><a title="obitools.obischemas.options
|
|
||||||
obitools.oligo.options
|
|
||||||
obitools.options" class="py-name" href="#" onclick="return doclink('link-43', 'options', 'link-15');">options</a></tt><tt class="py-op">.</tt><tt class="py-name">rejectedOligo</tt><tt class="py-op">.</tt><tt id="link-44" class="py-name"><a title="obitools.align.Alignement.append" class="py-name" href="#" onclick="return doclink('link-44', 'append', 'link-7');">append</a></tt><tt class="py-op">(</tt><tt id="link-45" class="py-name"><a title="obitools.oligo.predicat" class="py-name" href="#" onclick="return doclink('link-45', 'predicat', 'link-6');">predicat</a></tt><tt class="py-op">.</tt><tt id="link-46" class="py-name" targets="Function obitools.oligo.predicat.gcUpperBondGenerator()=obitools.oligo.predicat-module.html#gcUpperBondGenerator"><a title="obitools.oligo.predicat.gcUpperBondGenerator" class="py-name" href="#" onclick="return doclink('link-46', 'gcUpperBondGenerator', 'link-46');">gcUpperBondGenerator</a></tt><tt class="py-op">(</tt><tt id="link-47" class="py-name"><a title="obitools.obischemas.options
|
|
||||||
obitools.oligo.options
|
|
||||||
obitools.options" class="py-name" href="#" onclick="return doclink('link-47', 'options', 'link-15');">options</a></tt><tt class="py-op">.</tt><tt class="py-name">gcMax</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
|
|
||||||
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> </tt>
|
|
||||||
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-48" class="py-name"><a title="obitools.oligo.wordSelector" class="py-name" href="#" onclick="return doclink('link-48', 'wordSelector', 'link-2');">wordSelector</a></tt><tt class="py-op">(</tt><tt class="py-name">words</tt><tt class="py-op">,</tt> <tt id="link-49" class="py-name"><a title="obitools.obischemas.options
|
|
||||||
obitools.oligo.options
|
|
||||||
obitools.options" class="py-name" href="#" onclick="return doclink('link-49', 'options', 'link-15');">options</a></tt><tt class="py-op">.</tt><tt class="py-name">acceptedOligo</tt><tt class="py-op">,</tt> <tt id="link-50" class="py-name"><a title="obitools.obischemas.options
|
|
||||||
obitools.oligo.options
|
|
||||||
obitools.options" class="py-name" href="#" onclick="return doclink('link-50', 'options', 'link-15');">options</a></tt><tt class="py-op">.</tt><tt class="py-name">rejectedOligo</tt><tt class="py-op">)</tt> </tt>
|
|
||||||
</div><a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> </tt><script type="text/javascript">
|
|
||||||
<!--
|
|
||||||
expandto(location.href);
|
|
||||||
// -->
|
|
||||||
</script>
|
|
||||||
</pre>
|
|
||||||
<br />
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|
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<!-- ==================== NAVIGATION BAR ==================== -->
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// Private objects are initially displayed (because if
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<a href="obitools.oligo-module.html">Package oligo</a> ::
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Module predicat
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<h1 class="epydoc">Module predicat</h1><span class="codelink"><a href="obitools.oligo.predicat-pysrc.html">source code</a></span><br /><br />
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<td><span class="summary-sig"><a name="rePredicatGenerator"></a><span class="summary-sig-name">rePredicatGenerator</span>(<span class="summary-sig-arg">regex</span>)</span></td>
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<td><span class="summary-sig"><a name="gcUpperBondGenerator"></a><span class="summary-sig-name">gcUpperBondGenerator</span>(<span class="summary-sig-arg">count</span>)</span></td>
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<h1 class="epydoc">Source Code for <a href="obitools.oligo.predicat-module.html">Module obitools.oligo.predicat</a></h1>
|
|
||||||
<pre class="py-src">
|
|
||||||
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">re</tt> </tt>
|
|
||||||
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package obitools=obitools-module.html"><a title="obitools" class="py-name" href="#" onclick="return doclink('link-0', 'obitools', 'link-0');">obitools</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Package obitools.oligo=obitools.oligo-module.html"><a title="obitools.oligo" class="py-name" href="#" onclick="return doclink('link-1', 'oligo', 'link-1');">oligo</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name" targets="Function obitools.oligo.wordDist()=obitools.oligo-module.html#wordDist"><a title="obitools.oligo.wordDist" class="py-name" href="#" onclick="return doclink('link-2', 'wordDist', 'link-2');">wordDist</a></tt> </tt>
|
|
||||||
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"> </tt>
|
|
||||||
