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Module FormatConvert
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<h1 class="epydoc">Source Code for <a href="Bio.Align.FormatConvert-module.html">Module Bio.Align.FormatConvert</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">Utility for conversion between different formats for representing alignments.</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 class="py-docstring">classes:</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-docstring">FormatConverter</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">"""</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 class="py-comment"># biopython</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Package Bio.Fasta=Bio.Fasta-module.html"><a title="Bio.Fasta" class="py-name" href="#" onclick="return doclink('link-1', 'Fasta', 'link-1');">Fasta</a></tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Module Bio.Fasta.FastaAlign=Bio.Fasta.FastaAlign-module.html"><a title="Bio.Fasta.FastaAlign" class="py-name" href="#" onclick="return doclink('link-2', 'FastaAlign', 'link-2');">FastaAlign</a></tt> <tt class="py-keyword">import</tt> <tt id="link-3" class="py-name" targets="Class Bio.Fasta.FastaAlign.FastaAlignment=Bio.Fasta.FastaAlign.FastaAlignment-class.html"><a title="Bio.Fasta.FastaAlign.FastaAlignment" class="py-name" href="#" onclick="return doclink('link-3', 'FastaAlignment', 'link-3');">FastaAlignment</a></tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-4" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-4', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Package Bio.Clustalw=Bio.Clustalw-module.html"><a title="Bio.Clustalw" class="py-name" href="#" onclick="return doclink('link-5', 'Clustalw', 'link-5');">Clustalw</a></tt> <tt class="py-keyword">import</tt> <tt id="link-6" class="py-name" targets="Class Bio.Clustalw.ClustalAlignment=Bio.Clustalw.ClustalAlignment-class.html"><a title="Bio.Clustalw.ClustalAlignment" class="py-name" href="#" onclick="return doclink('link-6', 'ClustalAlignment', 'link-6');">ClustalAlignment</a></tt> </tt>
<a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"> </tt>
<a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"> </tt>
<a name="FormatConverter"></a><div id="FormatConverter-def"><a name="L13"></a><tt class="py-lineno">13</tt> <a class="py-toggle" href="#" id="FormatConverter-toggle" onclick="return toggle('FormatConverter');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Align.FormatConvert.FormatConverter-class.html">FormatConverter</a><tt class="py-op">:</tt> </tt>
</div><div id="FormatConverter-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="FormatConverter-expanded"><a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"> <tt class="py-docstring">"""Convert between different alignment representation formats.</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"> The basic idea behind the converter is that it takes a given format,</tt> </tt>
<a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"><tt class="py-docstring"> converts it into the base Alignment class, and then can return an object</tt> </tt>
<a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"><tt class="py-docstring"> in any other supported format with the info from the basal alignment.</tt> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"><tt class="py-docstring"> Supported formats are:</tt> </tt>
<a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"><tt class="py-docstring"> o Clustal format (*.aln)</tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"><tt class="py-docstring"> o Fasta format (*.fasta)</tt> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="FormatConverter.__init__"></a><div id="FormatConverter.__init__-def"><a name="L24"></a><tt class="py-lineno">24</tt> <a class="py-toggle" href="#" id="FormatConverter.__init__-toggle" onclick="return toggle('FormatConverter.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Align.FormatConvert.FormatConverter-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">to_convert</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FormatConverter.__init__-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="FormatConverter.__init__-expanded"><a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"> <tt class="py-docstring">"""Initialize a converter with a given object.</tt> </tt>
<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"> Arguments:</tt> </tt>
<a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"><tt class="py-docstring"> o to_convert - The class which we are going to be converting.</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-name">self</tt><tt class="py-op">.</tt><tt class="py-name">orig_format</tt> <tt class="py-op">=</tt> <tt class="py-name">to_convert</tt> </tt>
<a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"> </tt>
<a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_base_alphabet</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_base_records</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name" targets="Method Bio.Align.FormatConvert.FormatConverter._get_base_info()=Bio.Align.FormatConvert.FormatConverter-class.html#_get_base_info"><a title="Bio.Align.FormatConvert.FormatConverter._get_base_info" class="py-name" href="#" onclick="return doclink('link-7', '_get_base_info', 'link-7');">_get_base_info</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"> </tt>
