Sophie: biopython-doc-1.47-2mdv2008.1 x86

biopython-doc-1.47-2mdv2008.1.x86_64.rpm

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        <a href="Bio-module.html">Package&nbsp;Bio</a> ::
        <a href="Bio.expressions-module.html">Package&nbsp;expressions</a> ::
        <a href="Bio.expressions.swissprot-module.html">Package&nbsp;swissprot</a> ::
        Module&nbsp;sprot40
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<h1 class="epydoc">Source Code for <a href="Bio.expressions.swissprot.sprot40-module.html">Module Bio.expressions.swissprot.sprot40</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">warnings</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</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="L3"></a><tt class="py-lineno"> 3</tt>  <tt class="py-line"> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt>  <tt class="py-line"> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-0" class="py-name" targets="Package Martel=Martel-module.html"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-0', 'Martel', 'link-0');">Martel</a></tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</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.Time=Martel.Time-module.html"><a title="Martel.Time" class="py-name" href="#" onclick="return doclink('link-2', 'Time', 'link-2');">Time</a></tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-3" class="py-name" targets="Module Bio.expressions.swissprot.sprot38=Bio.expressions.swissprot.sprot38-module.html,Variable Bio.formatdefs.swissprot.sprot38=Bio.formatdefs.swissprot-module.html#sprot38"><a title="Bio.expressions.swissprot.sprot38
Bio.formatdefs.swissprot.sprot38" class="py-name" href="#" onclick="return doclink('link-3', 'sprot38', 'link-3');">sprot38</a></tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt>  <tt class="py-line"> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt>  <tt class="py-line"><tt class="py-comment"># HAS2_CHICK has a DT line like this</tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># DT   30-MAY-2000 (REL. 39, Created)</tt> </tt>
<a name="L11"></a><tt class="py-lineno">11</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#                   ^^^ Note the upper-case "REL" instead of "Rel" !</tt> </tt>
<a name="L12"></a><tt class="py-lineno">12</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt id="link-4" class="py-name" targets="Variable Bio.expressions.swissprot.ipi.DT_created_exp=Bio.expressions.swissprot.ipi-module.html#DT_created_exp,Variable Bio.expressions.swissprot.sprot40.DT_created_exp=Bio.expressions.swissprot.sprot40-module.html#DT_created_exp"><a title="Bio.expressions.swissprot.ipi.DT_created_exp
Bio.expressions.swissprot.sprot40.DT_created_exp" class="py-name" href="#" onclick="return doclink('link-4', 'DT_created_exp', 'link-4');">DT_created_exp</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-5" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-5', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-6" 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-6', 'Str', 'link-6');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"DT   "</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L13"></a><tt class="py-lineno">13</tt>  <tt class="py-line">                  <tt id="link-7" class="py-name"><a title="Martel.Time" class="py-name" href="#" onclick="return doclink('link-7', 'Time', 'link-2');">Time</a></tt><tt class="py-op">.</tt><tt id="link-8" class="py-name" targets="Function Martel.Time.make_expression()=Martel.Time-module.html#make_expression,Function Martel.convert_re.make_expression()=Martel.convert_re-module.html#make_expression"><a title="Martel.Time.make_expression
Martel.convert_re.make_expression" class="py-name" href="#" onclick="return doclink('link-8', 'make_expression', 'link-8');">make_expression</a></tt><tt class="py-op">(</tt><tt class="py-string">"%(DD)-%(Jan)-%(YYYY)"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L14"></a><tt class="py-lineno">14</tt>  <tt class="py-line">                  <tt id="link-9" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-9', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-10" class="py-name" targets="Function Martel.Re()=Martel-module.html#Re"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-10', 'Re', 'link-10');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">" \(R[Ee][Ll]. (?P&lt;release&gt;\d\d), Created\)\R"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </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 id="link-11" class="py-name" targets="Variable Bio.expressions.swissprot.sprot40.OX_start=Bio.expressions.swissprot.sprot40-module.html#OX_start"><a title="Bio.expressions.swissprot.sprot40.OX_start" class="py-name" href="#" onclick="return doclink('link-11', 'OX_start', 'link-11');">OX_start</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-12" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-12', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-13" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-13', 'Str', 'link-6');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"OX   NCBI_TaxID="</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L18"></a><tt class="py-lineno">18</tt>  <tt class="py-line">            <tt id="link-14" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-14', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-15" class="py-name" targets="Function Martel.Rep1()=Martel-module.html#Rep1"><a title="Martel.Rep1" class="py-name" href="#" onclick="return doclink('link-15', 'Rep1', 'link-15');">Rep1</a></tt><tt class="py-op">(</tt><tt id="link-16" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-16', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-17" class="py-name" targets="Function Martel.Digits()=Martel-module.html#Digits"><a title="Martel.Digits" class="py-name" href="#" onclick="return