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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.expressions-module.html">Package expressions</a> ::
Module hmmpfam
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<h1 class="epydoc">Source Code for <a href="Bio.expressions.hmmpfam-module.html">Module Bio.expressions.hmmpfam</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-docstring">"""Martel expression for the hmmpfam database search program in hmmer.</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 has been tested with version 2.2g. I should also make it work with</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-docstring">2.1.1 output.</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">XXX This isn't completely finished and doesn't do everything quite right.</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring">The main two problems being that it isn't well tested for a wide variety of</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">outputs and that the family line is not parsed into it's respective parts </tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">(see multitude of comments on this below).</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring">"""</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 class="py-keyword">import</tt> <tt class="py-name">warnings</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</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="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"> </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 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="L18"></a><tt class="py-lineno"> 18</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="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-3" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-3', 'Bio', 'link-3');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-4" class="py-name" targets="Module Bio.Std=Bio.Std-module.html"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-4', 'Std', 'link-4');">Std</a></tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-comment"># -- header</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># hmmpfam - search one or more sequences against HMM database</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-5" class="py-name" targets="Variable Bio.expressions.hmmpfam.program_description=Bio.expressions.hmmpfam-module.html#program_description"><a title="Bio.expressions.hmmpfam.program_description" class="py-name" href="#" onclick="return doclink('link-5', 'program_description', 'link-5');">program_description</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-6" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-6', 'Std', 'link-4');">Std</a></tt><tt class="py-op">.</tt><tt id="link-7" class="py-name" targets="Function Bio.Std.application_name()=Bio.Std-module.html#application_name"><a title="Bio.Std.application_name" class="py-name" href="#" onclick="return doclink('link-7', 'application_name', 'link-7');">application_name</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">"hmmpfam"</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-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-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-comment"># HMMER 2.2g (August 2001)</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-10" class="py-name" targets="Variable Bio.expressions.hmmpfam.program_version=Bio.expressions.hmmpfam-module.html#program_version"><a title="Bio.expressions.hmmpfam.program_version" class="py-name" href="#" onclick="return doclink('link-10', 'program_version', 'link-10');">program_version</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-11" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-11', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"HMMER "</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-12" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-12', 'Std', 'link-4');">Std</a></tt><tt class="py-op">.</tt><tt id="link-13" class="py-name" targets="Function Bio.Std.application_version()=Bio.Std-module.html#application_version"><a title="Bio.Std.application_version" class="py-name" href="#" onclick="return doclink('link-13', 'application_version', 'link-13');">application_version</a></tt><tt class="py-op">(</tt><tt id="link-14" class="py-name" targets="Function Martel.Re()=Martel-module.html#Re"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-14', 'Re', 'link-14');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">r"\d\.\d\w"</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-15" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-15', 'Re', 'link-14');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">r"\d\.\d\.\d"</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-16" class="py-name"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-16', 'ToEol', 'link-9');">ToEol</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>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-comment"># Copyright (C) 1992-2001 HHMI/Washington University School of Medicine</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Freely distributed under the GNU General Public License (GPL)</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt id="link-17" class="py-name" targets="Variable Bio.expressions.hmmpfam.copyright=Bio.expressions.hmmpfam-module.html#copyright,Variable Martel.test.test_swissprot38.copyright=Martel.test.test_swissprot38-module.html#copyright"><a title="Bio.expressions.hmmpfam.copyright
Martel.test.test_swissprot38.copyright" class="py-name" href="#" onclick="return doclink('link-17', 'copyright', 'link-17');">copyright</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-18" class="py-name"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-18', 'ToEol', 'link-9');">ToEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt id="link-19" class="py-name"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-19', 'ToEol', 'link-9');">ToEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<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 class="py-comment"># - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># HMM file: /data/hmm/Pfam_fs</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Sequence file: hmmpfam_test.fasta</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - </tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt id="link-20" class="py-name" targets="Variable Bio.expressions.hmmpfam.files=Bio.expressions.hmmpfam-module.html#files"><a title="Bio.expressions.hmmpfam.files" class="py-name" href="#" onclick="return doclink('link-20', 'files', 'link-20');">files</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-21" class="py-name"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-21', 'ToEol', 'link-9');">ToEol</a></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-22" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-22', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"HMM file:"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-23" class="py-name" targets="Function Martel.Spaces()=Martel-module.html#Spaces"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-23', 'Spaces', 'link-23');">Spaces</a></tt><tt class="py-op">(</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-24" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-24', 'Std', 'link-4');">Std</a></tt><tt class="py-op">.