<a name="rePredicatGenerator"></a><div id="rePredicatGenerator-def"><a name="L4"></a><tt class="py-lineno"> 4</tt> <a class="py-toggle" href="#" id="rePredicatGenerator-toggle" onclick="return toggle('rePredicatGenerator');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.oligo.predicat-module.html#rePredicatGenerator">rePredicatGenerator</a><tt class="py-op">(</tt><tt class="py-param">regex</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
||||||
</div><div id="rePredicatGenerator-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="rePredicatGenerator-expanded"><a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"> <tt class="py-name">regex</tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">compile</tt><tt class="py-op">(</tt><tt class="py-name">regex</tt><tt class="py-op">,</tt><tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">I</tt><tt class="py-op">)</tt> </tt>
|
|
||||||
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"> <tt class="py-keyword">def</tt> <tt class="py-def-name">predicat</tt><tt class="py-op">(</tt><tt class="py-param">w</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
||||||
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">bool</tt><tt class="py-op">(</tt><tt class="py-name">regex</tt><tt class="py-op">.</tt><tt class="py-name">search</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
|
|
||||||
</div><a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-3" class="py-name" targets="Module obitools.oligo.predicat=obitools.oligo.predicat-module.html"><a title="obitools.oligo.predicat" class="py-name" href="#" onclick="return doclink('link-3', 'predicat', 'link-3');">predicat</a></tt> </tt>
|
|
||||||
</div><a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"> </tt>
|
|
||||||
<a name="gcUpperBondGenerator"></a><div id="gcUpperBondGenerator-def"><a name="L10"></a><tt class="py-lineno">10</tt> <a class="py-toggle" href="#" id="gcUpperBondGenerator-toggle" onclick="return toggle('gcUpperBondGenerator');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.oligo.predicat-module.html#gcUpperBondGenerator">gcUpperBondGenerator</a><tt class="py-op">(</tt><tt class="py-param">count</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
||||||
</div><div id="gcUpperBondGenerator-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="gcUpperBondGenerator-expanded"><a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"> <tt class="py-keyword">def</tt> <tt class="py-def-name">predicat</tt><tt class="py-op">(</tt><tt class="py-param">w</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
||||||
<a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"> <tt class="py-name">c</tt> <tt class="py-op">=</tt> <tt class="py-name">w</tt><tt class="py-op">.</tt><tt class="py-name">count</tt><tt class="py-op">(</tt><tt class="py-string">'g'</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-name">w</tt><tt class="py-op">.</tt><tt class="py-name">count</tt><tt class="py-op">(</tt><tt class="py-string">'c'</tt><tt class="py-op">)</tt> </tt>
|
|
||||||
<a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">c</tt> <tt class="py-op"><=</tt> <tt class="py-name">count</tt> </tt>
|
|
||||||
</div><a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-4" class="py-name"><a title="obitools.oligo.predicat" class="py-name" href="#" onclick="return doclink('link-4', 'predicat', 'link-3');">predicat</a></tt> </tt>
|
|
||||||
</div><a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"> </tt>
|
|
||||||
<a name="homoPolymerGenerator"></a><div id="homoPolymerGenerator-def"><a name="L16"></a><tt class="py-lineno">16</tt> <a class="py-toggle" href="#" id="homoPolymerGenerator-toggle" onclick="return toggle('homoPolymerGenerator');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.oligo.predicat-module.html#homoPolymerGenerator">homoPolymerGenerator</a><tt class="py-op">(</tt><tt class="py-param">count</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
||||||
</div><div id="homoPolymerGenerator-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="homoPolymerGenerator-expanded"><a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"> <tt class="py-name">pattern</tt> <tt class="py-op">=</tt> <tt class="py-string">'(.)'</tt> <tt class="py-op">+</tt> <tt class="py-string">'\\1'</tt> <tt class="py-op">*</tt> <tt class="py-op">(</tt><tt class="py-name">count</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
|
|
||||||
<a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-5" class="py-name" targets="Function obitools.oligo.predicat.rePredicatGenerator()=obitools.oligo.predicat-module.html#rePredicatGenerator"><a title="obitools.oligo.predicat.rePredicatGenerator" class="py-name" href="#" onclick="return doclink('link-5', 'rePredicatGenerator', 'link-5');">rePredicatGenerator</a></tt><tt class="py-op">(</tt><tt class="py-name">pattern</tt><tt class="py-op">)</tt> </tt>
|
|
||||||
</div><a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"> </tt>
|
|
||||||
