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        <a href="Bio-module.html">Package&nbsp;Bio</a> ::
        <a href="Bio.expressions-module.html">Package&nbsp;expressions</a> ::
        Module&nbsp;fasta
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<h1 class="epydoc">Source Code for <a href="Bio.expressions.fasta-module.html">Module Bio.expressions.fasta</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno">  1</tt>  <tt class="py-line"><tt class="py-comment"># Read a FASTA description</tt> </tt>
<a name="L2"></a><tt class="py-lineno">  2</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L3"></a><tt class="py-lineno">  3</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">warnings</tt> </tt>
<a name="L4"></a><tt class="py-lineno">  4</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="L5"></a><tt class="py-lineno">  5</tt>  <tt class="py-line"> </tt>
<a name="L6"></a><tt class="py-lineno">  6</tt>  <tt class="py-line"> </tt>
<a name="L7"></a><tt class="py-lineno">  7</tt>  <tt class="py-line"> </tt>
<a name="L8"></a><tt class="py-lineno">  8</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">operator</tt> </tt>
<a name="L9"></a><tt class="py-lineno">  9</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="L10"></a><tt class="py-lineno"> 10</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-1" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-1', 'Bio', 'link-1');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name" targets="Module Bio.Std=Bio.Std-module.html"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-2', 'Std', 'link-2');">Std</a></tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt>  <tt class="py-line"> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt>  <tt class="py-line"><tt class="py-comment">### Parse dbxrefs given the NCBI|descr|line as explained</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">### in ftp://ncbi.nlm.nih.gov/blast/db/README and augmented</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">### by experience</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="make_2id"></a><div id="make_2id-def"><a name="L16"></a><tt class="py-lineno"> 16</tt> <a class="py-toggle" href="#" id="make_2id-toggle" onclick="return toggle('make_2id');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.expressions.fasta-module.html#make_2id">make_2id</a><tt class="py-op">(</tt><tt class="py-param">s</tt><tt class="py-op">,</tt> <tt class="py-param">dbname</tt><tt class="py-op">,</tt> <tt class="py-param">primary_name</tt><tt class="py-op">,</tt> <tt class="py-param">secondary_name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="make_2id-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="make_2id-expanded"><a name="L17"></a><tt class="py-lineno"> 17</tt>  <tt class="py-line">    <tt class="py-keyword">assert</tt> <tt class="py-name">secondary_name</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">primary_name</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-3" 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-3', 'Str', 'link-3');">Str</a></tt><tt class="py-op">(</tt><tt id="link-4" class="py-name" targets="Variable Martel.test.test_swissprot38.s=Martel.test.test_swissprot38-module.html#s"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-4', 's', 'link-4');">s</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="L20"></a><tt class="py-lineno"> 20</tt>  <tt class="py-line">               <tt id="link-5" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-5', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-6" class="py-name" targets="Function Bio.Std.dbxref_dbid()=Bio.Std-module.html#dbxref_dbid"><a title="Bio.Std.dbxref_dbid" class="py-name" href="#" onclick="return doclink('link-6', 'dbxref_dbid', 'link-6');">dbxref_dbid</a></tt><tt class="py-op">(</tt><tt id="link-7" class="py-name" targets="Function Martel.UntilSep()=Martel-module.html#UntilSep"><a title="Martel.UntilSep" class="py-name" href="#" onclick="return doclink('link-7', 'UntilSep', 'link-7');">UntilSep</a></tt><tt class="py-op">(</tt><tt class="py-name">sep</tt> <tt class="py-op">=</tt> <tt class="py-string">"| "</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-string">"dbname"</tt><tt class="py-op">:</tt> <tt class="py-name">dbname</tt><tt class="py-op">,</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt>  <tt class="py-line">                                                      <tt class="py-string">"type"</tt><tt class="py-op">:</tt> <tt class="py-name">secondary_name</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>