</tt><tt id="link-25" class="py-name" targets="Function Bio.Std.database_name()=Bio.Std-module.html#database_name"><a title="Bio.Std.database_name" class="py-name" href="#" onclick="return doclink('link-25', 'database_name', 'link-25');">database_name</a></tt><tt class="py-op">(</tt><tt id="link-26" class="py-name" targets="Function Martel.UntilEol()=Martel-module.html#UntilEol"><a title="Martel.UntilEol" class="py-name" href="#" onclick="return doclink('link-26', 'UntilEol', 'link-26');">UntilEol</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-27" 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-27', 'AnyEol', 'link-27');">AnyEol</a></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-28" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-28', '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-29" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-29', 'Spaces', 'link-23');">Spaces</a></tt><tt class="py-op">(</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-30" 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-30', 'Group', 'link-30');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"inputfile_name"</tt><tt class="py-op">,</tt> <tt id="link-31" class="py-name"><a title="Martel.UntilEol" class="py-name" href="#" onclick="return doclink('link-31', 'UntilEol', 'link-26');">UntilEol</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-32" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-32', 'AnyEol', 'link-27');">AnyEol</a></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-33" class="py-name"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-33', 'ToEol', 'link-9');">ToEol</a></tt><tt class="py-op">(</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>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt id="link-34" class="py-name" targets="Variable Bio.Wise.dnal.Statistics.header=Bio.Wise.dnal.Statistics-class.html#header,Variable Bio.expressions.blast.ncbiblast.header=Bio.expressions.blast.ncbiblast-module.html#header,Variable Bio.expressions.blast.wublast.header=Bio.expressions.blast.wublast-module.html#header,Variable Bio.expressions.blocks.header=Bio.expressions.blocks-module.html#header,Variable Bio.expressions.genbank.header=Bio.expressions.genbank-module.html#header,Variable Bio.expressions.hmmpfam.header=Bio.expressions.hmmpfam-module.html#header"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-34', 'header', 'link-34');">header</a></tt> <tt class="py-op">=</tt> <tt id="link-35" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-35', 'Std', 'link-4');">Std</a></tt><tt class="py-op">.</tt><tt id="link-36" class="py-name" targets="Function Bio.Std.search_header()=Bio.Std-module.html#search_header"><a title="Bio.Std.search_header" class="py-name" href="#" onclick="return doclink('link-36', 'search_header', 'link-36');">search_header</a></tt><tt class="py-op">(</tt><tt id="link-37" class="py-name"><a title="Bio.expressions.hmmpfam.program_description" class="py-name" href="#" onclick="return doclink('link-37', 'program_description', 'link-5');">program_description</a></tt> <tt class="py-op">+</tt> <tt id="link-38" class="py-name"><a title="Bio.expressions.hmmpfam.program_version" class="py-name" href="#" onclick="return doclink('link-38', 'program_version', 'link-10');">program_version</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt id="link-39" class="py-name"><a title="Bio.expressions.hmmpfam.copyright
Martel.test.test_swissprot38.copyright" class="py-name" href="#" onclick="return doclink('link-39', 'copyright', 'link-17');">copyright</a></tt> <tt class="py-op">+</tt> <tt id="link-40" class="py-name"><a title="Bio.expressions.hmmpfam.files" class="py-name" href="#" onclick="return doclink('link-40', 'files', 'link-20');">files</a></tt><tt class="py-op">)</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"><tt class="py-comment"># -- record</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Query sequence: AT1G01040</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Accession: [none]</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Description: Test Sequence for hmmpfam</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"><tt id="link-41" class="py-name" targets="Variable Bio.Emboss.primersearch_format.sequence_info=Bio.Emboss.primersearch_format-module.html#sequence_info,Variable Bio.expressions.hmmpfam.sequence_info=Bio.expressions.hmmpfam-module.html#sequence_info"><a title="Bio.Emboss.primersearch_format.sequence_info
Bio.expressions.hmmpfam.sequence_info" class="py-name" href="#" onclick="return doclink('link-41', 'sequence_info', 'link-41');">sequence_info</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-42" class="py-name"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-42', 'ToEol', 'link-9');">ToEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-comment"># blank line</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt id="link-43" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-43', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"Query sequence:"</tt><tt class="py-op">)</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-23');">Spaces</a></tt><tt class="py-op">(</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 id="link-45" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-45', 'Group', 'link-30');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"query_name"</tt><tt class="py-op">,</tt> <tt id="link-46" class="py-name"><a title="Martel.UntilEol" class="py-name" href="#" onclick="return doclink('link-46', 'UntilEol', 'link-26');">UntilEol</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-47" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-47', 'AnyEol', 'link-27');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt id="link-48" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-48', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"Accession:"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-49" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-49', 'Spaces', 'link-23');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt id="link-50" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-50', 'Group', 'link-30');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"query_accession"</tt><tt class="py-op">,</tt> <tt id="link-51" class="py-name"><a title="Martel.UntilEol" class="py-name" href="#" onclick="return doclink('link-51', 'UntilEol', 'link-26');">UntilEol</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-52" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-52', 'AnyEol', 'link-27');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt id="link-53" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-53', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"Description:"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-54" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-54', 'Spaces', 'link-23');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt id="link-55" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-55', 'Std', 'link-4');">Std</a></tt><tt class="py-op">.