<a name="distMinGenerator"></a><div id="distMinGenerator-def"><a name="L20"></a><tt class="py-lineno">20</tt> <a class="py-toggle" href="#" id="distMinGenerator-toggle" onclick="return toggle('distMinGenerator');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.oligo.predicat-module.html#distMinGenerator">distMinGenerator</a><tt class="py-op">(</tt><tt class="py-param">word</tt><tt class="py-op">,</tt><tt class="py-param">dmin</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
||||||
</div><div id="distMinGenerator-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="distMinGenerator-expanded"><a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"> <tt class="py-keyword">def</tt> <tt class="py-def-name">predicat</tt><tt class="py-op">(</tt><tt class="py-param">w</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
||||||
<a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">w</tt><tt class="py-op">==</tt><tt class="py-name">word</tt> <tt class="py-keyword">or</tt> <tt id="link-6" class="py-name"><a title="obitools.oligo.wordDist" class="py-name" href="#" onclick="return doclink('link-6', 'wordDist', 'link-2');">wordDist</a></tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">,</tt> <tt class="py-name">word</tt><tt class="py-op">)</tt> <tt class="py-op">>=</tt> <tt class="py-name">dmin</tt> </tt>
|
|
||||||
</div><a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-7" class="py-name"><a title="obitools.oligo.predicat" class="py-name" href="#" onclick="return doclink('link-7', 'predicat', 'link-3');">predicat</a></tt> </tt>
|
|
||||||
</div><a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"> </tt><script type="text/javascript">
|
|
||||||
<!--
|
|
||||||
expandto(location.href);
|
|
||||||
// -->
|
|
||||||
</script>
|
|
||||||
</pre>
|
|
||||||
<br />
|
|
||||||
<!-- ==================== NAVIGATION BAR ==================== -->
|
|
||||||
<table class="navbar" border="0" width="100%" cellpadding="0"
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|
||||||
bgcolor="#a0c0ff" cellspacing="0">
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|
||||||
<tr valign="middle">
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|
||||||
<!-- Home link -->
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|
||||||
<th> <a
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|
||||||
href="obitools-module.html">Home</a> </th>
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|
||||||
|
|
||||||
<!-- Tree link -->
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|
||||||
<th> <a
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|
||||||
href="module-tree.html">Trees</a> </th>
|
|
||||||
|
|
||||||
<!-- Index link -->
|
|
||||||
<th> <a
|
|
||||||
href="identifier-index.html">Indices</a> </th>
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|
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|
||||||
<!-- Help link -->
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|
||||||
<th> <a
|
|
||||||
href="help.html">Help</a> </th>
|
|
||||||
|
|
||||||
<!-- Project homepage -->
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|
||||||
<th class="navbar" align="right" width="100%">
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|
||||||
<table border="0" cellpadding="0" cellspacing="0">
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|
||||||
<tr><th class="navbar" align="center"
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><a class="navbar" target="_top" href="http://www.grenoble.prabi.fr/trac/OBITools">OBITools</a></th>
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|
||||||
</tr></table></th>
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|
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</tr>
|
|
||||||
</table>
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|
||||||
<table border="0" cellpadding="0" cellspacing="0" width="100%%">
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<tr>
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<td align="left" class="footer">
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<a href="epydoc-log.html">Generated by Epydoc
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|
||||||
3.0beta1 on Thu Jan 10 09:55:33 2008</a>
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|
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</td>
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|
||||||
<td align="right" class="footer">
|
|
||||||
<a href="http://epydoc.sourceforge.net">http://epydoc.sourceforge.net</a>
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|
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</td>
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|
||||||
</tr>
|
|
||||||
</table>
|
|
||||||
|
|
||||||
<script type="text/javascript">
|
|
||||||
<!--
|
|
||||||
// Private objects are initially displayed (because if
|
|
||||||
// javascript is turned off then we want them to be
|
|
||||||
// visible); but by default, we want to hide them. So hide
|
|
||||||
// them unless we have a cookie that says to show them.