<a name="L23"></a><tt class="py-lineno"> 23</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-8" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-8', 'Str', 'link-3');">Str</a></tt><tt class="py-op">(</tt><tt id="link-9" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-9', 's', 'link-4');">s</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="L24"></a><tt class="py-lineno"> 24</tt>  <tt class="py-line">           <tt id="link-10" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-10', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-11" class="py-name"><a title="Bio.Std.dbxref_dbid" class="py-name" href="#" onclick="return doclink('link-11', 'dbxref_dbid', 'link-6');">dbxref_dbid</a></tt><tt class="py-op">(</tt><tt id="link-12" class="py-name"><a title="Martel.UntilSep" class="py-name" href="#" onclick="return doclink('link-12', 'UntilSep', 'link-7');">UntilSep</a></tt><tt class="py-op">(</tt><tt class="py-name">sep</tt> <tt class="py-op">=</tt> <tt class="py-string">"|"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-string">"dbname"</tt><tt class="py-op">:</tt> <tt class="py-name">dbname</tt><tt class="py-op">,</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt>  <tt class="py-line">                                                 <tt class="py-string">"type"</tt><tt class="py-op">:</tt> <tt class="py-name">primary_name</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-13" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-13', 'Str', 'link-3');">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="L27"></a><tt class="py-lineno"> 27</tt>  <tt class="py-line">           <tt id="link-14" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-14', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-15" class="py-name"><a title="Bio.Std.dbxref_dbid" class="py-name" href="#" onclick="return doclink('link-15', 'dbxref_dbid', 'link-6');">dbxref_dbid</a></tt><tt class="py-op">(</tt><tt id="link-16" class="py-name"><a title="Martel.UntilSep" class="py-name" href="#" onclick="return doclink('link-16', 'UntilSep', 'link-7');">UntilSep</a></tt><tt class="py-op">(</tt><tt class="py-name">sep</tt> <tt class="py-op">=</tt> <tt class="py-string">"| "</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-string">"dbname"</tt><tt class="py-op">:</tt> <tt class="py-name">dbname</tt><tt class="py-op">,</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt>  <tt class="py-line">                                                  <tt class="py-string">"type"</tt><tt class="py-op">:</tt> <tt class="py-name">secondary_name</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> </tt>
</div><a name="L29"></a><tt class="py-lineno"> 29</tt>  <tt class="py-line"> </tt>
<a name="make_1id"></a><div id="make_1id-def"><a name="L30"></a><tt class="py-lineno"> 30</tt> <a class="py-toggle" href="#" id="make_1id-toggle" onclick="return toggle('make_1id');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.expressions.fasta-module.html#make_1id">make_1id</a><tt class="py-op">(</tt><tt class="py-param">s</tt><tt class="py-op">,</tt> <tt class="py-param">dbname</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="make_1id-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="make_1id-expanded"><a name="L31"></a><tt class="py-lineno"> 31</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-17" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-17', 'Str', 'link-3');">Str</a></tt><tt class="py-op">(</tt><tt id="link-18" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-18', 's', 'link-4');">s</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="L32"></a><tt class="py-lineno"> 32</tt>  <tt class="py-line">           <tt id="link-19" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-19', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-20" class="py-name"><a title="Bio.Std.dbxref_dbid" class="py-name" href="#" onclick="return doclink('link-20', 'dbxref_dbid', 'link-6');">dbxref_dbid</a></tt><tt class="py-op">(</tt><tt id="link-21" class="py-name"><a title="Martel.UntilSep" class="py-name" href="#" onclick="return doclink('link-21', 'UntilSep', 'link-7');">UntilSep</a></tt><tt class="py-op">(</tt><tt class="py-name">sep</tt> <tt class="py-op">=</tt> <tt class="py-string">"| "</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-string">"dbname"</tt><tt class="py-op">:</tt> <tt class="py-name">dbname</tt><tt class="py-op">,</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt>  <tt class="py-line">                                                  <tt class="py-string">"type"</tt><tt class="py-op">:</tt> <tt id="link-22" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.name=Bio.Encodings.IUPACEncoding-module.html#name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-22', 'name', 'link-22');">name</a></tt><tt class="py-op">}</tt><tt class="py-op">)</tt> </tt>
</div><a name="L34"></a><tt class="py-lineno"> 34</tt>  <tt class="py-line">                                     </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt>  <tt class="py-line"><tt id="link-23" class="py-name" targets="Variable Bio.expressions.fasta.ids=Bio.expressions.fasta-module.html#ids"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-23', 'ids', 'link-23');">ids</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 class="py-comment"># gene identifier              gi|id  # This isn't in the README</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt id="link-24" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-24', 'ids', 'link-23');">ids</a></tt><tt class="py-op">.