</tt><tt id="link-56" class="py-name" targets="Function Bio.Std.query_description()=Bio.Std-module.html#query_description"><a title="Bio.Std.query_description" class="py-name" href="#" onclick="return doclink('link-56', 'query_description', 'link-56');">query_description</a></tt><tt class="py-op">(</tt><tt id="link-57" class="py-name"><a title="Martel.UntilEol" class="py-name" href="#" onclick="return doclink('link-57', 'UntilEol', 'link-26');">UntilEol</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-58" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-58', 'AnyEol', 'link-27');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"><tt class="py-comment"># generic name for models</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># most model names are something like PFwhatever, but we also have some</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># different kinds like AAA and Sigma54_activat</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-59" class="py-name" targets="Variable Bio.expressions.hmmpfam.model_name=Bio.expressions.hmmpfam-module.html#model_name"><a title="Bio.expressions.hmmpfam.model_name" class="py-name" href="#" onclick="return doclink('link-59', 'model_name', 'link-59');">model_name</a></tt> <tt class="py-op">=</tt> <tt id="link-60" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-60', 'Re', 'link-14');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">r"[\w-]+"</tt><tt class="py-op">)</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Scores for sequence family classification (score includes all domains):</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Model Description Score E-value N </tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># -------- ----------- ----- ------- ---</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"><tt id="link-61" class="py-name" targets="Variable Bio.expressions.hmmpfam.family_header=Bio.expressions.hmmpfam-module.html#family_header"><a title="Bio.expressions.hmmpfam.family_header" class="py-name" href="#" onclick="return doclink('link-61', 'family_header', 'link-61');">family_header</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-62" class="py-name"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-62', 'ToEol', 'link-9');">ToEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-comment"># blank line</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt id="link-63" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-63', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"Scores"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-64" class="py-name"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-64', 'ToEol', 'link-9');">ToEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</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">"Model"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-66" class="py-name"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-66', 'ToEol', 'link-9');">ToEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt id="link-67" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-67', '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-68" class="py-name"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-68', 'ToEol', 'link-9');">ToEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"><tt class="py-comment"># family lines can either be a hit:</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># PF00636 RNase3 domain 354.9 1.1e-118 2</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># or no hit:</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># [no hits above thresholds]</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"><tt id="link-69" class="py-name" targets="Variable Bio.expressions.hmmpfam.no_hit_line=Bio.expressions.hmmpfam-module.html#no_hit_line"><a title="Bio.expressions.hmmpfam.no_hit_line" class="py-name" href="#" onclick="return doclink('link-69', 'no_hit_line', 'link-69');">no_hit_line</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-70" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-70', 'Spaces', 'link-23');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-71" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-71', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"[no hits above thresholds]"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-72" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-72', 'AnyEol', 'link-27');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"><tt id="link-73" class="py-name" targets="Variable Bio.expressions.hmmpfam.family_hit_line=Bio.expressions.hmmpfam-module.html#family_hit_line"><a title="Bio.expressions.hmmpfam.family_hit_line" class="py-name" href="#" onclick="return doclink('link-73', 'family_hit_line', 'link-73');">family_hit_line</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-74" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-74', 'Group', 'link-30');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"family_model"</tt><tt class="py-op">,</tt> <tt id="link-75" class="py-name"><a title="Bio.expressions.hmmpfam.model_name" class="py-name" href="#" onclick="return doclink('link-75', 'model_name', 'link-59');">model_name</a></tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-76" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-76', 'Spaces', 'link-23');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-comment"># XXX This is a pain in the ass, so I gave up</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-comment"># We need to match descriptions but stop when we get to the</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-comment"># score value.</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-comment"># This is very difficult since the description can contain</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-comment"># letters, numbers, (, ), /, - and periods. The numbers and</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-comment"># periods leave me unable to think of a way to distinguish</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-comment"># a "description word" from a score word.</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-comment"># You also can't use spaces as descriptions can have 2</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-comment"># spaces in them (not just one separating every word) and</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-comment"># the description to score value can also be separated by</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-comment"># only 2 spaces.