<?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>Bio.HMM.Utilities</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"> <!-- 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> <th class="navbar" width="100%"></th> </tr> </table> <table width="100%" cellpadding="0" cellspacing="0"> <tr valign="top"> <td width="100%"> <span class="breadcrumbs"> <a href="Bio-module.html">Package Bio</a> :: <a href="Bio.HMM-module.html">Package HMM</a> :: Module Utilities </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="Bio.HMM.Utilities-pysrc.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <h1 class="epydoc">Source Code for <a href="Bio.HMM.Utilities-module.html">Module Bio.HMM.Utilities</a></h1> <pre class="py-src"> <a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-docstring">"""Generic functions which are useful for working with HMMs.</tt> </tt> <a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-docstring">This just collects general functions which you might like to use in</tt> </tt> <a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-docstring">dealing with HMMs.</tt> </tt> <a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt> <a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-comment"># standard modules</tt> </tt> <a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">import</tt> <tt class="py-name">string</tt> </tt> <a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"> </tt> <a name="pretty_print_prediction"></a><div id="pretty_print_prediction-def"><a name="L9"></a><tt class="py-lineno"> 9</tt> <a class="py-toggle" href="#" id="pretty_print_prediction-toggle" onclick="return toggle('pretty_print_prediction');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.HMM.Utilities-module.html#pretty_print_prediction">pretty_print_prediction</a><tt class="py-op">(</tt><tt class="py-param">emissions</tt><tt class="py-op">,</tt> <tt class="py-param">real_state</tt><tt class="py-op">,</tt> <tt class="py-param">predicted_state</tt><tt class="py-op">,</tt> </tt> <a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"> <tt class="py-param">emission_title</tt> <tt class="py-op">=</tt> <tt class="py-string">"Emissions"</tt><tt class="py-op">,</tt> </tt> <a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"> <tt class="py-param">real_title</tt> <tt class="py-op">=</tt> <tt class="py-string">"Real State"</tt><tt class="py-op">,</tt> </tt> <a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"> <tt class="py-param">predicted_title</tt> <tt class="py-op">=</tt> <tt class="py-string">"Predicted State"</tt><tt class="py-op">,</tt> </tt> <a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"> <tt class="py-param">line_width</tt> <tt class="py-op">=</tt> <tt class="py-number">75</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="pretty_print_prediction-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="pretty_print_prediction-expanded"><a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"> <tt class="py-docstring">"""Print out a state sequence prediction in a nice manner.</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"> Arguments:</tt> </tt> <a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt> <a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"><tt class="py-docstring"> o emissions -- The sequence of emissions of the sequence you are</tt> </tt> <a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"><tt class="py-docstring"> dealing with.</tt> </tt> <a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"><tt class="py-docstring"> o real_state -- The actual state path that generated the emissions.</tt> </tt> <a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"><tt class="py-docstring"> o predicted_state -- A state path predicted by some kind of HMM model.</tt> </tt> <a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"> <tt class="py-comment"># calculate the length of the titles and sequences</tt> </tt> <a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">title_length</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">emission_title</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">real_title</tt><tt class="py-op">)</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">len</tt><tt class="py-op">(</tt><tt class="py-name">predicted_title</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt> </tt> <a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"> <tt class="py-name">seq_length</tt> <tt class="py-op">=</tt> <tt class="py-name">line_width</tt> <tt class="py-op">-</tt> <tt class="py-name">title_length</tt> </tt> <a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"> </tt> <a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"> <tt class="py-comment"># set up the titles so they'll print right</tt> </tt> <a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">emission_title</tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">ljust</tt><tt class="py-op">(</tt><tt class="py-name">emission_title</tt><tt class="py-op">,</tt> <tt class="py-name">title_length</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">real_title</tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">ljust</tt><tt class="py-op">(</tt><tt class="py-name">real_title</tt><tt class="py-op">,</tt> <tt class="py-name">title_length</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">predicted_title</tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">ljust</tt><tt class="py-op">(</tt><tt class="py-name">predicted_title</tt><tt class="py-op">,</tt> <tt class="py-name">title_length</tt><tt class="py-op">)</tt> </tt> <a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"> </tt> <a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"> <tt class="py-name">cur_position</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt> <a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"> <tt class="py-comment"># while we still have more than seq_length characters to print</tt> </tt> <a name="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt> <a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt class="py-name">cur_position</tt> <tt class="py-op">+</tt> <tt class="py-name">seq_length</tt><tt class="py-op">)</tt> <tt class="py-op"><</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">emissions</tt><tt class="py-op">)</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">extension</tt> <tt class="py-op">=</tt> <tt class="py-name">seq_length</tt> </tt> <a name="L40"></a><tt class="py-lineno">40</tt> <tt class="py-line"> <tt class="py-keyword">else</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">extension</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">emissions</tt><tt class="py-op">)</tt> <tt class="py-op">-</tt> <tt class="py-name">cur_position</tt> </tt> <a name="L42"></a><tt class="py-lineno">42</tt> <tt class="py-line"> </tt> <a name="L43"></a><tt class="py-lineno">43</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"%s%s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">emission_title</tt><tt class="py-op">,</tt> </tt> <a name="L44"></a><tt class="py-lineno">44</tt> <tt class="py-line"> <tt class="py-name">emissions</tt><tt class="py-op">.</tt><tt id="link-0" class="py-name" targets="Variable BioSQL.BioSeq.DBSeq.data=BioSQL.BioSeq.DBSeq-class.html#data"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-0', 'data', 'link-0');">data</a></tt><tt class="py-op">[</tt><tt class="py-name">cur_position</tt><tt class="py-op">:</tt><tt class="py-name">cur_position</tt> <tt class="py-op">+</tt> <tt class="py-name">seq_length</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt> <a name="L45"></a><tt class="py-lineno">45</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"%s%s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">real_title</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">real_state</tt><tt class="py-op">.</tt><tt id="link-1" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-1', 'data', 'link-0');">data</a></tt><tt class="py-op">[</tt><tt class="py-name">cur_position</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">cur_position</tt> <tt class="py-op">+</tt> <tt class="py-name">seq_length</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">print</tt> <tt class="py-string">"%s%s\n"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">predicted_title</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">predicted_state</tt><tt class="py-op">.</tt><tt id="link-2" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-2', 'data', 'link-0');">data</a></tt><tt class="py-op">[</tt><tt class="py-name">cur_position</tt><tt class="py-op">:</tt> </tt> <a name="L50"></a><tt class="py-lineno">50</tt> <tt class="py-line"> <tt class="py-name">cur_position</tt> <tt class="py-op">+</tt> <tt class="py-name">seq_length</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> <a name="L52"></a><tt class="py-lineno">52</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">emissions</tt><tt class="py-op">)</tt> <tt class="py-op"><</tt> <tt class="py-op">(</tt><tt class="py-name">cur_position</tt> <tt class="py-op">+</tt> <tt class="py-name">seq_length</tt><tt class="py-op">)</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-keyword">break</tt> </tt> <a name="L54"></a><tt class="py-lineno">54</tt> <tt class="py-line"> </tt> <a name="L55"></a><tt class="py-lineno">55</tt> <tt class="py-line"> <tt class="py-name">cur_position</tt> <tt class="py-op">+=</tt> <tt class="py-name">seq_length</tt> </tt> </div><a name="L56"></a><tt class="py-lineno">56</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"> <!-- Tree link --> <th> <a href="module-tree.html">Trees</a> 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