</tt><tt id="link-25" class="py-name" targets="Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-class.html#append,Method Bio.EUtils.POM.ElementNode.append()=Bio.EUtils.POM.ElementNode-class.html#append,Method Bio.EUtils.sourcegen.SourceFile.append()=Bio.EUtils.sourcegen.SourceFile-class.html#append,Method Bio.SCOP.Raf.SeqMap.append()=Bio.SCOP.Raf.SeqMap-class.html#append,Method Bio.Seq.MutableSeq.append()=Bio.Seq.MutableSeq-class.html#append,Method Bio.Wise.psw.Alignment.append()=Bio.Wise.psw.Alignment-class.html#append,Method Bio.Wise.psw.AlignmentColumn.append()=Bio.Wise.psw.AlignmentColumn-class.html#append,Method Martel.msre_parse.SubPattern.append()=Martel.msre_parse.SubPattern-class.html#append"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-25', 'append', 'link-25');">append</a></tt><tt class="py-op">(</tt><tt id="link-26" class="py-name" targets="Function Bio.expressions.fasta.make_1id()=Bio.expressions.fasta-module.html#make_1id"><a title="Bio.expressions.fasta.make_1id" class="py-name" href="#" onclick="return doclink('link-26', 'make_1id', 'link-26');">make_1id</a></tt><tt class="py-op">(</tt><tt class="py-string">"gi"</tt><tt class="py-op">,</tt> <tt class="py-string">"x-gi"</tt><tt class="py-op">,</tt> <tt class="py-string">"primary"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt>  <tt class="py-line"> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt>  <tt class="py-line"><tt class="py-comment"># GenBank                      gb|accession|locus</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"># gb|U37104|APU37104</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt id="link-27" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-27', 'ids', 'link-23');">ids</a></tt><tt class="py-op">.</tt><tt id="link-28" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-28', 'append', 'link-25');">append</a></tt><tt class="py-op">(</tt><tt id="link-29" class="py-name" targets="Function Bio.expressions.fasta.make_2id()=Bio.expressions.fasta-module.html#make_2id"><a title="Bio.expressions.fasta.make_2id" class="py-name" href="#" onclick="return doclink('link-29', 'make_2id', 'link-29');">make_2id</a></tt><tt class="py-op">(</tt><tt class="py-string">"gb"</tt><tt class="py-op">,</tt> <tt class="py-string">"gb"</tt><tt class="py-op">,</tt> <tt class="py-string">"primary"</tt><tt class="py-op">,</tt> <tt class="py-string">"secondary"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt>  <tt class="py-line"> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt>  <tt class="py-line"><tt class="py-comment"># EMBL Data Library            emb|accession|locus</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># emb|F19596|HSPD04201</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt id="link-30" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-30', 'ids', 'link-23');">ids</a></tt><tt class="py-op">.</tt><tt id="link-31" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-31', 'append', 'link-25');">append</a></tt><tt class="py-op">(</tt><tt id="link-32" class="py-name"><a title="Bio.expressions.fasta.make_2id" class="py-name" href="#" onclick="return doclink('link-32', 'make_2id', 'link-29');">make_2id</a></tt><tt class="py-op">(</tt><tt class="py-string">"emb"</tt><tt class="py-op">,</tt> <tt class="py-string">"embl"</tt><tt class="py-op">,</tt> <tt class="py-string">"primary"</tt><tt class="py-op">,</tt> <tt class="py-string">"secondary"</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>
<a name="L47"></a><tt class="py-lineno"> 47</tt>  <tt class="py-line"><tt class="py-comment"># DDBJ, DNA Database of Japan  dbj|accession|locus</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt id="link-33" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-33', 'ids', 'link-23');">ids</a></tt><tt class="py-op">.</tt><tt id="link-34" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-34', 'append', 'link-25');">append</a></tt><tt class="py-op">(</tt><tt id="link-35" class="py-name"><a title="Bio.expressions.fasta.make_2id" class="py-name" href="#" onclick="return doclink('link-35', 'make_2id', 'link-29');">make_2id</a></tt><tt class="py-op">(</tt><tt class="py-string">"dbj"</tt><tt class="py-op">,</tt> <tt class="py-string">"ddbj"</tt><tt class="py-op">,</tt> <tt class="py-string">"primary"</tt><tt class="py-op">,</tt> <tt class="py-string">"secondary"</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 class="py-comment"># NBRF PIR                     pir||entry</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt id="link-36" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-36', 'ids', 'link-23');">ids</a></tt><tt class="py-op">.</tt><tt id="link-37" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-37', 'append', 'link-25');">append</a></tt><tt class="py-op">(</tt><tt id="link-38" class="py-name"><a title="Bio.expressions.fasta.make_2id" class="py-name" href="#" onclick="return doclink('link-38', 'make_2id', 'link-29');">make_2id</a></tt><tt class="py-op">(</tt><tt class="py-string">"pir"</tt><tt class="py-op">,</tt> <tt class="py-string">"pir"</tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-string">"primary"</tt><tt class="py-op">)</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"># Protein Research Foundation  prf||name</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt id="link-39" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-39', 'ids', 'link-23');">ids</a></tt><tt class="py-op">.</tt><tt id="link-40" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-40', 'append', 'link-25');">append</a></tt><tt class="py-op">(</tt><tt id="link-41" class="py-name"><a title="Bio.expressions.fasta.make_2id" class="py-name" href="#" onclick="return doclink('link-41', 'make_2id', 'link-29');">make_2id</a></tt><tt class="py-op">(</tt><tt class="py-string">"prf"</tt><tt class="py-op">,</tt> <tt class="py-string">"x-prf"</tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-string">"primary"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt>  <tt class="py-line"> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt>  <tt class="py-line"><tt class="py-comment"># SWISS-PROT                   sp|accession|entry name</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt id="link-42" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-42', 'ids', 'link-23');">ids</a></tt><tt class="py-op">.