</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-comment"># I can't for the life of me figure this so I just</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-comment"># eat the rest of the line for right now and downstream</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-comment"># apps will have to get the information out from there.</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt id="link-77" class="py-name"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-77', 'ToEol', 'link-9');">ToEol</a></tt><tt class="py-op">(</tt><tt class="py-string">"family_information"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-comment">#Group("family_description",</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Rep1(Re(r"[a-zA-Z0-9_()/-]+") +</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Alt(Str(" "), Str(" ")))) +</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Alt(Spaces()) +</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Float("family_score") + Spaces() +</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Float("family_evalue") + Spaces() +</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Integer("family_n") + AnyEol())</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Parsed for domains:</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Model Domain seq-f seq-t hmm-f hmm-t score E-value</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># -------- ------- ----- ----- ----- ----- ----- -------</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-78" class="py-name" targets="Variable Bio.expressions.hmmpfam.domain_header=Bio.expressions.hmmpfam-module.html#domain_header"><a title="Bio.expressions.hmmpfam.domain_header" class="py-name" href="#" onclick="return doclink('link-78', 'domain_header', 'link-78');">domain_header</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-79" class="py-name"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-79', 'ToEol', 'link-9');">ToEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-comment"># blank line</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt id="link-80" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-80', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"Parsed for domains:"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-81" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-81', 'AnyEol', 'link-27');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <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">"Model"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-83" class="py-name"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-83', 'ToEol', 'link-9');">ToEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt id="link-84" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-84', '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-85" class="py-name"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-85', 'ToEol', 'link-9');">ToEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"><tt class="py-comment"># domain lines can also be either a hit:</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># PF00270 1/1 239 382 .. 1 141 [. 30.3 2.2e-09</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># or not hit:</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># [no hits above thresholds]</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"><tt class="py-comment"># I have no idea what these things exactly mean, but parse 'em anyways</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-86" class="py-name" targets="Variable Bio.expressions.hmmpfam.symbol_forward=Bio.expressions.hmmpfam-module.html#symbol_forward"><a title="Bio.expressions.hmmpfam.symbol_forward" class="py-name" href="#" onclick="return doclink('link-86', 'symbol_forward', 'link-86');">symbol_forward</a></tt> <tt class="py-op">=</tt> <tt id="link-87" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-87', '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-88" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-88', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"["</tt><tt class="py-op">)</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"><tt id="link-89" class="py-name" targets="Variable Bio.expressions.hmmpfam.symbol_reverse=Bio.expressions.hmmpfam-module.html#symbol_reverse"><a title="Bio.expressions.hmmpfam.symbol_reverse" class="py-name" href="#" onclick="return doclink('link-89', 'symbol_reverse', 'link-89');">symbol_reverse</a></tt> <tt class="py-op">=</tt> <tt id="link-90" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-90', '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-91" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-91', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"]"</tt><tt class="py-op">)</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"><tt id="link-92" class="py-name" targets="Variable Bio.expressions.hmmpfam.match_symbols=Bio.expressions.hmmpfam-module.html#match_symbols"><a title="Bio.expressions.hmmpfam.match_symbols" class="py-name" href="#" onclick="return doclink('link-92', 'match_symbols', 'link-92');">match_symbols</a></tt> <tt class="py-op">=</tt> <tt id="link-93" class="py-name"><a title="Bio.expressions.hmmpfam.symbol_forward" class="py-name" href="#" onclick="return doclink('link-93', 'symbol_forward', 'link-86');">symbol_forward</a></tt> <tt class="py-op">+</tt> <tt id="link-94" class="py-name"><a title="Bio.expressions.hmmpfam.symbol_reverse" class="py-name" href="#" onclick="return doclink('link-94', 'symbol_reverse', 'link-89');">symbol_reverse</a></tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"><tt id="link-95" class="py-name" targets="Variable Bio.expressions.hmmpfam.domain_hit_line=Bio.expressions.hmmpfam-module.html#domain_hit_line"><a title="Bio.expressions.hmmpfam.domain_hit_line" class="py-name" href="#" onclick="return doclink('link-95', 'domain_hit_line', 'link-95');">domain_hit_line</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-96" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-96', 'Group', 'link-30');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"domain_model"</tt><tt class="py-op">,</tt> <tt id="link-97" class="py-name"><a title="Bio.expressions.hmmpfam.model_name" class="py-name" href="#" onclick="return doclink('link-97', 'model_name', 'link-59');">model_name</a></tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-98" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-98', 'Spaces', 'link-23');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt id="link-99" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-99', 'Group', 'link-30');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"domain_domain"</tt><tt class="py-op">,</tt> <tt id="link-100" 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-100', 'Integer', 'link-100');">Integer</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-101" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-101', '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-102" class="py-name"><a title="Bio.Decode.Integer
