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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.expressions-module.html">Package expressions</a> ::
Module transfac
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<h1 class="epydoc">Source Code for <a href="Bio.expressions.transfac-module.html">Module Bio.expressions.transfac</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-docstring">"""A Martel format to parse the output from transfac.</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">Formats:</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-docstring">format Format for a whole file.</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-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-keyword">import</tt> <tt class="py-name">warnings</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-name">warnings</tt><tt class="py-op">.</tt><tt class="py-name">warn</tt><tt class="py-op">(</tt><tt class="py-string">"Bio.expressions was deprecated, as it does not work with recent versions of mxTextTools. If you want to continue to use this module, please get in contact with the Biopython developers at biopython-dev@biopython.org to avoid permanent removal of this module from Biopython"</tt><tt class="py-op">,</tt> <tt class="py-name">DeprecationWarning</tt><tt class="py-op">)</tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"> </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 class="py-keyword">import</tt> <tt class="py-name">sys</tt> </tt>
<a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Martel=Martel-module.html"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-0', 'Martel', 'link-0');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt>
<a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-1" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-1', 'Martel', 'link-0');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name" targets="Module Martel.RecordReader=Martel.RecordReader-module.html,Class Martel.RecordReader.RecordReader=Martel.RecordReader.RecordReader-class.html"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-2', 'RecordReader', 'link-2');">RecordReader</a></tt> </tt>
<a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"> </tt>
<a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"><tt id="link-3" class="py-name" targets="Variable Bio.Emboss.primer3_format.blank_line=Bio.Emboss.primer3_format-module.html#blank_line,Variable Bio.Emboss.primersearch_format.blank_line=Bio.Emboss.primersearch_format-module.html#blank_line,Variable Bio.MetaTool.metatool_format.blank_line=Bio.MetaTool.metatool_format-module.html#blank_line,Variable Bio.expressions.transfac.blank_line=Bio.expressions.transfac-module.html#blank_line"><a title="Bio.Emboss.primer3_format.blank_line
Bio.Emboss.primersearch_format.blank_line
Bio.MetaTool.metatool_format.blank_line
Bio.expressions.transfac.blank_line" class="py-name" href="#" onclick="return doclink('link-3', 'blank_line', 'link-3');">blank_line</a></tt> <tt class="py-op">=</tt> <tt id="link-4" class="py-name" targets="Function Martel.Opt()=Martel-module.html#Opt"><a title="Martel.Opt" class="py-name" href="#" onclick="return doclink('link-4', 'Opt', 'link-4');">Opt</a></tt><tt class="py-op">(</tt><tt id="link-5" class="py-name" targets="Function Martel.Spaces()=Martel-module.html#Spaces"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-5', 'Spaces', 'link-5');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-6" class="py-name" targets="Class Martel.Expression.AnyEol=Martel.Expression.AnyEol-class.html"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-6', 'AnyEol', 'link-6');">AnyEol</a></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>
<a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"><tt id="link-7" class="py-name" targets="Variable Bio.expressions.transfac.MATRIX_LINE=Bio.expressions.transfac-module.html#MATRIX_LINE"><a title="Bio.expressions.transfac.MATRIX_LINE" class="py-name" href="#" onclick="return doclink('link-7', 'MATRIX_LINE', 'link-7');">MATRIX_LINE</a></tt> <tt class="py-op">=</tt> <tt id="link-8" class="py-name" targets="Class Martel.Expression.Str=Martel.Expression.Str-class.html,Function Martel.Str()=Martel-module.html#Str"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-8', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"Search for sites by WeightMatrix library:"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-9" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-9', 