</tt><tt id="link-43" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-43', 'append', 'link-25');">append</a></tt><tt class="py-op">(</tt><tt id="link-44" class="py-name"><a title="Bio.expressions.fasta.make_2id" class="py-name" href="#" onclick="return doclink('link-44', 'make_2id', 'link-29');">make_2id</a></tt><tt class="py-op">(</tt><tt class="py-string">"sp"</tt><tt class="py-op">,</tt> <tt class="py-string">"sp"</tt><tt class="py-op">,</tt> <tt class="py-string">"primary"</tt><tt class="py-op">,</tt> <tt class="py-string">"secondary"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt>  <tt class="py-line"> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt>  <tt class="py-line"><tt class="py-comment"># Brookhaven Protein Data Bank pdb|entry|chain</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt id="link-45" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-45', 'ids', 'link-23');">ids</a></tt><tt class="py-op">.</tt><tt id="link-46" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-46', 'append', 'link-25');">append</a></tt><tt class="py-op">(</tt><tt id="link-47" class="py-name"><a title="Bio.expressions.fasta.make_2id" class="py-name" href="#" onclick="return doclink('link-47', 'make_2id', 'link-29');">make_2id</a></tt><tt class="py-op">(</tt><tt class="py-string">"pdb"</tt><tt class="py-op">,</tt> <tt class="py-string">"x-pdb"</tt><tt class="py-op">,</tt> <tt class="py-string">"primary"</tt><tt class="py-op">,</tt> <tt class="py-string">"secondary"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt>  <tt class="py-comment"># XXX not correct</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt>  <tt class="py-line"> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt>  <tt class="py-line"><tt class="py-comment"># Patents                      pat|country|number </tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt id="link-48" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-48', 'ids', 'link-23');">ids</a></tt><tt class="py-op">.</tt><tt id="link-49" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-49', 'append', 'link-25');">append</a></tt><tt class="py-op">(</tt><tt id="link-50" class="py-name"><a title="Bio.expressions.fasta.make_2id" class="py-name" href="#" onclick="return doclink('link-50', 'make_2id', 'link-29');">make_2id</a></tt><tt class="py-op">(</tt><tt class="py-string">"pat"</tt><tt class="py-op">,</tt> <tt class="py-string">"x-pat"</tt><tt class="py-op">,</tt> <tt class="py-string">"primary"</tt><tt class="py-op">,</tt> <tt class="py-string">"secondary"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt>  <tt class="py-comment"># XXX not correct</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt>  <tt class="py-line"> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt>  <tt class="py-line"><tt class="py-comment"># GenInfo Backbone Id          bbs|number </tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt id="link-51" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-51', 'ids', 'link-23');">ids</a></tt><tt class="py-op">.</tt><tt id="link-52" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-52', 'append', 'link-25');">append</a></tt><tt class="py-op">(</tt><tt id="link-53" class="py-name"><a title="Bio.expressions.fasta.make_1id" class="py-name" href="#" onclick="return doclink('link-53', 'make_1id', 'link-26');">make_1id</a></tt><tt class="py-op">(</tt><tt class="py-string">"bbs"</tt><tt class="py-op">,</tt> <tt class="py-string">"x-bbs"</tt><tt class="py-op">,</tt> <tt class="py-string">"primary"</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"># General database identifier  gnl|database|identifier</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt id="link-54" class="py-name" targets="Variable Bio.expressions.fasta.gnl_id=Bio.expressions.fasta-module.html#gnl_id"><a title="Bio.expressions.fasta.gnl_id" class="py-name" href="#" onclick="return doclink('link-54', 'gnl_id', 'link-54');">gnl_id</a></tt> <tt class="py-op">=</tt> <tt id="link-55" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-55', 'Str', 'link-3');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"gnl|"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt>  <tt class="py-line">         <tt id="link-56" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-56', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-57" class="py-name" targets="Function Bio.Std.dbxref_dbname()=Bio.Std-module.html#dbxref_dbname"><a title="Bio.Std.dbxref_dbname" class="py-name" href="#" onclick="return doclink('link-57', 'dbxref_dbname', 'link-57');">dbxref_dbname</a></tt><tt class="py-op">(</tt><tt id="link-58" class="py-name"><a title="Martel.UntilSep" class="py-name" href="#" onclick="return doclink('link-58', 'UntilSep', 'link-7');">UntilSep</a></tt><tt class="py-op">(</tt><tt class="py-name">sep</tt> <tt class="py-op">=</tt> <tt class="py-string">"| "</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt>  <tt class="py-line">         <tt id="link-59" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-59', 'Str', 'link-3');">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="L72"></a><tt