<a name="FormatConverter._get_base_info"></a><div id="FormatConverter._get_base_info-def"><a name="L34"></a><tt class="py-lineno">34</tt> <a class="py-toggle" href="#" id="FormatConverter._get_base_info-toggle" onclick="return toggle('FormatConverter._get_base_info');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Align.FormatConvert.FormatConverter-class.html#_get_base_info">_get_base_info</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FormatConverter._get_base_info-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="FormatConverter._get_base_info-expanded"><a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"> <tt class="py-docstring">"""Retrieve all of the basal (ie Generic.Alignment) info.</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-docstring"> The idea is that this info is present in all of the classes and</tt> </tt>
<a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"><tt class="py-docstring"> this is the information that will be retained in a conversion.</tt> </tt>
<a name="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"><tt class="py-docstring"> Format specific information will be lost.</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-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">orig_format</tt><tt class="py-op">.</tt><tt id="link-8" class="py-name" targets="Method Bio.MEME.Motif.Motif._alphabet()=Bio.MEME.Motif.Motif-class.html#_alphabet,Method Bio.MEME.Parser.MASTRecord._alphabet()=Bio.MEME.Parser.MASTRecord-class.html#_alphabet,Method Bio.MEME.Parser._MEMEConsumer._alphabet()=Bio.MEME.Parser._MEMEConsumer-class.html#_alphabet"><a title="Bio.MEME.Motif.Motif._alphabet
Bio.MEME.Parser.MASTRecord._alphabet
Bio.MEME.Parser._MEMEConsumer._alphabet" class="py-name" href="#" onclick="return doclink('link-8', '_alphabet', 'link-8');">_alphabet</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">orig_format</tt><tt class="py-op">.</tt><tt class="py-name">_records</tt> </tt>
</div><a name="L42"></a><tt class="py-lineno">42</tt> <tt class="py-line"> </tt>
<a name="FormatConverter.to_fasta"></a><div id="FormatConverter.to_fasta-def"><a name="L43"></a><tt class="py-lineno">43</tt> <a class="py-toggle" href="#" id="FormatConverter.to_fasta-toggle" onclick="return toggle('FormatConverter.to_fasta');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Align.FormatConvert.FormatConverter-class.html#to_fasta">to_fasta</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FormatConverter.to_fasta-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="FormatConverter.to_fasta-expanded"><a name="L44"></a><tt class="py-lineno">44</tt> <tt class="py-line"> <tt class="py-docstring">"""Convert the current info into a FastaAlignment object.</tt> </tt>
<a name="L45"></a><tt class="py-lineno">45</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L46"></a><tt class="py-lineno">46</tt> <tt class="py-line"> <tt class="py-name">return_format</tt> <tt class="py-op">=</tt> <tt id="link-9" class="py-name"><a title="Bio.Fasta.FastaAlign.FastaAlignment" class="py-name" href="#" onclick="return doclink('link-9', 'FastaAlignment', 'link-3');">FastaAlignment</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_base_alphabet</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">return_format</tt><tt class="py-op">.</tt><tt class="py-name">_records</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_base_records</tt> </tt>
<a name="L48"></a><tt class="py-lineno">48</tt> <tt class="py-line"> </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">return_format</tt> </tt>
</div><a name="L50"></a><tt class="py-lineno">50</tt> <tt class="py-line"> </tt>
<a name="FormatConverter.to_clustal"></a><div id="FormatConverter.to_clustal-def"><a name="L51"></a><tt class="py-lineno">51</tt> <a class="py-toggle" href="#" id="FormatConverter.to_clustal-toggle" onclick="return toggle('FormatConverter.to_clustal');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Align.FormatConvert.FormatConverter-class.html#to_clustal">to_clustal</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FormatConverter.to_clustal-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="FormatConverter.to_clustal-expanded"><a name="L52"></a><tt class="py-lineno">52</tt> <tt class="py-line"> <tt class="py-docstring">"""Convert the current info into a ClustalAlignment object.</tt> </tt>
<a name="L53"></a><tt class="py-lineno">53</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L54"></a><tt class="py-lineno">54</tt> <tt class="py-line"> <tt class="py-name">return_format</tt> <tt class="py-op">=</tt> <tt id="link-10" class="py-name"><a title="Bio.Clustalw.ClustalAlignment" class="py-name" href="#" onclick="return doclink('link-10', 'ClustalAlignment', 'link-6');">ClustalAlignment</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_base_alphabet</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">return_format</tt><tt class="py-op">.</tt><tt class="py-name">_records</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_base_records</tt> </tt>
<a name="L56"></a><tt class="py-lineno">56</tt> <tt class="py-line"> </tt>
<a name="L57"></a><tt class="py-lineno">57</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">return_format</tt> </tt>
</div></div><a name="L58"></a><tt class="py-lineno">58</tt> <tt class="py-line"> </tt><script type="text/javascript">
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