'Spaces', 'link-5');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"> <tt id="link-10" class="py-name" targets="Function Martel.UntilEol()=Martel-module.html#UntilEol"><a title="Martel.UntilEol" class="py-name" href="#" onclick="return doclink('link-10', 'UntilEol', 'link-10');">UntilEol</a></tt><tt class="py-op">(</tt><tt class="py-string">"matrix_file"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-11" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-11', 'AnyEol', 'link-6');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"><tt id="link-12" class="py-name" targets="Variable Bio.expressions.transfac.SEQUENCE_LINE=Bio.expressions.transfac-module.html#SEQUENCE_LINE"><a title="Bio.expressions.transfac.SEQUENCE_LINE" class="py-name" href="#" onclick="return doclink('link-12', 'SEQUENCE_LINE', 'link-12');">SEQUENCE_LINE</a></tt> <tt class="py-op">=</tt> <tt id="link-13" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-13', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"Sequence file:"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-14" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-14', 'Spaces', 'link-5');">Spaces</a></tt><tt class="py-op">(</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 id="link-15" class="py-name"><a title="Martel.UntilEol" class="py-name" href="#" onclick="return doclink('link-15', 'UntilEol', 'link-10');">UntilEol</a></tt><tt class="py-op">(</tt><tt class="py-string">"sequence_file"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-16" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-16', 'AnyEol', 'link-6');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"><tt id="link-17" class="py-name" targets="Variable Bio.expressions.transfac.PROFILE_LINE=Bio.expressions.transfac-module.html#PROFILE_LINE"><a title="Bio.expressions.transfac.PROFILE_LINE" class="py-name" href="#" onclick="return doclink('link-17', 'PROFILE_LINE', 'link-17');">PROFILE_LINE</a></tt> <tt class="py-op">=</tt> <tt id="link-18" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-18', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"Site selection profile:"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-19" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-19', 'Spaces', 'link-5');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"> <tt id="link-20" class="py-name" targets="Function Martel.UntilSep()=Martel-module.html#UntilSep"><a title="Martel.UntilSep" class="py-name" href="#" onclick="return doclink('link-20', 'UntilSep', 'link-20');">UntilSep</a></tt><tt class="py-op">(</tt><tt class="py-string">"profile_file"</tt><tt class="py-op">,</tt> <tt class="py-name">sep</tt><tt class="py-op">=</tt><tt class="py-string">" "</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-21" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-21', 'Spaces', 'link-5');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"> <tt id="link-22" class="py-name"><a title="Martel.UntilEol" class="py-name" href="#" onclick="return doclink('link-22', 'UntilEol', 'link-10');">UntilEol</a></tt><tt class="py-op">(</tt><tt class="py-string">"profile_description"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-23" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-23', 'AnyEol', 'link-6');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"> </tt>
<a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"><tt id="link-24" class="py-name" targets="Variable Bio.expressions.transfac.TITLE_LINE=Bio.expressions.transfac-module.html#TITLE_LINE"><a title="Bio.expressions.transfac.TITLE_LINE" class="py-name" href="#" onclick="return doclink('link-24', 'TITLE_LINE', 'link-24');">TITLE_LINE</a></tt> <tt class="py-op">=</tt> <tt id="link-25" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-25', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"Inspecting sequence ID"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-26" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-26', 'Spaces', 'link-5');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"> <tt id="link-27" class="py-name"><a title="Martel.UntilSep" class="py-name" href="#" onclick="return doclink('link-27', 'UntilSep', 'link-20');">UntilSep</a></tt><tt class="py-op">(</tt><tt class="py-string">"entryname"</tt><tt class="py-op">,</tt> <tt class="py-name">sep</tt><tt class="py-op">=</tt><tt