|
|
||||||
checkCookie()
|
|
||||||
// -->
|
|
||||||
</script>
|
|
||||||
|
|
||||||
</body>
|
|
||||||
</html>
|
|
||||||
@ -59,7 +59,7 @@ class BioSequence(object):
|
|||||||
self._seq=str(seq).lower()
|
self._seq=str(seq).lower()
|
||||||
self._info = dict(info)
|
self._info = dict(info)
|
||||||
self.definition=definition
|
self.definition=definition
|
||||||
self._id=id
|
self.id=id
|
||||||
|
|
||||||
def getDefinition(self):
|
def getDefinition(self):
|
||||||
'''
|
'''
|
||||||
|
|||||||
@ -14,21 +14,21 @@ _H= _A + _C + _T
|
|||||||
_V= _A + _C + _G
|
_V= _A + _C + _G
|
||||||
_N= _A + _C + _G + _T
|
_N= _A + _C + _G + _T
|
||||||
|
|
||||||
_dnahash={'A':_A,
|
_dnahash={'a':_A,
|
||||||
'C':_C,
|
'c':_C,
|
||||||
'G':_G,
|
'g':_G,
|
||||||
'T':_T,
|
't':_T,
|
||||||
'R':_R,
|
'r':_R,
|
||||||
'Y':_Y,
|
'y':_Y,
|
||||||
'M':_M,
|
'm':_M,
|
||||||
'K':_K,
|
'k':_K,
|
||||||
'W':_W,
|
'w':_W,
|
||||||
'S':_S,
|
's':_S,
|
||||||
'B':_B,
|
'b':_B,
|
||||||
'D':_D,
|
'd':_D,
|
||||||
'H':_H,
|
'h':_H,
|
||||||
'V':_V,
|
'v':_V,
|
||||||
'N':_N,
|
'n':_N,
|
||||||
}
|
}
|
||||||
|
|
||||||
def hashCodeIterator(sequence,wsize,degeneratemax=0,offset=0):
|
def hashCodeIterator(sequence,wsize,degeneratemax=0,offset=0):
|
||||||
@ -44,7 +44,7 @@ def hashCodeIterator(sequence,wsize,degeneratemax=0,offset=0):
|
|||||||
hashmask +=3
|
hashmask +=3
|
||||||
|
|
||||||
for l in sequence:
|
for l in sequence:
|
||||||
l = l.upper()
|
l = l.lower()
|
||||||
hl = _dnahash[l]
|
hl = _dnahash[l]
|
||||||
|
|
||||||
if emask[epointer]:
|
if emask[epointer]:
|
||||||
|
|||||||
@ -218,6 +218,12 @@ class Graph(object):
|
|||||||
if index is None:
|
if index is None:
|
||||||
index=self.getNode(node).index
|
index=self.getNode(node).index
|
||||||
return self._node[index]
|
return self._node[index]
|
||||||
|
|
||||||
|
def edgeCount(self):
|
||||||
|
n = reduce(lambda x,y:x+y, (len(z) for z in self._node.itervalues()),0)
|
||||||
|
if not self._directed:
|
||||||
|
n=n/2
|
||||||
|
return n
|
||||||
|
|
||||||
def subgraph(self,nodes,name='G'):
|
def subgraph(self,nodes,name='G'):
|
||||||
sub = Graph(name,self._directed,self._index)
|
sub = Graph(name,self._directed,self._index)
|
||||||
|
|||||||
@ -3,25 +3,30 @@ import time
|
|||||||
import sys
|
import sys
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
_maxsize=0
|
_maxsize=0
|
||||||
_solution=0
|
_solution=0
|
||||||
|
_notbound=0
|
||||||
|
_sizebound=0
|
||||||
|
|
||||||
def cliqueIterator(graph,minsize=1,node=None):
|
def cliqueIterator(graph,minsize=1,node=None):
|
||||||
global _maxsize,_solution
|
global _maxsize,_solution,_notbound,_sizebound
|
||||||
_maxsize=0
|
_maxsize=0
|
||||||
_solution=0
|
_solution=0
|
||||||
|
_notbound=0
|
||||||
|
_sizebound=0
|
||||||
starttime = time.time()
|
starttime = time.time()
|
||||||
|
|
||||||
if node:
|
if node:
|
||||||
node = graph.getNode(node)
|
node = graph.getNode(node)
|
||||||
index = node.index
|
index = node.index
|
||||||
clique= set([index])
|
clique= set([index])
|
||||||
candidates= graph.neighbourIndexSet(index=index)