Bio.GenBank.LocationParser.Integer
Martel.Integer" class="py-name" href="#" onclick="return doclink('link-102', 'Integer', 'link-100');">Integer</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="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt id="link-103" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-103', 'Spaces', 'link-23');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt id="link-104" class="py-name"><a title="Bio.Decode.Integer
Bio.GenBank.LocationParser.Integer
Martel.Integer" class="py-name" href="#" onclick="return doclink('link-104', 'Integer', 'link-100');">Integer</a></tt><tt class="py-op">(</tt><tt class="py-string">"domain_seq-f"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-105" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-105', 'Spaces', 'link-23');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt id="link-106" class="py-name"><a title="Bio.Decode.Integer
Bio.GenBank.LocationParser.Integer
Martel.Integer" class="py-name" href="#" onclick="return doclink('link-106', 'Integer', 'link-100');">Integer</a></tt><tt class="py-op">(</tt><tt class="py-string">"domain_seq-r"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-107" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-107', 'Spaces', 'link-23');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt id="link-108" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-108', 'Group', 'link-30');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"domain_seq_symbols"</tt><tt class="py-op">,</tt> <tt id="link-109" class="py-name"><a title="Bio.expressions.hmmpfam.match_symbols" class="py-name" href="#" onclick="return doclink('link-109', 'match_symbols', 'link-92');">match_symbols</a></tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-110" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-110', 'Spaces', 'link-23');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt id="link-111" class="py-name"><a title="Bio.Decode.Integer
Bio.GenBank.LocationParser.Integer
Martel.Integer" class="py-name" href="#" onclick="return doclink('link-111', 'Integer', 'link-100');">Integer</a></tt><tt class="py-op">(</tt><tt class="py-string">"domain_hmm-f"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-112" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-112', 'Spaces', 'link-23');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt id="link-113" class="py-name"><a title="Bio.Decode.Integer
Bio.GenBank.LocationParser.Integer
Martel.Integer" class="py-name" href="#" onclick="return doclink('link-113', 'Integer', 'link-100');">Integer</a></tt><tt class="py-op">(</tt><tt class="py-string">"domain_hmm-t"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-114" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-114', 'Spaces', 'link-23');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt id="link-115" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-115', 'Group', 'link-30');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"domain_hmm_symbols"</tt><tt class="py-op">,</tt> <tt id="link-116" class="py-name"><a title="Bio.expressions.hmmpfam.match_symbols" class="py-name" href="#" onclick="return doclink('link-116', 'match_symbols', 'link-92');">match_symbols</a></tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-117" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-117', 'Spaces', 'link-23');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt id="link-118" 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-118', 'Float', 'link-118');">Float</a></tt><tt class="py-op">(</tt><tt class="py-string">"domain_score"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-119" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-119', 'Spaces', 'link-23');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt id="link-120" class="py-name"><a title="Bio.Decode.Float
Martel.Float" class="py-name" href="#" onclick="return doclink('link-120', 'Float', 'link-118');">Float</a></tt><tt class="py-op">(</tt><tt class="py-string">"domain_evalue"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-121" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-121', 'AnyEol', 'link-27');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"><tt class="py-comment"># </tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Alignments of top-scoring domains:</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-122" class="py-name" targets="Variable Bio.expressions.hmmpfam.alignment_header=Bio.expressions.hmmpfam-module.html#alignment_header"><a title="Bio.expressions.hmmpfam.alignment_header" class="py-name" href="#" onclick="return doclink('link-122', 'alignment_header', 'link-122');">alignment_header</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-123" class="py-name"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-123', 'ToEol', 'link-9');">ToEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-comment"># empty line</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt id="link-124" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-124', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"Alignments of top-scoring domains:"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> <tt id="link-125" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-125', 'AnyEol', 'link-27');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"><tt class="py-comment"># PF00271: domain 1 of 1, from 686 to 767: score 58.6, E = 8.9e-17</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># *->ell.epgikvarlhG.....glsqeeReeilekFrngkskvLvaTdv</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># el ++ i++a++ G+++++++++++ ++++ kFr+g + +LvaT+v</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># AT1G01040 686 ELPsLSFIRCASMIGhnnsqEMKSSQMQDTISKFRDGHVTLLVATSV 732 </tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># </tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># aarGlDipdvnlVInydlpwnpesyiQRiGRaGRaG<-*</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># a++GlDi ++n+V +dl +++ yiQ +GR +R </tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># AT1G01040 733 AEEGLDIRQCNVVMRFDLAKTVLAYIQSRGR-ARKP 767</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-126" class="py-name" targets="Variable Bio.expressions.hmmpfam.domain_align_header=Bio.expressions.hmmpfam-module.html#domain_align_header"><a title="Bio.expressions.hmmpfam.domain_align_header" class="py-name" href="#" onclick="return doclink('link-126', 'domain_align_header', 'link-126');">domain_align_header</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-127" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-127', 'Group', 'link-30');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"dalign_name"</tt><tt class="py-op">,</tt> <tt id="link-128" class="py-name"><a title="Bio.expressions.hmmpfam.model_name" class="py-name" href="#" onclick="return doclink('link-128', 'model_name', 'link-59');">model_name</a></tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt id="link-129" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-129', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">": domain "</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt id="link-130" class="py-name"><a title="Bio.Decode.Integer