class="py-lineno"> 72</tt>  <tt class="py-line">         <tt id="link-60" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-60', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-61" class="py-name"><a title="Bio.Std.dbxref_dbid" class="py-name" href="#" onclick="return doclink('link-61', 'dbxref_dbid', 'link-6');">dbxref_dbid</a></tt><tt class="py-op">(</tt><tt id="link-62" class="py-name"><a title="Martel.UntilSep" class="py-name" href="#" onclick="return doclink('link-62', 'UntilSep', 'link-7');">UntilSep</a></tt><tt class="py-op">(</tt><tt class="py-name">sep</tt> <tt class="py-op">=</tt> <tt class="py-string">"| "</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt>  <tt class="py-line"><tt id="link-63" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-63', 'ids', 'link-23');">ids</a></tt><tt class="py-op">.</tt><tt id="link-64" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-64', 'append', 'link-25');">append</a></tt><tt class="py-op">(</tt><tt id="link-65" class="py-name"><a title="Bio.expressions.fasta.gnl_id" class="py-name" href="#" onclick="return doclink('link-65', 'gnl_id', 'link-54');">gnl_id</a></tt><tt class="py-op">)</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt>  <tt class="py-line"> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt>  <tt class="py-line"><tt class="py-comment"># NCBI Reference Sequence      ref|accession|locus</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt id="link-66" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-66', 'ids', 'link-23');">ids</a></tt><tt class="py-op">.</tt><tt id="link-67" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-67', 'append', 'link-25');">append</a></tt><tt class="py-op">(</tt><tt id="link-68" class="py-name"><a title="Bio.expressions.fasta.make_2id" class="py-name" href="#" onclick="return doclink('link-68', 'make_2id', 'link-29');">make_2id</a></tt><tt class="py-op">(</tt><tt class="py-string">"ref"</tt><tt class="py-op">,</tt> <tt class="py-string">"x-ref"</tt><tt class="py-op">,</tt> <tt class="py-string">"primary"</tt><tt class="py-op">,</tt> <tt class="py-string">"secondary"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt>  <tt class="py-line"> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt>  <tt class="py-line"><tt class="py-comment"># Local Sequence identifier    lcl|identifier</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt id="link-69" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-69', 'ids', 'link-23');">ids</a></tt><tt class="py-op">.</tt><tt id="link-70" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-70', 'append', 'link-25');">append</a></tt><tt class="py-op">(</tt><tt id="link-71" class="py-name"><a title="Bio.expressions.fasta.make_1id" class="py-name" href="#" onclick="return doclink('link-71', 'make_1id', 'link-26');">make_1id</a></tt><tt class="py-op">(</tt><tt class="py-string">"lcl"</tt><tt class="py-op">,</tt> <tt class="py-string">"local"</tt><tt class="py-op">,</tt> <tt class="py-string">"primary"</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>
<a name="L81"></a><tt class="py-lineno"> 81</tt>  <tt class="py-line"><tt class="py-comment"># "|" them all together</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt id="link-72" class="py-name" targets="Variable Bio.expressions.fasta.ncbi_word=Bio.expressions.fasta-module.html#ncbi_word"><a title="Bio.expressions.fasta.ncbi_word" class="py-name" href="#" onclick="return doclink('link-72', 'ncbi_word', 'link-72');">ncbi_word</a></tt> <tt class="py-op">=</tt> <tt id="link-73" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-73', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-74" class="py-name" targets="Function Bio.Std.dbxref()=Bio.Std-module.html#dbxref"><a title="Bio.Std.dbxref" class="py-name" href="#" onclick="return doclink('link-74', 'dbxref', 'link-74');">dbxref</a></tt><tt class="py-op">(</tt><tt class="py-name">reduce</tt><tt class="py-op">(</tt><tt class="py-name">operator</tt><tt class="py-op">.</tt><tt class="py-name">or_</tt><tt class="py-op">,</tt> <tt id="link-75" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-75', 'ids', 'link-23');">ids</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt>  <tt class="py-line"> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt>  <tt class="py-line"><tt class="py-comment">#ncbi_term = Assert(Re("[^ \R]+\|")) + \</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt id="link-76" class="py-name" targets="Variable Bio.expressions.fasta.ncbi_term=Bio.expressions.fasta-module.html#ncbi_term"><a title="Bio.expressions.fasta.ncbi_term" class="py-name" href="#" onclick="return doclink('link-76', 'ncbi_term', 'link-76');">ncbi_term</a></tt> <tt class="py-op">=</tt>  <tt id="link-77" class="py-name"><a title="Bio.expressions.fasta.ncbi_word" class="py-name" href="#" onclick="return doclink('link-77', 'ncbi_word', 'link-72');">ncbi_word</a></tt> <tt class="py-op">+</tt> <tt id="link-78" 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-78', 'Rep', 'link-78');">Rep</a></tt><tt class="py-op">(</tt><tt id="link-79" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-79', 'Str', 'link-3');">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-80" class="py-name"><a title="Bio.expressions.fasta.ncbi_word" class="py-name" href="#" onclick="return doclink('link-80', 'ncbi_word', 'link-72');">ncbi_word</a></tt><tt