|
candidates= set(graph.neighbourIndexSet(index=index))
|
||||||
else:
|
else:
|
||||||
clique=set()
|
clique=set()
|
||||||
candidates = set(x.index for x in graph)
|
candidates = set(x.index for x in graph)
|
||||||
|
|
||||||
|
|
||||||
# candidates = set(x for x in candidates
|
# candidates = set(x for x in candidates
|
||||||
# if len(graph.neighbourIndexSet(index=x) & candidates) >= (minsize - 1))
|
# if len(graph.neighbourIndexSet(index=x) & candidates) >= (minsize - 1))
|
||||||
|
|
||||||
@ -33,12 +38,24 @@ def cliqueIterator(graph,minsize=1,node=None):
|
|||||||
|
|
||||||
|
|
||||||
|
|
||||||
def _cliqueIterator(graph,clique,candidates,notset,minsize=0,start=None):
|
def _cliqueIterator(graph,clique,candidates,notlist,minsize=0,start=None):
|
||||||
global _maxsize,_solution
|
global _maxsize,_solution,_notbound,_sizebound
|
||||||
|
|
||||||
|
# Speed indicator
|
||||||
if len(clique)>_maxsize or not _solution % 1000 :
|
lclique = len(clique)
|
||||||
lcandidates = len(candidates)
|
lcandidates = len(candidates)
|
||||||
|
notmin = lcandidates
|
||||||
|
notfix = None
|
||||||
|
|
||||||
|
for n in notlist:
|
||||||
|
nnc = candidates - graph.neighbourIndexSet(index=n)
|
||||||
|
nc = len(nnc)
|
||||||
|
if nc < notmin:
|
||||||
|
notmin=nc
|
||||||
|
notfix=n
|
||||||
|
notfixneib = nnc
|
||||||
|
|
||||||
|
if lclique > _maxsize or not _solution % 1000 :
|
||||||
if start is not None:
|
if start is not None:
|
||||||
top = time.time()
|
top = time.time()
|
||||||
delta = top - start
|
delta = top - start
|
||||||
@ -46,53 +63,59 @@ def _cliqueIterator(graph,clique,candidates,notset,minsize=0,start=None):
|
|||||||
start = top
|
start = top
|
||||||
else:
|
else:
|
||||||
speed = 0
|
speed = 0
|
||||||
print >>sys.stderr,"\rCandidates : %-5d Maximum clique size : %-5d Solutions explored : %10d speed = %5.2f solutions/sec " % (lcandidates,_maxsize,_solution,speed),
|
print >>sys.stderr,"\rCandidates : %-5d Maximum clique size : %-5d Solutions explored : %10d speed = %5.2f solutions/sec sizebound=%10d notbound=%10d " % (lcandidates,_maxsize,_solution,speed,_sizebound,_notbound),
|
||||||
sys.stderr.flush()
|
sys.stderr.flush()
|
||||||
if len(clique)>_maxsize:
|
if lclique > _maxsize:
|
||||||
_maxsize=len(clique)
|
_maxsize=lclique
|
||||||
|
|
||||||
|
# print >>sys.stderr,'koukou'
|
||||||
|
|
||||||
|
if not candidates and not notlist:
|
||||||
|
yield set(clique)
|
||||||
|
else:
|
||||||
|
while notmin and candidates and (lclique + len(candidates)) >= minsize:
|
||||||
|
# count explored solution
|
||||||
|
_solution+=1
|
||||||
|
|
||||||
if (len(clique)+len(candidates)) >= minsize:
|
if notfix is None:
|
||||||
|
|
||||||
if not candidates and not notset:
|
|
||||||
yield set(clique)
|
|
||||||
else:
|
|
||||||
while candidates:
|
|
||||||
# count explored solution
|
|
||||||
_solution+=1
|
|
||||||
|
|
||||||
nextcandidate = candidates.pop()
|
nextcandidate = candidates.pop()
|
||||||
|
else:
|
||||||
clique.add(nextcandidate)
|
nextcandidate = notfixneib.pop()
|
||||||