Bio.GenBank.LocationParser.Integer
Martel.Integer" class="py-name" href="#" onclick="return doclink('link-130', 'Integer', 'link-100');">Integer</a></tt><tt class="py-op">(</tt><tt class="py-string">"dalign_of_domain"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt id="link-131" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-131', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">" of "</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt id="link-132" class="py-name"><a title="Bio.Decode.Integer
Bio.GenBank.LocationParser.Integer
Martel.Integer" class="py-name" href="#" onclick="return doclink('link-132', 'Integer', 'link-100');">Integer</a></tt><tt class="py-op">(</tt><tt class="py-string">"dalign_total_domain"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt id="link-133" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-133', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">", from "</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt id="link-134" class="py-name"><a title="Bio.Decode.Integer
Bio.GenBank.LocationParser.Integer
Martel.Integer" class="py-name" href="#" onclick="return doclink('link-134', 'Integer', 'link-100');">Integer</a></tt><tt class="py-op">(</tt><tt class="py-string">"dalign_domain_start"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt id="link-135" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-135', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">" to "</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> <tt id="link-136" class="py-name"><a title="Bio.Decode.Integer
Bio.GenBank.LocationParser.Integer
Martel.Integer" class="py-name" href="#" onclick="return doclink('link-136', 'Integer', 'link-100');">Integer</a></tt><tt class="py-op">(</tt><tt class="py-string">"dalign_domain_end"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt id="link-137" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-137', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">": score "</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt id="link-138" class="py-name"><a title="Bio.Decode.Float
Martel.Float" class="py-name" href="#" onclick="return doclink('link-138', 'Float', 'link-118');">Float</a></tt><tt class="py-op">(</tt><tt class="py-string">"dalign_score"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt id="link-139" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-139', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">", E = "</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt id="link-140" class="py-name"><a title="Bio.Decode.Float
Martel.Float" class="py-name" href="#" onclick="return doclink('link-140', 'Float', 'link-118');">Float</a></tt><tt class="py-op">(</tt><tt class="py-string">"dalign_evalue"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt id="link-141" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-141', 'AnyEol', 'link-27');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"><tt class="py-comment"># occasionally we have a line like:</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># preceeding the alignment. I'm not sure what this means.</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-142" class="py-name" targets="Variable Bio.expressions.hmmpfam.rf_line=Bio.expressions.hmmpfam-module.html#rf_line"><a title="Bio.expressions.hmmpfam.rf_line" class="py-name" href="#" onclick="return doclink('link-142', 'rf_line', 'link-142');">rf_line</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-143" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-143', 'Spaces', 'link-23');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-144" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-144', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"RF "</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-145" class="py-name"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-145', 'ToEol', 'link-9');">ToEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"><tt id="link-146" class="py-name" targets="Variable Bio.expressions.hmmpfam.domain_align_top=Bio.expressions.hmmpfam-module.html#domain_align_top"><a title="Bio.expressions.hmmpfam.domain_align_top" class="py-name" href="#" onclick="return doclink('link-146', 'domain_align_top', 'link-146');">domain_align_top</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-147" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-147', 'Spaces', 'link-23');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt id="link-148" class="py-name"><a title="Martel.UntilEol" class="py-name" href="#" onclick="return doclink('link-148', 'UntilEol', 'link-26');">UntilEol</a></tt><tt class="py-op">(</tt><tt class="py-string">"dalign_match_top"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-149" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-149', 'AnyEol', 'link-27');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"><tt id="link-150" class="py-name" targets="Variable Bio.expressions.hmmpfam.domain_align_middle=Bio.expressions.hmmpfam-module.html#domain_align_middle"><a title="Bio.expressions.hmmpfam.domain_align_middle" class="py-name" href="#" onclick="return doclink('link-150', 'domain_align_middle', 'link-150');">domain_align_middle</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-151" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-151', 'Spaces', 'link-23');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt id="link-152" class="py-name"><a title="Martel.UntilEol" class="py-name" href="#" onclick="return doclink('link-152', 'UntilEol', 'link-26');">UntilEol</a></tt><tt class="py-op">(</tt><tt class="py-string">"dalign_match_middle"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-153" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-153', 'AnyEol', 'link-27');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"><tt id="link-154" class="py-name" targets="Variable Bio.expressions.hmmpfam.domain_align_bottom=Bio.expressions.hmmpfam-module.html#domain_align_bottom"><a title="Bio.expressions.hmmpfam.domain_align_bottom" class="py-name" href="#" onclick="return doclink('link-154', 'domain_align_bottom', 'link-154');">domain_align_bottom</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-155" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-155', 'Spaces', 'link-23');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt id="link-156" class="py-name" targets="Function Martel.ToSep()=Martel-module.html#ToSep"><a