class="py-string">" "</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-28" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-28', 'Spaces', 'link-5');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"> <tt id="link-29" class="py-name"><a title="Martel.UntilSep" class="py-name" href="#" onclick="return doclink('link-29', 'UntilSep', 'link-20');">UntilSep</a></tt><tt class="py-op">(</tt><tt class="py-string">"dataclass"</tt><tt class="py-op">,</tt> <tt class="py-name">sep</tt><tt class="py-op">=</tt><tt class="py-string">";"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-30" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-30', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">";"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-31" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-31', 'Spaces', 'link-5');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"> <tt id="link-32" class="py-name"><a title="Martel.UntilSep" class="py-name" href="#" onclick="return doclink('link-32', 'UntilSep', 'link-20');">UntilSep</a></tt><tt class="py-op">(</tt><tt class="py-string">"molecule"</tt><tt class="py-op">,</tt> <tt class="py-name">sep</tt><tt class="py-op">=</tt><tt class="py-string">";"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-33" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-33', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">";"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-34" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-34', 'Spaces', 'link-5');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"> <tt id="link-35" class="py-name"><a title="Martel.UntilSep" class="py-name" href="#" onclick="return doclink('link-35', 'UntilSep', 'link-20');">UntilSep</a></tt><tt class="py-op">(</tt><tt class="py-string">"division"</tt><tt class="py-op">,</tt> <tt class="py-name">sep</tt><tt class="py-op">=</tt><tt class="py-string">";"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-36" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-36', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">";"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-37" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-37', 'Spaces', 'link-5');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"> <tt id="link-38" class="py-name"><a title="Martel.UntilSep" class="py-name" href="#" onclick="return doclink('link-38', 'UntilSep', 'link-20');">UntilSep</a></tt><tt class="py-op">(</tt><tt class="py-string">"sequencelength"</tt><tt class="py-op">,</tt> <tt class="py-name">sep</tt><tt class="py-op">=</tt><tt class="py-string">" "</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-39" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-39', 'Spaces', 'link-5');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-40" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-40', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"BP"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"> <tt id="link-41" class="py-name"><a title="Martel.UntilEol" class="py-name" href="#" onclick="return doclink('link-41', 'UntilEol', 'link-10');">UntilEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-42" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-42', 'AnyEol', 'link-6');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"> </tt>
<a name="SS"></a><div id="SS-def"><a name="L35"></a><tt class="py-lineno">35</tt> <a class="py-toggle" href="#" id="SS-toggle" onclick="return toggle('SS');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.expressions.transfac-module.html#SS">SS</a><tt class="py-op">(</tt><tt class="py-param">exp</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-comment"># expression surrounded by optional spaces.</tt> </tt>
</div><a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-43" class="py-name"><a title="Martel.Opt" class="py-name" href="#" onclick="return doclink('link-43', 'Opt', 'link-4');">Opt</a></tt><tt class="py-op">(</tt><tt id="link-44" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-44', 'Spaces', 'link-5');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-45" class="py-name" targets="Variable Bio.Affy.CelFile.exp=Bio.Affy.CelFile-module.html#exp,Variable Bio.LogisticRegression.exp=Bio.LogisticRegression-module.html#exp,Variable Bio.MarkovModel.exp=Bio.MarkovModel-module.html#exp,Variable Bio.MaxEntropy.exp=Bio.MaxEntropy-module.html#exp,Variable Bio.NaiveBayes.exp=Bio.NaiveBayes-module.html#exp,Variable Bio.Statistics.lowess.exp=Bio.Statistics.lowess-module.html#exp,Variable Bio.distance.exp=Bio.distance-module.html#exp,Variable Bio.kNN.exp=Bio.kNN-module.html#exp"><a title="Bio.Affy.CelFile.exp