doclink('link-17', 'Digits', 'link-17');">Digits</a></tt><tt class="py-op">(</tt><tt class="py-string">"ncbi_taxid"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt>  <tt class="py-line">                        <tt id="link-18" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-18', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-19" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-19', 'Re', 'link-10');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">"[,; ]+"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L20"></a><tt class="py-lineno">20</tt>  <tt class="py-line">            <tt id="link-20" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-20', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-21" 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-21', 'AnyEol', 'link-21');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L21"></a><tt class="py-lineno">21</tt>  <tt class="py-line"><tt id="link-22" class="py-name" targets="Variable Bio.expressions.swissprot.sprot40.OX_cont=Bio.expressions.swissprot.sprot40-module.html#OX_cont"><a title="Bio.expressions.swissprot.sprot40.OX_cont" class="py-name" href="#" onclick="return doclink('link-22', 'OX_cont', 'link-22');">OX_cont</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-23" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-23', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-24" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-24', 'Str', 'link-6');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"OX   "</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt>  <tt class="py-line">           <tt id="link-25" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-25', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-26" class="py-name"><a title="Martel.Rep1" class="py-name" href="#" onclick="return doclink('link-26', 'Rep1', 'link-15');">Rep1</a></tt><tt class="py-op">(</tt><tt id="link-27" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-27', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-28" class="py-name"><a title="Martel.Digits" class="py-name" href="#" onclick="return doclink('link-28', 'Digits', 'link-17');">Digits</a></tt><tt class="py-op">(</tt><tt class="py-string">"ncbi_taxid"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt>  <tt class="py-line">                       <tt id="link-29" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-29', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-30" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-30', 'Re', 'link-10');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">"[,; ]+"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt>  <tt class="py-line">           <tt id="link-31" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-31', 'Martel', 'link-0');">Martel</a></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-21');">AnyEol</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 id="link-33" class="py-name" targets="Variable Bio.expressions.swissprot.sprot40.OX_exp=Bio.expressions.swissprot.sprot40-module.html#OX_exp"><a title="Bio.expressions.swissprot.sprot40.OX_exp" class="py-name" href="#" onclick="return doclink('link-33', 'OX_exp', 'link-33');">OX_exp</a></tt> <tt class="py-op">=</tt> <tt id="link-34" class="py-name"><a title="Bio.expressions.swissprot.sprot40.OX_start" class="py-name" href="#" onclick="return doclink('link-34', 'OX_start', 'link-11');">OX_start</a></tt> <tt class="py-op">+</tt> <tt id="link-35" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-35', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-36" 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-36', 'Rep', 'link-36');">Rep</a></tt><tt class="py-op">(</tt><tt id="link-37" class="py-name"><a title="Bio.expressions.swissprot.sprot40.OX_cont" class="py-name" href="#" onclick="return doclink('link-37', 'OX_cont', 'link-22');">OX_cont</a></tt><tt class="py-op">)</tt> </tt>
<a name="L27"></a><tt class="py-lineno">27</tt>  <tt class="py-line"> </tt>
<a name="L28"></a><tt class="py-lineno">28</tt>  <tt class="py-line"><tt class="py-comment"># 0 or 1</tt> </tt>
<a name="L29"></a><tt class="py-lineno">29</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># in 40 the line changed to look like this</tt> </tt>
<a name="L30"></a><tt class="py-lineno">30</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  RX   MEDLINE=93305731; PubMed=7916637;</tt> </tt>
<a name="L31"></a><tt class="py-lineno">31</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  RX   PubMed=11001938;</tt> </tt>
<a name="L32"></a><tt class="py-lineno">32</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt id="link-38" class="py-name" targets="Variable Bio.expressions.swissprot.sprot40.bib=Bio.expressions.swissprot.sprot40-module.html#bib"><a title="Bio.expressions.swissprot.sprot40.bib" class="py-name" href="#" onclick="return doclink('link-38', 'bib', 'link-38');">bib</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-39" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-39', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-40" class="py-name" targets="Function Martel.Word()=Martel-module.html#Word"><a title="Martel.Word" class="py-name" href="#" onclick="return doclink('link-40', 'Word', 'link-40');">Word</a></tt><tt class="py-op">(</tt><tt class="py-string">"bibliographic_database_name"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-41" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-41', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-42" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-42', 'Str', 'link-6');">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="L33"></a><tt class="py-lineno">33</tt>  <tt class="py-line">       <tt id="link-43" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-43', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-44" class="py-name" targets="Function Martel.ToSep()=Martel-module.html#ToSep"><a title="Martel.ToSep" class="py-name" href="#" onclick="return doclink('link-44', 'ToSep', 'link-44');">ToSep</a></tt><tt class="py-op">(</tt><tt class="py-string">"bibliographic_identifier"</tt><tt class="py-op">,</tt> <tt class="py-string">";"</tt><tt class="py-op">)</tt> </tt>