title="Martel.ToSep" class="py-name" href="#" onclick="return doclink('link-156', 'ToSep', 'link-156');">ToSep</a></tt><tt class="py-op">(</tt><tt class="py-string">"dalign_query_name"</tt><tt class="py-op">,</tt> <tt class="py-string">" "</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-157" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-157', 'Spaces', 'link-23');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> <tt class="py-comment"># some match ends can have:</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> <tt class="py-comment"># AT1G01230 - -</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt class="py-comment"># instead of an actual line, so there are fixes</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> <tt class="py-comment"># in here for that messed up case</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt id="link-158" class="py-name" targets="Function Martel.Alt()=Martel-module.html#Alt,Class Martel.Expression.Alt=Martel.Expression.Alt-class.html"><a title="Martel.Alt
Martel.Expression.Alt" class="py-name" href="#" onclick="return doclink('link-158', 'Alt', 'link-158');">Alt</a></tt><tt class="py-op">(</tt><tt id="link-159" class="py-name"><a title="Bio.Decode.Integer
Bio.GenBank.LocationParser.Integer
Martel.Integer" class="py-name" href="#" onclick="return doclink('link-159', 'Integer', 'link-100');">Integer</a></tt><tt class="py-op">(</tt><tt class="py-string">"dalign_query_start"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-160" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-160', 'Spaces', 'link-23');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt id="link-161" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-161', 'Group', 'link-30');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"dalign_match_bottom"</tt><tt class="py-op">,</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt id="link-162" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-162', 'Re', 'link-14');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">"[\w\-]+"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-163" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-163', 'Spaces', 'link-23');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt id="link-164" class="py-name"><a title="Bio.Decode.Integer
Bio.GenBank.LocationParser.Integer
Martel.Integer" class="py-name" href="#" onclick="return doclink('link-164', 'Integer', 'link-100');">Integer</a></tt><tt class="py-op">(</tt><tt class="py-string">"dalign_query_end"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt id="link-165" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-165', 'Spaces', 'link-23');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-166" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-166', 'AnyEol', 'link-27');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt id="link-167" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-167', '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-168" class="py-name"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-168', 'ToEol', 'link-9');">ToEol</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="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt id="link-169" class="py-name"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-169', 'ToEol', 'link-9');">ToEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-comment"># blank line</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"><tt id="link-170" class="py-name" targets="Variable Bio.expressions.hmmpfam.domain_alignment=Bio.expressions.hmmpfam-module.html#domain_alignment"><a title="Bio.expressions.hmmpfam.domain_alignment" class="py-name" href="#" onclick="return doclink('link-170', 'domain_alignment', 'link-170');">domain_alignment</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-171" class="py-name"><a title="Bio.expressions.hmmpfam.domain_align_header" class="py-name" href="#" onclick="return doclink('link-171', 'domain_align_header', 'link-126');">domain_align_header</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt id="link-172" class="py-name" targets="Function Martel.Rep1()=Martel-module.html#Rep1"><a title="Martel.Rep1" class="py-name" href="#" onclick="return doclink('link-172', 'Rep1', 'link-172');">Rep1</a></tt><tt class="py-op">(</tt><tt id="link-173" class="py-name" targets="Function Martel.Opt()=Martel-module.html#Opt"><a title="Martel.Opt" class="py-name" href="#" onclick="return doclink('link-173', 'Opt', 'link-173');">Opt</a></tt><tt class="py-op">(</tt><tt id="link-174" class="py-name"><a title="Bio.expressions.hmmpfam.rf_line" class="py-name" href="#" onclick="return doclink('link-174', 'rf_line', 'link-142');">rf_line</a></tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt id="link-175" class="py-name"><a title="Bio.expressions.hmmpfam.domain_align_top" class="py-name" href="#" onclick="return doclink('link-175', 'domain_align_top', 'link-146');">domain_align_top</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt id="link-176" class="py-name"><a title="Bio.expressions.hmmpfam.domain_align_middle" class="py-name" href="#" onclick="return doclink('link-176', 'domain_align_middle', 'link-150');">domain_align_middle</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt id="link-177" class="py-name"><a title="Bio.expressions.hmmpfam.domain_align_bottom" class="py-name" href="#" onclick="return doclink('link-177', 'domain_align_bottom', 'link-154');">domain_align_bottom</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"><tt class="py-comment"># //</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-178" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.record_end()=Bio.GenBank._FeatureConsumer-class.html#record_end,Method Bio.GenBank._RecordConsumer.record_end()=Bio.GenBank._RecordConsumer-class.html#record_end,Variable Bio.expressions.genbank.record_end=Bio.expressions.genbank-module.html#record_end,Variable Bio.expressions.hmmpfam.record_end=Bio.expressions.hmmpfam-module.html#record_end"><a title="Bio.GenBank._FeatureConsumer.record_end
Bio.GenBank._RecordConsumer.record_end
Bio.expressions.genbank.record_end