class="py-op">)</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt>  <tt class="py-line"> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt>  <tt class="py-line"><tt class="py-comment"># Anything else</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt id="link-81" class="py-name" targets="Variable Bio.expressions.fasta.generic_term=Bio.expressions.fasta-module.html#generic_term"><a title="Bio.expressions.fasta.generic_term" class="py-name" href="#" onclick="return doclink('link-81', 'generic_term', 'link-81');">generic_term</a></tt> <tt class="py-op">=</tt> <tt id="link-82" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-82', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-83" class="py-name"><a title="Bio.Std.dbxref" class="py-name" href="#" onclick="return doclink('link-83', 'dbxref', 'link-74');">dbxref</a></tt><tt class="py-op">(</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt>  <tt class="py-line">                 <tt id="link-84" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-84', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-85" class="py-name"><a title="Bio.Std.dbxref_dbid" class="py-name" href="#" onclick="return doclink('link-85', 'dbxref_dbid', 'link-6');">dbxref_dbid</a></tt><tt class="py-op">(</tt><tt id="link-86" class="py-name"><a title="Martel.UntilSep" class="py-name" href="#" onclick="return doclink('link-86', 'UntilSep', 'link-7');">UntilSep</a></tt><tt class="py-op">(</tt><tt class="py-name">sep</tt> <tt class="py-op">=</tt> <tt class="py-string">" "</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-string">"dbname"</tt><tt class="py-op">:</tt> <tt class="py-string">"local"</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt>  <tt class="py-line">               <tt class="py-op">)</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt>  <tt class="py-line"><tt id="link-87" class="py-name" targets="Variable Bio.expressions.fasta.id_term=Bio.expressions.fasta-module.html#id_term"><a title="Bio.expressions.fasta.id_term" class="py-name" href="#" onclick="return doclink('link-87', 'id_term', 'link-87');">id_term</a></tt> <tt class="py-op">=</tt> <tt id="link-88" class="py-name"><a title="Bio.expressions.fasta.ncbi_term" class="py-name" href="#" onclick="return doclink('link-88', 'ncbi_term', 'link-76');">ncbi_term</a></tt> <tt class="py-op">|</tt> <tt id="link-89" class="py-name"><a title="Bio.expressions.fasta.generic_term" class="py-name" href="#" onclick="return doclink('link-89', 'generic_term', 'link-81');">generic_term</a></tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt>  <tt class="py-line"><tt class="py-comment">###########################################################</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt>  <tt class="py-line"><tt id="link-90" 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-90', 'comment_lines', 'link-90');">comment_lines</a></tt> <tt class="py-op">=</tt> <tt id="link-91" class="py-name"><a title="Bio.Pathway.Rep
Martel.Rep" class="py-name" href="#" onclick="return doclink('link-91', 'Rep', 'link-78');">Rep</a></tt><tt class="py-op">(</tt><tt id="link-92" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-92', 'Str', 'link-3');">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-93" class="py-name" targets="Function Martel.ToEol()=Martel-module.html#ToEol"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-93', 'ToEol', 'link-93');">ToEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt>  <tt class="py-line"><tt id="link-94" class="py-name" targets="Method Bio.Blast.NCBIStandalone._AlignmentConsumer.title()=Bio.Blast.NCBIStandalone._AlignmentConsumer-class.html#title,Method Bio.GenBank._FeatureConsumer.title()=Bio.GenBank._FeatureConsumer-class.html#title,Method Bio.GenBank._RecordConsumer.title()=Bio.GenBank._RecordConsumer-class.html#title,Method Bio.Medline._RecordConsumer.title()=Bio.Medline._RecordConsumer-class.html#title,Variable Bio.expressions.fasta.title=Bio.expressions.fasta-module.html#title"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title
Bio.Medline._RecordConsumer.title
Bio.expressions.fasta.title" class="py-name" href="#" onclick="return doclink('link-94', 'title', 'link-94');">title</a></tt> <tt class="py-op">=</tt> <tt id="link-95" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-95', 'Str', 'link-3');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"&gt;"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-96" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-96', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-97" class="py-name" targets="Function Bio.Std.description_line()=Bio.Std-module.html#description_line"><a title="Bio.Std.description_line" class="py-name" href="#" onclick="return doclink('link-97', 'description_line', 'link-97');">description_line</a></tt><tt class="py-op">(</tt><tt id="link-98" class="py-name"><a title="Bio.expressions.fasta.id_term" class="py-name" href="#" onclick="return doclink('link-98', 'id_term', 'link-87');">id_term</a></tt> <tt class="py-op">+</tt> <tt id="link-99" class="py-name" targets="Function Martel.UntilEol()=Martel-module.html#UntilEol"><a title="Martel.UntilEol" class="py-name" href="#" onclick="return doclink('link-99', 'UntilEol', 'link-99');">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-100" 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-100', 'AnyEol', 