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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.IntelliGenetics-module.html">Package IntelliGenetics</a> ::
Module intelligenetics_format
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<h1 class="epydoc">Source Code for <a href="Bio.IntelliGenetics.intelligenetics_format-module.html">Module Bio.IntelliGenetics.intelligenetics_format</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright 2001 by Katharine Lindner. All rights reserved.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">"""Martel regular expression for Intelligenetic format.</tt> </tt>
<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">http://hiv-web.lanl.gov/ALIGN_97/HIV12SIV-index.html</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"><tt class="py-comment"># standard library</tt> </tt>
<a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#http://immuno.bme.nwu.edu/seqhunt.html</tt> </tt>
<a name="L12"></a><tt class="py-lineno">12</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="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-comment"># Martel</tt> </tt>
<a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">import</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>
<a name="L16"></a><tt class="py-lineno">16</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="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"> </tt>
<a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"><tt class="py-comment"># --- first set up some helper constants and functions</tt> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-3" class="py-name" targets="Variable Bio.Emboss.primer3_format.comment_line=Bio.Emboss.primer3_format-module.html#comment_line,Variable Bio.IntelliGenetics.intelligenetics_format.comment_line=Bio.IntelliGenetics.intelligenetics_format-module.html#comment_line,Variable Bio.NBRF.nbrf_format.comment_line=Bio.NBRF.nbrf_format-module.html#comment_line,Variable Bio.Saf.saf_format.comment_line=Bio.Saf.saf_format-module.html#comment_line"><a title="Bio.Emboss.primer3_format.comment_line
Bio.IntelliGenetics.intelligenetics_format.comment_line
Bio.NBRF.nbrf_format.comment_line
Bio.Saf.saf_format.comment_line" class="py-name" href="#" onclick="return doclink('link-3', 'comment_line', 'link-3');">comment_line</a></tt> <tt class="py-op">=</tt> <tt id="link-4" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-4', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-5" 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-5', 'Group', 'link-5');">Group</a></tt><tt class="py-op">(</tt> <tt class="py-string">"comment_line"</tt><tt class="py-op">,</tt> \ </tt>
<a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"> <tt id="link-6" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-6', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-7" 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-7', 'Str', 'link-7');">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="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"> <tt id="link-8" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-8', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Function Martel.ToEol()=Martel-module.html#ToEol"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-9', 'ToEol', 'link-9');">ToEol</a></tt><tt class="py-op">(</tt> <tt class="py-string">"comment"</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-10" class="py-name" targets="Variable Bio.IntelliGenetics.intelligenetics_format.comment_lines=Bio.IntelliGenetics.intelligenetics_format-module.html#comment_lines,Variable Bio.expressions.fasta.comment_lines=Bio.expressions.fasta-module.html#comment_lines"><a title="Bio.IntelliGenetics.intelligenetics_format.comment_lines
Bio.expressions.fasta.comment_lines" class="py-name" href="#" onclick="return doclink('link-10', 'comment_lines', 'link-10');">comment_lines</a></tt> <tt class="py-op">=</tt> <tt id="link-11" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-11', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-12" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-12', 'Group', 'link-5');">Group</a></tt><tt class="py-op">(</tt> <tt class="py-string">"comment_lines"</tt><tt class="py-op">,</tt> <tt id="link-13" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-13', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-14" 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-14', 'Rep', 'link-14');">Rep</a></tt><tt class="py-op">(</tt> <tt id="link-15" class="py-name"><a title="Bio.Emboss.primer3_format.comment_line
Bio.IntelliGenetics.intelligenetics_format.comment_line
Bio.NBRF.nbrf_format.comment_line
Bio.Saf.saf_format.comment_line" class="py-name" href="#" onclick="return doclink('link-15', 'comment_line', 'link-3');">comment_line</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-16" class="py-name" targets="Method Bio.IntelliGenetics._RecordConsumer.title_line()=Bio.IntelliGenetics._RecordConsumer-class.html#title_line,Variable Bio.IntelliGenetics.intelligenetics_format.title_line=Bio.IntelliGenetics.intelligenetics_format-module.html#title_line"><a title="Bio.IntelliGenetics._RecordConsumer.title_line
Bio.IntelliGenetics.intelligenetics_format.title_line" class="py-name" href="#" onclick="return doclink('link-16', 'title_line', 'link-16');">title_line</a></tt> <tt class="py-op">=</tt> <tt id="link-17" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-17', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-18" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-18', 'Group', 'link-5');">Group</a></tt><tt class="py-op">(</tt> <tt class="py-string">"title_line"</tt><tt class="py-op">,</tt> \ </tt>
<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"> <tt id="link-19" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-19', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-20" class="py-name" targets="Class Bio.EUtils.Datatypes.Expression=Bio.EUtils.Datatypes.Expression-class.html,Module Martel.Expression=Martel.Expression-module.html,Class Martel.Expression.Expression=Martel.Expression.Expression-class.html"><a title="Bio.EUtils.Datatypes.Expression