Bio.expressions.hmmpfam.record_end" class="py-name" href="#" onclick="return doclink('link-178', 'record_end', 'link-178');">record_end</a></tt> <tt class="py-op">=</tt> <tt id="link-179" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-179', '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-180" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-180', 'AnyEol', 'link-27');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"><tt id="link-181" class="py-name" targets="Variable Bio.Emboss.primer3_format.record=Bio.Emboss.primer3_format-module.html#record,Variable Bio.Emboss.primersearch_format.record=Bio.Emboss.primersearch_format-module.html#record,Method Bio.GFF.Feature.record()=Bio.GFF.Feature-class.html#record,Variable Bio.LocusLink.web_parse.record=Bio.LocusLink.web_parse-module.html#record,Variable Bio.Ndb.record=Bio.Ndb-module.html#record,Function Bio.Std.record()=Bio.Std-module.html#record,Variable Bio.expressions.blocks.record=Bio.expressions.blocks-module.html#record,Variable Bio.expressions.embl.embl65.record=Bio.expressions.embl.embl65-module.html#record,Variable Bio.expressions.fasta.record=Bio.expressions.fasta-module.html#record,Variable Bio.expressions.genbank.record=Bio.expressions.genbank-module.html#record,Variable Bio.expressions.hmmpfam.record=Bio.expressions.hmmpfam-module.html#record,Variable Bio.expressions.swissprot.ipi.record=Bio.expressions.swissprot.ipi-module.html#record,Variable Bio.expressions.swissprot.speclist.record=Bio.expressions.swissprot.speclist-module.html#record,Variable Bio.expressions.swissprot.sprot38.record=Bio.expressions.swissprot.sprot38-module.html#record,Variable Bio.expressions.swissprot.sprot40.record=Bio.expressions.swissprot.sprot40-module.html#record,Variable Martel.test.test_swissprot38.record=Martel.test.test_swissprot38-module.html#record,Variable Martel.test.testformats.swissprot38.record=Martel.test.testformats.swissprot38-module.html#record"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-181', 'record', 'link-181');">record</a></tt> <tt class="py-op">=</tt> <tt id="link-182" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-182', 'Std', 'link-4');">Std</a></tt><tt class="py-op">.</tt><tt id="link-183" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-183', 'record', 'link-181');">record</a></tt><tt class="py-op">(</tt><tt id="link-184" 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-184', 'Rep', 'link-184');">Rep</a></tt><tt class="py-op">(</tt><tt id="link-185" class="py-name"><a title="Bio.Emboss.primersearch_format.sequence_info
Bio.expressions.hmmpfam.sequence_info" class="py-name" href="#" onclick="return doclink('link-185', 'sequence_info', 'link-41');">sequence_info</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt id="link-186" class="py-name"><a title="Bio.expressions.hmmpfam.family_header" class="py-name" href="#" onclick="return doclink('link-186', 'family_header', 'link-61');">family_header</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt id="link-187" class="py-name"><a title="Bio.expressions.hmmpfam.no_hit_line" class="py-name" href="#" onclick="return doclink('link-187', 'no_hit_line', 'link-69');">no_hit_line</a></tt> <tt class="py-op">|</tt> <tt id="link-188" class="py-name"><a title="Martel.Rep1" class="py-name" href="#" onclick="return doclink('link-188', 'Rep1', 'link-172');">Rep1</a></tt><tt class="py-op">(</tt><tt id="link-189" class="py-name"><a title="Bio.expressions.hmmpfam.family_hit_line" class="py-name" href="#" onclick="return doclink('link-189', 'family_hit_line', 'link-73');">family_hit_line</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt id="link-190" class="py-name"><a title="Bio.expressions.hmmpfam.domain_header" class="py-name" href="#" onclick="return doclink('link-190', 'domain_header', 'link-78');">domain_header</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt id="link-191" class="py-name"><a title="Bio.expressions.hmmpfam.no_hit_line" class="py-name" href="#" onclick="return doclink('link-191', 'no_hit_line', 'link-69');">no_hit_line</a></tt> <tt class="py-op">|</tt> <tt id="link-192" class="py-name"><a title="Martel.Rep1" class="py-name" href="#" onclick="return doclink('link-192', 'Rep1', 'link-172');">Rep1</a></tt><tt class="py-op">(</tt><tt id="link-193" class="py-name"><a title="Bio.expressions.hmmpfam.domain_hit_line" class="py-name" href="#" onclick="return doclink('link-193', 'domain_hit_line', 'link-95');">domain_hit_line</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt id="link-194" class="py-name"><a title="Bio.expressions.hmmpfam.alignment_header" class="py-name" href="#" onclick="return doclink('link-194', 'alignment_header', 'link-122');">alignment_header</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt id="link-195" class="py-name"><a title="Bio.expressions.hmmpfam.no_hit_line" class="py-name" href="#" onclick="return doclink('link-195', 'no_hit_line', 'link-69');">no_hit_line</a></tt> <tt class="py-op">|</tt> <tt id="link-196" class="py-name"><a title="Martel.Rep1" class="py-name" href="#" onclick="return doclink('link-196', 'Rep1', 'link-172');">Rep1</a></tt><tt class="py-op">(</tt><tt id="link-197" class="py-name"><a title="Bio.expressions.hmmpfam.domain_alignment" class="py-name" href="#" onclick="return doclink('link-197', 'domain_alignment', 'link-170');">domain_alignment</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt id="link-198" class="py-name"><a title="Bio.GenBank._FeatureConsumer.record_end
Bio.GenBank._RecordConsumer.record_end
Bio.expressions.genbank.record_end
Bio.expressions.hmmpfam.record_end" class="py-name" href="#" onclick="return doclink('link-198', 'record_end', 'link-178');">record_end</a></tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"><tt id="link-199" 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-199', 'format', 'link-199');">format</a></tt> <tt class="py-op">=</tt> <tt id="link-200" class="py-name" targets="Class Martel.Expression.HeaderFooter=Martel.Expression.HeaderFooter-class.html"><a title="Martel.Expression.HeaderFooter" class="py-name" href="#" onclick="return doclink('link-200', 'HeaderFooter', 'link-200');">HeaderFooter</a></tt><tt class="py-op">(</tt><tt class="py-string">"hmmpfam"</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">,</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt id="link-201" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-201', 'header', 'link-34');">header</a></tt><tt class="py-op">,</tt> <tt id="link-202" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-202', 'RecordReader', 'link-2');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-203" class="py-name" targets="Class Martel.RecordReader.CountLines=Martel.RecordReader.CountLines-class.html"><a title="Martel.RecordReader.CountLines" class="py-name" href="#" onclick="return doclink('link-203', 'CountLines', 'link-203');">CountLines</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-number">8</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt id="link-204" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-204', 'record', 'link-181');">record</a></tt><tt class="py-op">,</tt> <tt id="link-205" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-205', 'RecordReader', 'link-2');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-206" class="py-name" targets="Class Martel.RecordReader.EndsWith=Martel.RecordReader.EndsWith-class.html"><a title="Martel.RecordReader.EndsWith" class="py-name" href="#" onclick="return doclink('link-206', 'EndsWith', 'link-206');">EndsWith</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-string">"//\n"</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> </tt><script type="text/javascript">
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