Bio.LogisticRegression.exp
Bio.MarkovModel.exp
Bio.MaxEntropy.exp
Bio.NaiveBayes.exp
Bio.Statistics.lowess.exp
Bio.distance.exp
Bio.kNN.exp" class="py-name" href="#" onclick="return doclink('link-45', 'exp', 'link-45');">exp</a></tt> <tt class="py-op">+</tt> <tt id="link-46" class="py-name"><a title="Martel.Opt" class="py-name" href="#" onclick="return doclink('link-46', 'Opt', 'link-4');">Opt</a></tt><tt class="py-op">(</tt><tt id="link-47" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-47', 'Spaces', 'link-5');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"> </tt>
<a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"> </tt>
<a name="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"><tt id="link-48" class="py-name" targets="Variable Bio.expressions.transfac.DATA_LINE=Bio.expressions.transfac-module.html#DATA_LINE"><a title="Bio.expressions.transfac.DATA_LINE" class="py-name" href="#" onclick="return doclink('link-48', 'DATA_LINE', 'link-48');">DATA_LINE</a></tt> <tt class="py-op">=</tt> \ </tt>
<a name="L40"></a><tt class="py-lineno">40</tt> <tt class="py-line"> <tt id="link-49" class="py-name" targets="Function Bio.expressions.transfac.SS()=Bio.expressions.transfac-module.html#SS"><a title="Bio.expressions.transfac.SS" class="py-name" href="#" onclick="return doclink('link-49', 'SS', 'link-49');">SS</a></tt><tt class="py-op">(</tt><tt id="link-50" class="py-name"><a title="Martel.UntilSep" class="py-name" href="#" onclick="return doclink('link-50', 'UntilSep', 'link-20');">UntilSep</a></tt><tt class="py-op">(</tt><tt class="py-string">"matrix_identifier"</tt><tt class="py-op">,</tt> <tt class="py-name">sep</tt><tt class="py-op">=</tt><tt class="py-string">" |"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L41"></a><tt class="py-lineno">41</tt> <tt class="py-line"> <tt id="link-51" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-51', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"|"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L42"></a><tt class="py-lineno">42</tt> <tt class="py-line"> <tt id="link-52" class="py-name"><a title="Bio.expressions.transfac.SS" class="py-name" href="#" onclick="return doclink('link-52', 'SS', 'link-49');">SS</a></tt><tt class="py-op">(</tt><tt id="link-53" class="py-name"><a title="Martel.UntilSep" class="py-name" href="#" onclick="return doclink('link-53', 'UntilSep', 'link-20');">UntilSep</a></tt><tt class="py-op">(</tt><tt class="py-string">"position"</tt><tt class="py-op">,</tt> <tt class="py-name">sep</tt><tt class="py-op">=</tt><tt class="py-string">" "</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 id="link-54" class="py-name"><a title="Bio.expressions.transfac.SS" class="py-name" href="#" onclick="return doclink('link-54', 'SS', 'link-49');">SS</a></tt><tt class="py-op">(</tt><tt id="link-55" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-55', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"("</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-56" class="py-name" targets="Class Martel.Expression.Group=Martel.Expression.Group-class.html,Function Martel.Group()=Martel-module.html#Group"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-56', 'Group', 'link-56');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"strand"</tt><tt class="py-op">,</tt> <tt id="link-57" class="py-name" targets="Function Martel.Any()=Martel-module.html#Any,Class Martel.Expression.Any=Martel.Expression.Any-class.html"><a title="Martel.Any
Martel.Expression.Any" class="py-name" href="#" onclick="return doclink('link-57', 'Any', 'link-57');">Any</a></tt><tt class="py-op">(</tt><tt class="py-string">"+-"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-58" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-58', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">")"</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 id="link-59" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-59', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"|"</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 id="link-60" class="py-name"><a title="Bio.expressions.transfac.SS" class="py-name" href="#" onclick="return doclink('link-60', 'SS', 'link-49');">SS</a></tt><tt class="py-op">(</tt><tt id="link-61" class="py-name" targets="Class Bio.Decode.Float=Bio.Decode.Float-class.html,Function Martel.Float()=Martel-module.html#Float"><a title="Bio.Decode.Float