|
candidates.remove(nextcandidate)
|
||||||
# Speed indicator
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
nextcandidates= candidates & graph.neighbourIndexSet(index=nextcandidate)
|
|
||||||
nextnot = notset & graph.neighbourIndexSet(index=nextcandidate)
|
|
||||||
|
|
||||||
|
|
||||||
# potentialClique = nextcandidates | clique
|
clique.add(nextcandidate)
|
||||||
# nextcandidates = set(x for x in nextcandidates
|
|
||||||
# if len(graph.neighbourIndexSet(index=x) & potentialClique) >= (minsize - 1))
|
neighbours = graph.neighbourIndexSet(index=nextcandidate)
|
||||||
#
|
|
||||||
#
|
nextcandidates = candidates & neighbours
|
||||||
#
|
nextnot = notlist & neighbours
|
||||||
# if (len(nextcandidates) + len(clique)) >= minsize:
|
|
||||||
#
|
nnc = candidates - neighbours
|
||||||
# if nextcandidates:
|
lnnc=len(nnc)
|
||||||
|
|
||||||
|
for c in _cliqueIterator(graph,
|
||||||
for c in _cliqueIterator(graph,
|
set(clique),
|
||||||
set(clique),
|
nextcandidates,
|
||||||
nextcandidates,
|
nextnot,
|
||||||
nextnot,
|
minsize,
|
||||||
minsize,
|
start):
|
||||||
start):
|
yield c
|
||||||
yield c
|
|
||||||
|
|
||||||
|
clique.remove(nextcandidate)
|
||||||
|
|
||||||
|
notmin-=1
|
||||||
|
|
||||||
|
if lnnc < notmin:
|
||||||
|
notmin = lnnc
|
||||||
|
notfix = nextcandidate
|
||||||
|
notfixneib = nnc
|
||||||
|
|
||||||
clique.remove(nextcandidate)
|
if notmin==0:
|
||||||
notset.add(nextcandidate)
|
_notbound+=1
|
||||||
|
|
||||||
|
notlist.add(nextcandidate)
|
||||||
|
else:
|
||||||
|
if (lclique + len(candidates)) < minsize:
|
||||||
|
_sizebound+=1
|
||||||
|
|
||||||
|
|||||||
@ -2,8 +2,9 @@ from logging import debug,root,DEBUG
|
|||||||
|
|
||||||
|
|
||||||
|
|
||||||
from obitools.word import wordSelector,wordIterator
|
from obitools.word import wordSelector,allWordIterator
|
||||||
from obitools.word import predicat
|
from obitools.word import predicat
|
||||||
|
import sys
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
@ -80,16 +81,16 @@ def dnaWordIterator(options):
|
|||||||
assert options.familySize is not None,"option -f or --family-size must be specified"
|
assert options.familySize is not None,"option -f or --family-size must be specified"
|
||||||
assert options.oligoDist is not None,"option -d or --distance must be specified"
|
assert options.oligoDist is not None,"option -d or --distance must be specified"
|
||||||
|
|
||||||
words = wordIterator(options.oligoSize)
|
words = allWordIterator(options.oligoSize)
|
||||||
seed = 'a' * options.oligoSize
|
#seed = 'a' * options.oligoSize
|
||||||
|
|
||||||
if not hasattr(options, "acceptedOligo"):
|
if not hasattr(options, "acceptedOligo") or options.acceptedOligo is None:
|
||||||
options.acceptedOligo=[]
|
options.acceptedOligo=[]
|
||||||
|
|
||||||
if not hasattr(options, "rejectedOligo"):
|
if not hasattr(options, "rejectedOligo") or options.rejectedOligo is None:
|
||||||
options.rejectedOligo=[]
|
options.rejectedOligo=[]
|
||||||
|
|
||||||
options.acceptedOligo.append(predicat.distMinGenerator(seed, options.oligoDist))