'link-100');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt>  <tt class="py-line"><tt id="link-101" class="py-name" targets="Variable Bio.expressions.fasta.seqline=Bio.expressions.fasta-module.html#seqline"><a title="Bio.expressions.fasta.seqline" class="py-name" href="#" onclick="return doclink('link-101', 'seqline', 'link-101');">seqline</a></tt> <tt class="py-op">=</tt> <tt id="link-102" class="py-name" targets="Function Martel.AssertNot()=Martel-module.html#AssertNot"><a title="Martel.AssertNot" class="py-name" href="#" onclick="return doclink('link-102', 'AssertNot', 'link-102');">AssertNot</a></tt><tt class="py-op">(</tt><tt id="link-103" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-103', 'Str', 'link-3');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"&gt;"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-104" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-104', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-105" class="py-name" targets="Method Bio.AlignAce.Parser.AlignAceConsumer.sequence()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#sequence,Variable Bio.Emboss.primer3_format.sequence=Bio.Emboss.primer3_format-module.html#sequence,Method Bio.FSSP.FSSPAlignDict.sequence()=Bio.FSSP.FSSPAlignDict-class.html#sequence,Method Bio.GenBank._FeatureConsumer.sequence()=Bio.GenBank._FeatureConsumer-class.html#sequence,Method Bio.GenBank._RecordConsumer.sequence()=Bio.GenBank._RecordConsumer-class.html#sequence,Method Bio.IntelliGenetics._RecordConsumer.sequence()=Bio.IntelliGenetics._RecordConsumer-class.html#sequence,Method Bio.Rebase._RecordConsumer.sequence()=Bio.Rebase._RecordConsumer-class.html#sequence,Function Bio.Std.sequence()=Bio.Std-module.html#sequence,Module Bio.builders.SeqRecord.sequence=Bio.builders.SeqRecord.sequence-module.html,Variable Bio.expressions.fasta.sequence=Bio.expressions.fasta-module.html#sequence,Variable Bio.expressions.genbank.sequence=Bio.expressions.genbank-module.html#sequence,Variable Bio.expressions.swissprot.sprot38.sequence=Bio.expressions.swissprot.sprot38-module.html#sequence,Module Bio.formatdefs.sequence=Bio.formatdefs.sequence-module.html,Variable Bio.formatdefs.sequence.sequence=Bio.formatdefs.sequence-module.html#sequence,Variable Martel.test.test_swissprot38.sequence=Martel.test.test_swissprot38-module.html#sequence,Variable Martel.test.testformats.swissprot38.sequence=Martel.test.testformats.swissprot38-module.html#sequence"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-105', 'sequence', 'link-105');">sequence</a></tt><tt class="py-op">(</tt><tt id="link-106" class="py-name"><a title="Martel.UntilEol" class="py-name" href="#" onclick="return doclink('link-106', 'UntilEol', 'link-99');">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-107" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-107', 'AnyEol', 'link-100');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt>  <tt class="py-line"><tt class="py-comment"># can get a sequence line without an Eol at the end of a file</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt id="link-108" class="py-name" targets="Variable Bio.expressions.fasta.seqline_nonewline=Bio.expressions.fasta-module.html#seqline_nonewline"><a title="Bio.expressions.fasta.seqline_nonewline" class="py-name" href="#" onclick="return doclink('link-108', 'seqline_nonewline', 'link-108');">seqline_nonewline</a></tt> <tt class="py-op">=</tt> <tt id="link-109" class="py-name"><a title="Martel.AssertNot" class="py-name" href="#" onclick="return doclink('link-109', 'AssertNot', 'link-102');">AssertNot</a></tt><tt class="py-op">(</tt><tt id="link-110" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-110', 'Str', 'link-3');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"&gt;"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-111" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-111', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-112" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-112', 'sequence', 'link-105');">sequence</a></tt><tt class="py-op">(</tt><tt id="link-113" class="py-name" targets="Function Martel.Word()=Martel-module.html#Word"><a title="Martel.Word" class="py-name" href="#" onclick="return doclink('link-113', 'Word', 'link-113');">Word</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt>  <tt class="py-line"> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt>  <tt class="py-line"><tt id="link-114" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-114', 'sequence', 'link-105');">sequence</a></tt> <tt class="py-op">=</tt> <tt id="link-115" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-115', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-116" class="py-name" targets="Variable Bio.CDD.cdd_format.sequence_block=Bio.CDD.cdd_format-module.html#sequence_block,Variable Bio.NBRF.nbrf_format.sequence_block=Bio.NBRF.nbrf_format-module.html#sequence_block,Function Bio.Std.sequence_block()=Bio.Std-module.html#sequence_block"><a title="Bio.CDD.cdd_format.sequence_block
Bio.NBRF.nbrf_format.sequence_block
Bio.Std.sequence_block" class="py-name" href="#" onclick="return doclink('link-116', 'sequence_block', 'link-116');">sequence_block</a></tt><tt class="py-op">(</tt><tt id="link-117" class="py-name"><a title="Bio.Pathway.Rep