Martel.Float" class="py-name" href="#" onclick="return doclink('link-61', 'Float', 'link-61');">Float</a></tt><tt class="py-op">(</tt><tt class="py-string">"core_match"</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 id="link-62" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-62', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"|"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L47"></a><tt class="py-lineno">47</tt> <tt class="py-line"> <tt id="link-63" class="py-name"><a title="Bio.expressions.transfac.SS" class="py-name" href="#" onclick="return doclink('link-63', 'SS', 'link-49');">SS</a></tt><tt class="py-op">(</tt><tt id="link-64" class="py-name"><a title="Bio.Decode.Float
Martel.Float" class="py-name" href="#" onclick="return doclink('link-64', 'Float', 'link-61');">Float</a></tt><tt class="py-op">(</tt><tt class="py-string">"matrix_match"</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 id="link-65" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-65', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"|"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L49"></a><tt class="py-lineno">49</tt> <tt class="py-line"> <tt id="link-66" class="py-name"><a title="Martel.Opt" class="py-name" href="#" onclick="return doclink('link-66', 'Opt', 'link-4');">Opt</a></tt><tt class="py-op">(</tt><tt id="link-67" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-67', 'Spaces', 'link-5');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-68" class="py-name"><a title="Martel.UntilEol" class="py-name" href="#" onclick="return doclink('link-68', 'UntilEol', 'link-10');">UntilEol</a></tt><tt class="py-op">(</tt><tt class="py-string">"sequence"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-69" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-69', 'AnyEol', 'link-6');">AnyEol</a></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>
<a name="L51"></a><tt class="py-lineno">51</tt> <tt class="py-line"><tt id="link-70" class="py-name" targets="Variable Bio.expressions.transfac.SEQUENCES_LENGTH_LINE=Bio.expressions.transfac-module.html#SEQUENCES_LENGTH_LINE"><a title="Bio.expressions.transfac.SEQUENCES_LENGTH_LINE" class="py-name" href="#" onclick="return doclink('link-70', 'SEQUENCES_LENGTH_LINE', 'link-70');">SEQUENCES_LENGTH_LINE</a></tt> <tt class="py-op">=</tt> \ </tt>
<a name="L52"></a><tt class="py-lineno">52</tt> <tt class="py-line"> <tt id="link-71" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-71', 'Spaces', 'link-5');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-72" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-72', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"Total sequences length="</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-73" class="py-name" targets="Class Bio.Decode.Integer=Bio.Decode.Integer-class.html,Class Bio.GenBank.LocationParser.Integer=Bio.GenBank.LocationParser.Integer-class.html,Function Martel.Integer()=Martel-module.html#Integer"><a title="Bio.Decode.Integer
Bio.GenBank.LocationParser.Integer
Martel.Integer" class="py-name" href="#" onclick="return doclink('link-73', 'Integer', 'link-73');">Integer</a></tt><tt class="py-op">(</tt><tt class="py-string">"sequences_length"</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 id="link-74" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-74', 'AnyEol', 'link-6');">AnyEol</a></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>
<a name="L55"></a><tt class="py-lineno">55</tt> <tt class="py-line"><tt id="link-75" class="py-name" targets="Variable Bio.expressions.transfac.FOUND_SITES_LINE=Bio.expressions.transfac-module.html#FOUND_SITES_LINE"><a title="Bio.expressions.transfac.FOUND_SITES_LINE" class="py-name" href="#" onclick="return doclink('link-75', 'FOUND_SITES_LINE', 'link-75');">FOUND_SITES_LINE</a></tt> <tt class="py-op">=</tt> \ </tt>
<a name="L56"></a><tt class="py-lineno">56</tt> <tt class="py-line"> <tt id="link-76" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-76', 'Spaces', 'link-5');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-77" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-77', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"Total number of found sites="</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-78" class="py-name"><a title="Bio.Decode.Integer
