183 lines
19 KiB
HTML
183 lines
19 KiB
HTML
<?xml version="1.0" encoding="ascii"?>
|
|
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
|
|
"DTD/xhtml1-transitional.dtd">
|
|
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
|
|
<head>
|
|
<title>obitools.fast</title>
|
|
<link rel="stylesheet" href="epydoc.css" type="text/css" />
|
|
<script type="text/javascript" src="epydoc.js"></script>
|
|
</head>
|
|
|
|
<body bgcolor="white" text="black" link="blue" vlink="#204080"
|
|
alink="#204080">
|
|
<!-- ==================== NAVIGATION BAR ==================== -->
|
|
<table class="navbar" border="0" width="100%" cellpadding="0"
|
|
bgcolor="#a0c0ff" cellspacing="0">
|
|
<tr valign="middle">
|
|
<!-- Home link -->
|
|
<th> <a
|
|
href="obitools-module.html">Home</a> </th>
|
|
|
|
<!-- Tree link -->
|
|
<th> <a
|
|
href="module-tree.html">Trees</a> </th>
|
|
|
|
<!-- Index link -->
|
|
<th> <a
|
|
href="identifier-index.html">Indices</a> </th>
|
|
|
|
<!-- Help link -->
|
|
<th> <a
|
|
href="help.html">Help</a> </th>
|
|
|
|
<!-- Project homepage -->
|
|
<th class="navbar" align="right" width="100%">
|
|
<table border="0" cellpadding="0" cellspacing="0">
|
|
<tr><th class="navbar" align="center"
|
|
><a class="navbar" target="_top" href="http://www.grenoble.prabi.fr/trac/OBITools">OBITools</a></th>
|
|
</tr></table></th>
|
|
</tr>
|
|
</table>
|
|
<table width="100%" cellpadding="0" cellspacing="0">
|
|
<tr valign="top">
|
|
<td width="100%">
|
|
<span class="breadcrumbs">
|
|
<a href="obitools-module.html">Package obitools</a> ::
|
|
Module fast
|
|
</span>
|
|
</td>
|
|
<td>
|
|
<table cellpadding="0" cellspacing="0">
|
|
<!-- hide/show private -->
|
|
<tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
|
|
onclick="toggle_private();">hide private</a>]</span></td></tr>
|
|
<tr><td align="right"><span class="options"
|
|
>[<a href="frames.html" target="_top">frames</a
|
|
>] | <a href="obitools.fast-pysrc.html"
|
|
target="_top">no frames</a>]</span></td></tr>
|
|
</table>
|
|
</td>
|
|
</tr>
|
|
</table>
|
|
<h1 class="epydoc">Source Code for <a href="obitools.fast-module.html">Module obitools.fast</a></h1>
|
|
<pre class="py-src">
|
|
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
|
|
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-docstring"> implement fastn/fastp sililarity search algorithm for BioSequence.</tt> </tt>
|
|
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
|
|
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"> </tt>
|
|
<a name="Fast"></a><div id="Fast-def"><a name="L5"></a><tt class="py-lineno"> 5</tt> <a class="py-toggle" href="#" id="Fast-toggle" onclick="return toggle('Fast');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="obitools.fast.Fast-class.html">Fast</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="Fast-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="Fast-expanded"><a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"> </tt>
|
|
<a name="Fast.__init__"></a><div id="Fast.__init__-def"><a name="L7"></a><tt class="py-lineno"> 7</tt> <a class="py-toggle" href="#" id="Fast.__init__-toggle" onclick="return toggle('Fast.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.fast.Fast-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">seq</tt><tt class="py-op">,</tt><tt class="py-param">kup</tt><tt class="py-op">=</tt><tt class="py-number">2</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="Fast.__init__-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="Fast.__init__-expanded"><a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
|
|
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring"> @param seq: sequence to hash</tt> </tt>
|
|
<a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"><tt class="py-docstring"> @type seq: BioSequence</tt> </tt>
|
|
<a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"><tt class="py-docstring"> @param kup: word size used for hashing process</tt> </tt>
|
|
<a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"><tt class="py-docstring"> @type kup: int</tt> </tt>
|
|
<a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
|
|
<a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"> <tt class="py-name">hash</tt><tt class="py-op">=</tt><tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
|
|
<a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"> <tt id="link-0" class="py-name" targets="Variable obitools.BioSequence.seq=obitools.BioSequence-class.html#seq,Variable obitools.WrappedBioSequence.seq=obitools.WrappedBioSequence-class.html#seq"><a title="obitools.BioSequence.seq
|
|
obitools.WrappedBioSequence.seq" class="py-name" href="#" onclick="return doclink('link-0', 'seq', 'link-0');">seq</a></tt> <tt class="py-op">=</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-1" class="py-name"><a title="obitools.BioSequence.seq
|
|
obitools.WrappedBioSequence.seq" class="py-name" href="#" onclick="return doclink('link-1', 'seq', 'link-0');">seq</a></tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-2" class="py-name" targets="Package obitools.word=obitools.word-module.html"><a title="obitools.word" class="py-name" href="#" onclick="return doclink('link-2', 'word', 'link-2');">word</a></tt><tt class="py-op">,</tt><tt class="py-name">pos</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-3" class="py-name"><a title="obitools.BioSequence.seq