Martel.Rep" class="py-name" href="#" onclick="return doclink('link-117', 'Rep', 'link-78');">Rep</a></tt><tt class="py-op">(</tt><tt id="link-118" class="py-name"><a title="Bio.expressions.fasta.seqline" class="py-name" href="#" onclick="return doclink('link-118', 'seqline', 'link-101');">seqline</a></tt> <tt class="py-op">|</tt> <tt id="link-119" class="py-name"><a title="Bio.expressions.fasta.seqline_nonewline" class="py-name" href="#" onclick="return doclink('link-119', 'seqline_nonewline', 'link-108');">seqline_nonewline</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt>  <tt class="py-line"> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt>  <tt class="py-line"><tt id="link-120" 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-120', 'record', 'link-120');">record</a></tt> <tt class="py-op">=</tt> <tt id="link-121" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-121', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-122" 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-122', 'record', 'link-120');">record</a></tt><tt class="py-op">(</tt><tt id="link-123" class="py-name"><a title="Bio.IntelliGenetics.intelligenetics_format.comment_lines
Bio.expressions.fasta.comment_lines" class="py-name" href="#" onclick="return doclink('link-123', 'comment_lines', 'link-90');">comment_lines</a></tt> <tt class="py-op">+</tt> <tt id="link-124" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title
Bio.Medline._RecordConsumer.title
Bio.expressions.fasta.title" class="py-name" href="#" onclick="return doclink('link-124', 'title', 'link-94');">title</a></tt> <tt class="py-op">+</tt> <tt id="link-125" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-125', 'sequence', 'link-105');">sequence</a></tt> <tt class="py-op">+</tt> <tt id="link-126" class="py-name"><a title="Bio.Pathway.Rep
Martel.Rep" class="py-name" href="#" onclick="return doclink('link-126', 'Rep', 'link-78');">Rep</a></tt><tt class="py-op">(</tt><tt id="link-127" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-127', 'AnyEol', 'link-100');">AnyEol</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="L103"></a><tt class="py-lineno">103</tt>  <tt class="py-line"> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt>  <tt class="py-line"><tt class="py-comment"># define a format which reads records, but allows #-style comments in </tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># the FASTA file</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt id="link-128" 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-128', 'format', 'link-128');">format</a></tt> <tt class="py-op">=</tt> <tt id="link-129" 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-129', 'HeaderFooter', 'link-129');">HeaderFooter</a></tt><tt class="py-op">(</tt><tt class="py-string">"dataset"</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-string">"format"</tt><tt class="py-op">:</tt> <tt class="py-string">"fasta"</tt><tt class="py-op">}</tt><tt class="py-op">,</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt>  <tt class="py-line">                      <tt id="link-130" class="py-name"><a title="Bio.IntelliGenetics.intelligenetics_format.comment_lines
Bio.expressions.fasta.comment_lines" class="py-name" href="#" onclick="return doclink('link-130', 'comment_lines', 'link-90');">comment_lines</a></tt><tt class="py-op">,</tt> <tt id="link-131" 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-131', 'RecordReader', 'link-131');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-132" class="py-name" targets="Class Martel.RecordReader.Until=Martel.RecordReader.Until-class.html"><a title="Martel.RecordReader.Until" class="py-name" href="#" onclick="return doclink('link-132', 'Until', 'link-132');">Until</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-string">"&gt;"</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt>  <tt class="py-line">                      <tt id="link-133" 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-133', 'record', 'link-120');">record</a></tt><tt class="py-op">,</tt> <tt id="link-134" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-134', 'RecordReader', 'link-131');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-135" class="py-name" targets="Class Martel.RecordReader.StartsWith=Martel.RecordReader.StartsWith-class.html"><a title="Martel.RecordReader.StartsWith" class="py-name" href="#" onclick="return doclink('link-135', 'StartsWith', 'link-135');">StartsWith</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-string">"&gt;"</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt>  <tt class="py-line">                      <tt id="link-136" class="py-name"><a title="Bio.IntelliGenetics.intelligenetics_format.comment_lines
Bio.expressions.fasta.comment_lines" class="py-name" href="#" onclick="return doclink('link-136', 'comment_lines', 'link-90');">comment_lines</a></tt><tt class="py-op">,</tt> <tt id="link-137" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-137', 'RecordReader', 'link-131');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-138" class="py-name" targets="Class Martel.RecordReader.Everything=Martel.RecordReader.Everything-class.html"><a title="Martel.RecordReader.Everything" class="py-name" href="#" onclick="return doclink('link-138', 'Everything', 'link-138');">Everything</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt>  <tt class="py-line">                     <tt class="py-op">)</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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