Bio.GenBank.LocationParser.Integer
Martel.Integer" class="py-name" href="#" onclick="return doclink('link-78', 'Integer', 'link-73');">Integer</a></tt><tt class="py-op">(</tt><tt class="py-string">"found_sites"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L57"></a><tt class="py-lineno">57</tt> <tt class="py-line"> <tt id="link-79" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-79', 'AnyEol', 'link-6');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L58"></a><tt class="py-lineno">58</tt> <tt class="py-line"> </tt>
<a name="L59"></a><tt class="py-lineno">59</tt> <tt class="py-line"><tt id="link-80" class="py-name" targets="Variable Bio.expressions.transfac.SITE_FREQUENCY_LINE=Bio.expressions.transfac-module.html#SITE_FREQUENCY_LINE"><a title="Bio.expressions.transfac.SITE_FREQUENCY_LINE" class="py-name" href="#" onclick="return doclink('link-80', 'SITE_FREQUENCY_LINE', 'link-80');">SITE_FREQUENCY_LINE</a></tt> <tt class="py-op">=</tt> \ </tt>
<a name="L60"></a><tt class="py-lineno">60</tt> <tt class="py-line"> <tt id="link-81" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-81', 'Spaces', 'link-5');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-82" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-82', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"Frequency of sites per nucleotide="</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L61"></a><tt class="py-lineno">61</tt> <tt class="py-line"> <tt id="link-83" class="py-name"><a title="Bio.Decode.Float
Martel.Float" class="py-name" href="#" onclick="return doclink('link-83', 'Float', 'link-61');">Float</a></tt><tt class="py-op">(</tt><tt class="py-string">"sites_per_nucleotide"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-84" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-84', 'AnyEol', 'link-6');">AnyEol</a></tt><tt class="py-op">(</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 id="link-85" class="py-name" targets="Method Bio.Restriction.Restriction.RestrictionBatch.format()=Bio.Restriction.Restriction.RestrictionBatch-class.html#format,Variable Bio.expressions.blast.ncbiblast.format=Bio.expressions.blast.ncbiblast-module.html#format,Variable Bio.expressions.blast.wublast.format=Bio.expressions.blast.wublast-module.html#format,Variable Bio.expressions.blocks.format=Bio.expressions.blocks-module.html#format,Variable Bio.expressions.embl.embl65.format=Bio.expressions.embl.embl65-module.html#format,Variable Bio.expressions.fasta.format=Bio.expressions.fasta-module.html#format,Variable Bio.expressions.genbank.format=Bio.expressions.genbank-module.html#format,Variable Bio.expressions.hmmpfam.format=Bio.expressions.hmmpfam-module.html#format,Variable Bio.expressions.swissprot.ipi.format=Bio.expressions.swissprot.ipi-module.html#format,Variable Bio.expressions.swissprot.speclist.format=Bio.expressions.swissprot.speclist-module.html#format,Variable Bio.expressions.swissprot.sprot38.format=Bio.expressions.swissprot.sprot38-module.html#format,Variable Bio.expressions.swissprot.sprot40.format=Bio.expressions.swissprot.sprot40-module.html#format,Variable Bio.expressions.transfac.format=Bio.expressions.transfac-module.html#format,Variable Martel.test.test_swissprot38.format=Martel.test.test_swissprot38-module.html#format,Variable Martel.test.testformats.swissprot38.format=Martel.test.testformats.swissprot38-module.html#format"><a title="Bio.Restriction.Restriction.RestrictionBatch.format
Bio.expressions.blast.ncbiblast.format
Bio.expressions.blast.wublast.format
Bio.expressions.blocks.format
Bio.expressions.embl.embl65.format
Bio.expressions.fasta.format
Bio.expressions.genbank.format
Bio.expressions.hmmpfam.format
Bio.expressions.swissprot.ipi.format
Bio.expressions.swissprot.speclist.format
Bio.expressions.swissprot.sprot38.format
Bio.expressions.swissprot.sprot40.format
Bio.expressions.transfac.format
Martel.test.test_swissprot38.format
Martel.test.testformats.swissprot38.format" class="py-name" href="#" onclick="return doclink('link-85', 'format', 'link-85');">format</a></tt> <tt class="py-op">=</tt> <tt id="link-86" class="py-name"><a title="Bio.expressions.transfac.MATRIX_LINE" class="py-name" href="#" onclick="return doclink('link-86', 'MATRIX_LINE', 'link-7');">MATRIX_LINE</a></tt> <tt class="py-op">+</tt> \ </tt>