|
|
obitools.WrappedBioSequence.seq" class="py-name" href="#" onclick="return doclink('link-3', 'seq', 'link-0');">seq</a></tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">:</tt><tt class="py-name">i</tt><tt class="py-op">+</tt><tt class="py-name">kup</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">upper</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">i</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-4" class="py-name"><a title="obitools.BioSequence.seq
|
|
obitools.WrappedBioSequence.seq" class="py-name" href="#" onclick="return doclink('link-4', 'seq', 'link-0');">seq</a></tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-name">kup</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-5" class="py-name"><a title="obitools.word" class="py-name" href="#" onclick="return doclink('link-5', 'word', 'link-2');">word</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">hash</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">hash</tt><tt class="py-op">[</tt><tt id="link-6" class="py-name"><a title="obitools.word" class="py-name" href="#" onclick="return doclink('link-6', 'word', 'link-2');">word</a></tt><tt class="py-op">]</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,Method obitools.table.Table.append()=obitools.table.Table-class.html#append,Method obitools.table.TableRow.append()=obitools.table.TableRow-class.html#append,Method obitools.table._Row.append()=obitools.table._Row-class.html#append"><a title="obitools.align.Alignement.append
|
|
obitools.table.Table.append
|
|
obitools.table.TableRow.append
|
|
obitools.table._Row.append" class="py-name" href="#" onclick="return doclink('link-7', 'append', 'link-7');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">pos</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"> <tt class="py-name">hash</tt><tt class="py-op">[</tt><tt id="link-8" class="py-name"><a title="obitools.word" class="py-name" href="#" onclick="return doclink('link-8', 'word', 'link-2');">word</a></tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-name">pos</tt><tt class="py-op">]</tt> </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 class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_kup</tt> <tt class="py-op">=</tt> <tt class="py-name">kup</tt> </tt>
|
|
<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_hash</tt><tt class="py-op">=</tt> <tt class="py-name">hash</tt> </tt>
|
|
</div><a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"> </tt>
|
|
<a name="Fast.__call__"></a><div id="Fast.__call__-def"><a name="L25"></a><tt class="py-lineno">25</tt> <a class="py-toggle" href="#" id="Fast.__call__-toggle" onclick="return toggle('Fast.__call__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.fast.Fast-class.html#__call__">__call__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">seq</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="Fast.__call__-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="Fast.__call__-expanded"><a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
|
|
<a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"><tt class="py-docstring"> Align one sequence with the fast hash table.</tt> </tt>
|
|
<a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
|
|
<a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"><tt class="py-docstring"> @param seq: the sequence to align</tt> </tt>
|
|
<a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"><tt class="py-docstring"> @type seq: BioSequence</tt> </tt>
|
|
<a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
|
|
<a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"><tt class="py-docstring"> @return: where smax is the</tt> </tt>
|
|
<a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"><tt class="py-docstring"> score of the largest diagonal and pmax the</tt> </tt>
|
|
<a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"><tt class="py-docstring"> associated shift </tt> </tt>
|
|
<a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: a int tuple (smax,pmax)</tt> </tt>
|
|
<a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
|
|
<a name="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"> <tt class="py-name">histo</tt><tt class="py-op">=</tt><tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
|
|
<a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"> <tt id="link-9" class="py-name"><a title="obitools.BioSequence.seq
|
|
obitools.WrappedBioSequence.seq" class="py-name" href="#" onclick="return doclink('link-9', 'seq', 'link-0');">seq</a></tt> <tt class="py-op">=</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-10" class="py-name"><a title="obitools.BioSequence.seq
|
|
obitools.WrappedBioSequence.seq" class="py-name" href="#" onclick="return doclink('link-10', 'seq', 'link-0');">seq</a></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">hash</tt><tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_hash</tt> </tt>
|
|
<a name="L40"></a><tt class="py-lineno">40</tt> <tt class="py-line"> <tt class="py-name">kup</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_kup</tt> </tt>
|
|