Martel.Expression
Martel.Expression.Expression" class="py-name" href="#" onclick="return doclink('link-20', 'Expression', 'link-20');">Expression</a></tt><tt class="py-op">.</tt><tt id="link-21" class="py-name" targets="Function Martel.Assert()=Martel-module.html#Assert,Class Martel.Expression.Assert=Martel.Expression.Assert-class.html"><a title="Martel.Assert
Martel.Expression.Assert" class="py-name" href="#" onclick="return doclink('link-21', 'Assert', 'link-21');">Assert</a></tt><tt class="py-op">(</tt> <tt id="link-22" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-22', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-23" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-23', 'Str', 'link-7');">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-number">1</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-24" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-24', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-25" class="py-name"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-25', 'ToEol', 'link-9');">ToEol</a></tt><tt class="py-op">(</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 id="link-26" class="py-name" targets="Variable Bio.IntelliGenetics.intelligenetics_format.residue_line=Bio.IntelliGenetics.intelligenetics_format-module.html#residue_line"><a title="Bio.IntelliGenetics.intelligenetics_format.residue_line" class="py-name" href="#" onclick="return doclink('link-26', 'residue_line', 'link-26');">residue_line</a></tt> <tt class="py-op">=</tt> <tt id="link-27" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-27', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-28" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-28', 'Group', 'link-5');">Group</a></tt><tt class="py-op">(</tt> <tt class="py-string">"residue_line"</tt><tt class="py-op">,</tt> \ </tt>
<a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"> <tt id="link-29" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-29', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-30" class="py-name"><a title="Bio.EUtils.Datatypes.Expression
Martel.Expression
Martel.Expression.Expression" class="py-name" href="#" onclick="return doclink('link-30', 'Expression', 'link-20');">Expression</a></tt><tt class="py-op">.</tt><tt id="link-31" class="py-name"><a title="Martel.Assert
Martel.Expression.Assert" class="py-name" href="#" onclick="return doclink('link-31', 'Assert', 'link-21');">Assert</a></tt><tt class="py-op">(</tt> <tt id="link-32" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-32', 'Martel', 'link-0');">Martel</a></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-7');">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-number">1</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-34" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-34', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-35" class="py-name"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-35', 'ToEol', 'link-9');">ToEol</a></tt><tt class="py-op">(</tt> <tt class="py-string">"sequence"</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-36" class="py-name" targets="Variable Bio.IntelliGenetics.intelligenetics_format.residue_lines=Bio.IntelliGenetics.intelligenetics_format-module.html#residue_lines"><a title="Bio.IntelliGenetics.intelligenetics_format.residue_lines" class="py-name" href="#" onclick="return doclink('link-36', 'residue_lines', 'link-36');">residue_lines</a></tt> <tt class="py-op">=</tt> <tt id="link-37" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-37', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-38" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-38', 'Group', 'link-5');">Group</a></tt><tt class="py-op">(</tt> <tt class="py-string">"residue_lines"</tt><tt class="py-op">,</tt> <tt id="link-39" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-39', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-40" class="py-name" targets="Function Martel.Rep1()=Martel-module.html#Rep1"><a title="Martel.Rep1" class="py-name" href="#" onclick="return doclink('link-40', 'Rep1', 'link-40');">Rep1</a></tt><tt class="py-op">(</tt> <tt id="link-41" class="py-name"><a title="Bio.IntelliGenetics.intelligenetics_format.residue_line" class="py-name" href="#" onclick="return doclink('link-41', 'residue_line', 'link-26');">residue_line</a></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-42" class="py-name" targets="Variable Bio.IntelliGenetics.intelligenetics_format.intelligenetics_record=Bio.IntelliGenetics.intelligenetics_format-module.html#intelligenetics_record"><a title="Bio.IntelliGenetics.intelligenetics_format.intelligenetics_record" class="py-name" href="#" onclick="return doclink('link-42', 'intelligenetics_record', 'link-42');">intelligenetics_record</a></tt> <tt class="py-op">=</tt> <tt id="link-43" class="py-name"><a title="Bio.IntelliGenetics.intelligenetics_format.comment_lines
Bio.expressions.fasta.comment_lines" class="py-name" href="#" onclick="return doclink('link-43', 'comment_lines', 'link-10');">comment_lines</a></tt> <tt class="py-op">+</tt> <tt id="link-44" class="py-name"><a title="Bio.IntelliGenetics._RecordConsumer.title_line
Bio.IntelliGenetics.intelligenetics_format.title_line" class="py-name" href="#" onclick="return doclink('link-44', 'title_line', 'link-16');">title_line</a></tt> <tt class="py-op">+</tt> <tt id="link-45" class="py-name"><a title="Bio.IntelliGenetics.intelligenetics_format.residue_lines" class="py-name" href="#" onclick="return doclink('link-45', 'residue_lines', 'link-36');">residue_lines</a></tt> </tt>
<a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"> </tt><script type="text/javascript">
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