<a name="L64"></a><tt class="py-lineno">64</tt> <tt class="py-line"> <tt id="link-87" class="py-name"><a title="Bio.expressions.transfac.SEQUENCE_LINE" class="py-name" href="#" onclick="return doclink('link-87', 'SEQUENCE_LINE', 'link-12');">SEQUENCE_LINE</a></tt> <tt class="py-op">+</tt> \ </tt>
<a name="L65"></a><tt class="py-lineno">65</tt> <tt class="py-line"> <tt id="link-88" class="py-name"><a title="Bio.expressions.transfac.PROFILE_LINE" class="py-name" href="#" onclick="return doclink('link-88', 'PROFILE_LINE', 'link-17');">PROFILE_LINE</a></tt> <tt class="py-op">+</tt> \ </tt>
<a name="L66"></a><tt class="py-lineno">66</tt> <tt class="py-line"> <tt id="link-89" class="py-name"><a title="Bio.Emboss.primer3_format.blank_line
Bio.Emboss.primersearch_format.blank_line
Bio.MetaTool.metatool_format.blank_line
Bio.expressions.transfac.blank_line" class="py-name" href="#" onclick="return doclink('link-89', 'blank_line', 'link-3');">blank_line</a></tt> <tt class="py-op">+</tt> \ </tt>
<a name="L67"></a><tt class="py-lineno">67</tt> <tt class="py-line"> <tt id="link-90" class="py-name"><a title="Bio.expressions.transfac.TITLE_LINE" class="py-name" href="#" onclick="return doclink('link-90', 'TITLE_LINE', 'link-24');">TITLE_LINE</a></tt> <tt class="py-op">+</tt> \ </tt>
<a name="L68"></a><tt class="py-lineno">68</tt> <tt class="py-line"> <tt id="link-91" class="py-name"><a title="Bio.Emboss.primer3_format.blank_line
Bio.Emboss.primersearch_format.blank_line
Bio.MetaTool.metatool_format.blank_line
Bio.expressions.transfac.blank_line" class="py-name" href="#" onclick="return doclink('link-91', 'blank_line', 'link-3');">blank_line</a></tt> <tt class="py-op">+</tt> \ </tt>
<a name="L69"></a><tt class="py-lineno">69</tt> <tt class="py-line"> <tt id="link-92" class="py-name" targets="Package Bio.Pathway.Rep=Bio.Pathway.Rep-module.html,Function Martel.Rep()=Martel-module.html#Rep"><a title="Bio.Pathway.Rep
Martel.Rep" class="py-name" href="#" onclick="return doclink('link-92', 'Rep', 'link-92');">Rep</a></tt><tt class="py-op">(</tt><tt id="link-93" class="py-name"><a title="Bio.expressions.transfac.DATA_LINE" class="py-name" href="#" onclick="return doclink('link-93', 'DATA_LINE', 'link-48');">DATA_LINE</a></tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L70"></a><tt class="py-lineno">70</tt> <tt class="py-line"> <tt id="link-94" class="py-name"><a title="Bio.Emboss.primer3_format.blank_line
Bio.Emboss.primersearch_format.blank_line
Bio.MetaTool.metatool_format.blank_line
Bio.expressions.transfac.blank_line" class="py-name" href="#" onclick="return doclink('link-94', 'blank_line', 'link-3');">blank_line</a></tt> <tt class="py-op">+</tt> \ </tt>
<a name="L71"></a><tt class="py-lineno">71</tt> <tt class="py-line"> <tt id="link-95" class="py-name"><a title="Bio.expressions.transfac.SEQUENCES_LENGTH_LINE" class="py-name" href="#" onclick="return doclink('link-95', 'SEQUENCES_LENGTH_LINE', 'link-70');">SEQUENCES_LENGTH_LINE</a></tt> <tt class="py-op">+</tt> \ </tt>
<a name="L72"></a><tt class="py-lineno">72</tt> <tt class="py-line"> <tt id="link-96" class="py-name"><a title="Bio.Emboss.primer3_format.blank_line
Bio.Emboss.primersearch_format.blank_line
Bio.MetaTool.metatool_format.blank_line
Bio.expressions.transfac.blank_line" class="py-name" href="#" onclick="return doclink('link-96', 'blank_line', 'link-3');">blank_line</a></tt> <tt class="py-op">+</tt> \ </tt>
<a name="L73"></a><tt class="py-lineno">73</tt> <tt class="py-line"> <tt id="link-97" class="py-name"><a title="Bio.expressions.transfac.FOUND_SITES_LINE" class="py-name" href="#" onclick="return doclink('link-97', 'FOUND_SITES_LINE', 'link-75');">FOUND_SITES_LINE</a></tt> <tt class="py-op">+</tt> \ </tt>
<a name="L74"></a><tt class="py-lineno">74</tt> <tt class="py-line"> <tt id="link-98" class="py-name"><a title="Bio.Emboss.primer3_format.blank_line
Bio.Emboss.primersearch_format.blank_line
Bio.MetaTool.metatool_format.blank_line
Bio.expressions.transfac.blank_line" class="py-name" href="#" onclick="return doclink('link-98', 'blank_line', 'link-3');">blank_line</a></tt> <tt class="py-op">+</tt> \ </tt>
<a name="L75"></a><tt class="py-lineno">75</tt> <tt class="py-line"> <tt id="link-99" class="py-name"><a title="Bio.expressions.transfac.SITE_FREQUENCY_LINE" class="py-name" href="#" onclick="return doclink('link-99', 'SITE_FREQUENCY_LINE', 'link-80');">SITE_FREQUENCY_LINE</a></tt> </tt>
<a name="L76"></a><tt class="py-lineno">76</tt> <tt class="py-line"> </tt><script type="text/javascript">
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