|
#options.acceptedOligo.append(predicat.distMinGenerator(seed, options.oligoDist))
|
||||||
|
|
||||||
if options.homopolymere:
|
if options.homopolymere:
|
||||||
options.rejectedOligo.append(predicat.homoPolymerGenerator(options.homopolymere))
|
options.rejectedOligo.append(predicat.homoPolymerGenerator(options.homopolymere))
|
||||||
|
|||||||
78
src/oligoTag.py
Executable file
78
src/oligoTag.py
Executable file
@ -0,0 +1,78 @@
|
|||||||
|
#!/usr/local/bin/python
|
||||||
|
|
||||||
|
import sys
|
||||||
|
import re
|
||||||
|
from logging import root,DEBUG
|
||||||
|
|
||||||
|
from obitools.options import getOptionManager
|
||||||
|
|
||||||
|
from obitools import oligo
|
||||||
|
|
||||||
|
from obitools.word.options import addOligoOptions
|
||||||
|
from obitools.word.options import dnaWordIterator,wordSelector
|
||||||
|
|
||||||
|
from obitools.word import wordDist
|
||||||
|
from obitools.word.predicat import distMinGenerator
|
||||||
|
|
||||||
|
from obitools.graph.algorithms.clique import cliqueIterator
|
||||||
|
from obitools.graph import Graph
|
||||||
|
|
||||||
|
def edgeIterator(words,distmin=1):
|
||||||
|
words=[x for x in words]
|
||||||
|
|
||||||
|
for i in xrange(len(words)):
|
||||||
|
for j in xrange(i+1,len(words)):
|
||||||
|
if wordDist(words[i], words[j])>=distmin:
|
||||||
|
yield words[i], words[j]
|
||||||
|
|
||||||
|
def readData(edges):
|
||||||
|
graph = Graph()
|
||||||
|
|
||||||
|
for x,y in edges:
|
||||||
|
graph.addEdge(x, y)
|
||||||
|
return graph
|
||||||
|
|
||||||
|
|
||||||
|
if __name__=='__main__':
|
||||||
|
|
||||||
|
try:
|
||||||
|
import psyco
|
||||||
|
psyco.full()
|
||||||
|
except ImportError:
|
||||||
|
pass
|
||||||
|
|
||||||
|
optionParser = getOptionManager([addOligoOptions],
|
||||||
|
)
|
||||||
|
(options, entries) = optionParser()
|
||||||
|
|
||||||
|
|
||||||
|
goodOligo = dnaWordIterator(options)
|
||||||
|
|
||||||
|
print >>sys.stderr,"Build good words graph..."
|
||||||
|
|
||||||
|
graph= readData(edgeIterator(goodOligo,options.oligoDist))
|
||||||
|
|
||||||
|
print >>sys.stderr,"Initial graph size : %d edge count : %d" % (len(graph),graph.edgeCount())
|
||||||
|
# print >>sys.stderr,"Component connexe count : %d" % len(connected_components(graph))
|
||||||
|
print >>sys.stderr
|
||||||
|
|
||||||
|
# startNode = graph.getNode(index=0).label
|
||||||
|
|
||||||
|
ci = cliqueIterator(graph, options.familySize)
|
||||||
|
|
||||||
|
try:
|
||||||
|
result = ci.next()
|
||||||
|
print >>sys.stderr
|
||||||
|
|
||||||
|
for word in result:
|
||||||
|
print graph.getNode(index=word).getLabel()
|
||||||
|
|
||||||
|
except StopIteration:
|
||||||
|
print >>sys.stderr
|
||||||
|
print >>sys.stderr,"-------------------------------------------"
|
||||||
|
print >>sys.stderr
|
||||||
|
print >>sys.stderr,"No solutions for this parametter set"
|
||||||
|
print >>sys.stderr
|
||||||
|
print >>sys.stderr,"-------------------------------------------"
|
||||||
|
print >>sys.stderr
|
||||||
|
|
||||||
Reference in New Issue
Block a user