<a name="L41"></a><tt class="py-lineno">41</tt> <tt class="py-line"> </tt>
|
|
<a name="L42"></a><tt class="py-lineno">42</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-11" class="py-name"><a title="obitools.word" class="py-name" href="#" onclick="return doclink('link-11', 'word', 'link-2');">word</a></tt><tt class="py-op">,</tt><tt class="py-name">pos</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-12" class="py-name"><a title="obitools.BioSequence.seq
|
|
obitools.WrappedBioSequence.seq" class="py-name" href="#" onclick="return doclink('link-12', 'seq', 'link-0');">seq</a></tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">:</tt><tt class="py-name">i</tt><tt class="py-op">+</tt><tt class="py-name">kup</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">i</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-13" class="py-name"><a title="obitools.BioSequence.seq
|
|
obitools.WrappedBioSequence.seq" class="py-name" href="#" onclick="return doclink('link-13', 'seq', 'link-0');">seq</a></tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-name">kup</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L43"></a><tt class="py-lineno">43</tt> <tt class="py-line"> <tt class="py-name">matchedpos</tt> <tt class="py-op">=</tt> <tt class="py-name">hash</tt><tt class="py-op">.</tt><tt id="link-14" class="py-name" targets="Method obitools.eutils.EFetch.get()=obitools.eutils.EFetch-class.html#get"><a title="obitools.eutils.EFetch.get" class="py-name" href="#" onclick="return doclink('link-14', 'get', 'link-14');">get</a></tt><tt class="py-op">(</tt><tt id="link-15" class="py-name"><a title="obitools.word" class="py-name" href="#" onclick="return doclink('link-15', 'word', 'link-2');">word</a></tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L44"></a><tt class="py-lineno">44</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">p</tt> <tt class="py-keyword">in</tt> <tt class="py-name">matchedpos</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">delta</tt> <tt class="py-op">=</tt> <tt class="py-name">pos</tt> <tt class="py-op">-</tt> <tt class="py-name">p</tt> </tt>
|
|
<a name="L46"></a><tt class="py-lineno">46</tt> <tt class="py-line"> <tt class="py-name">histo</tt><tt class="py-op">[</tt><tt class="py-name">delta</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">histo</tt><tt class="py-op">.</tt><tt id="link-16" class="py-name"><a title="obitools.eutils.EFetch.get" class="py-name" href="#" onclick="return doclink('link-16', 'get', 'link-14');">get</a></tt><tt class="py-op">(</tt><tt class="py-name">delta</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-number">1</tt> </tt>
|
|
<a name="L47"></a><tt class="py-lineno">47</tt> <tt class="py-line"> <tt class="py-name">smax</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">histo</tt><tt class="py-op">.</tt><tt class="py-name">values</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-name">pmax</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">x</tt> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">histo</tt> <tt class="py-keyword">if</tt> <tt class="py-name">histo</tt><tt class="py-op">[</tt><tt class="py-name">x</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-name">smax</tt><tt class="py-op">]</tt> </tt>
|
|
<a name="L49"></a><tt class="py-lineno">49</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">smax</tt><tt class="py-op">,</tt><tt class="py-name">pmax</tt> </tt>
|
|
</div></div><a name="L50"></a><tt class="py-lineno">50</tt> <tt class="py-line"> </tt><script type="text/javascript">
|
|
<!--
|
|
expandto(location.href);
|
|
// -->
|
|
</script>
|
|
</pre>
|
|
<br />
|
|
<!-- ==================== NAVIGATION BAR ==================== -->
|
|
<table class="navbar" border="0" width="100%" cellpadding="0"
|
|
bgcolor="#a0c0ff" cellspacing="0">
|
|
<tr valign="middle">
|
|
<!-- Home link -->
|
|
<th> <a
|
|
href="obitools-module.html">Home</a> </th>
|
|
|
|
<!-- Tree link -->
|
|
<th> <a
|
|
href="module-tree.html">Trees</a> </th>
|
|
|
|
<!-- Index link -->
|
|
<th> <a
|
|
href="identifier-index.html">Indices</a> </th>
|
|
|
|
<!-- Help link -->
|
|
<th> <a
|
|
href="help.html">Help</a> </th>
|
|
|
|
<!-- Project homepage -->
|
|
<th class="navbar" align="right" width="100%">
|
|
<table border="0" cellpadding="0" cellspacing="0">
|
|
<tr><th class="navbar" align="center"
|
|
><a class="navbar" target="_top" href="http://www.grenoble.prabi.fr/trac/OBITools">OBITools</a></th>
|
|
</tr></table></th>
|
|
</tr>
|
|
</table>
|
|
<table border="0" cellpadding="0" cellspacing="0" width="100%%">
|
|
<tr>
|
|
<td align="left" class="footer">
|
|
<a href="epydoc-log.html">Generated by Epydoc
|
|
3.0beta1 on Tue Apr 29 13:03:55 2008</a>
|
|
</td>
|
|
<td align="right" class="footer">
|
|
<a href="http://epydoc.sourceforge.net">http://epydoc.sourceforge.net</a>
|
|
</td>
|
|
</tr>
|
|
</table>
|
|
|
|
<script type="text/javascript">
|
|
<!--
|
|
// Private objects are initially displayed (because if
|
|
// javascript is turned off then we want them to be
|
|
// visible); but by default, we want to hide them. So hide
|
|
// them unless we have a cookie that says to show them.
|
|
checkCookie()
|
|
// -->
|
|
</script>
|
|
|
|
</body>
|
|
</html>
|