<a name="L34"></a><tt class="py-lineno">34</tt>  <tt class="py-line">       <tt class="py-op">)</tt> </tt>
<a name="L35"></a><tt class="py-lineno">35</tt>  <tt class="py-line"><tt id="link-45" class="py-name" targets="Variable Bio.expressions.swissprot.sprot40.RX_exp=Bio.expressions.swissprot.sprot40-module.html#RX_exp"><a title="Bio.expressions.swissprot.sprot40.RX_exp" class="py-name" href="#" onclick="return doclink('link-45', 'RX_exp', 'link-45');">RX_exp</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-46" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-46', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-47" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-47', 'Str', 'link-6');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"RX   "</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-48" class="py-name"><a title="Bio.expressions.swissprot.sprot40.bib" class="py-name" href="#" onclick="return doclink('link-48', 'bib', 'link-38');">bib</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L36"></a><tt class="py-lineno">36</tt>  <tt class="py-line">          <tt id="link-49" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-49', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-50" class="py-name" targets="Function Martel.Opt()=Martel-module.html#Opt"><a title="Martel.Opt" class="py-name" href="#" onclick="return doclink('link-50', 'Opt', 'link-50');">Opt</a></tt><tt class="py-op">(</tt><tt id="link-51" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-51', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-52" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-52', 'Str', 'link-6');">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-53" class="py-name"><a title="Bio.expressions.swissprot.sprot40.bib" class="py-name" href="#" onclick="return doclink('link-53', 'bib', 'link-38');">bib</a></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 id="link-54" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-54', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-55" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-55', 'AnyEol', 'link-21');">AnyEol</a></tt><tt class="py-op">(</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"># Here's the neq SQ line format -- uses a CRC64</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"># SQ   SEQUENCE   889 AA;  100368 MW;  ABD7E3CD53961B78 CRC64;</tt> </tt>
<a name="L41"></a><tt class="py-lineno">41</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt id="link-56" class="py-name" targets="Variable Bio.expressions.swissprot.sprot40.SQ_exp=Bio.expressions.swissprot.sprot40-module.html#SQ_exp"><a title="Bio.expressions.swissprot.sprot40.SQ_exp" class="py-name" href="#" onclick="return doclink('link-56', 'SQ_exp', 'link-56');">SQ_exp</a></tt> <tt class="py-op">=</tt> <tt id="link-57" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-57', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-58" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-58', 'Re', 'link-10');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">"SQ   SEQUENCE +(?P&lt;sequence_length&gt;\d+) AA;"</tt> \ </tt>
<a name="L42"></a><tt class="py-lineno">42</tt>  <tt class="py-line">                   <tt class="py-string">" +(?P&lt;molecular_weight&gt;\d+) MW;"</tt> \ </tt>
<a name="L43"></a><tt class="py-lineno">43</tt>  <tt class="py-line">                   <tt class="py-string">" +(?P&lt;crc?type=64&gt;\w+) CRC64;\R"</tt><tt class="py-op">)</tt> </tt>
<a name="L44"></a><tt class="py-lineno">44</tt>  <tt class="py-line"> </tt>
<a name="L45"></a><tt class="py-lineno">45</tt>  <tt class="py-line"><tt id="link-59" class="py-name" targets="Variable Bio.expressions.swissprot.ipi.replacements=Bio.expressions.swissprot.ipi-module.html#replacements,Variable Bio.expressions.swissprot.sprot40.replacements=Bio.expressions.swissprot.sprot40-module.html#replacements"><a title="Bio.expressions.swissprot.ipi.replacements
Bio.expressions.swissprot.sprot40.replacements" class="py-name" href="#" onclick="return doclink('link-59', 'replacements', 'link-59');">replacements</a></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 class="py-op">(</tt><tt class="py-string">"DT_created"</tt><tt class="py-op">,</tt> <tt id="link-60" class="py-name"><a title="Bio.expressions.swissprot.ipi.DT_created_exp
Bio.expressions.swissprot.sprot40.DT_created_exp" class="py-name" href="#" onclick="return doclink('link-60', 'DT_created_exp', 'link-4');">DT_created_exp</a></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 class="py-op">(</tt><tt class="py-string">"OX_block"</tt><tt class="py-op">,</tt> <tt id="link-61" class="py-name"><a title="Bio.expressions.swissprot.sprot40.OX_exp" class="py-name" href="#" onclick="return doclink('link-61', 'OX_exp', 'link-33');">OX_exp</a></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 class="py-op">(</tt><tt class="py-string">"RX"</tt><tt class="py-op">,</tt> <tt id="link-62" class="py-name"><a title="Bio.expressions.swissprot.sprot40.RX_exp" class="py-name" href="#" onclick="return doclink('link-62', 'RX_exp', 'link-45');">RX_exp</a></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 class="py-op">(</tt><tt class="py-string">"SQ"</tt><tt class="py-op">,</tt> <tt id="link-63" class="py-name"><a title="Bio.expressions.swissprot.sprot40.SQ_exp" class="py-name" href="#" onclick="return doclink('link-63', 'SQ_exp', 'link-56');">SQ_exp</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L50"></a><tt class="py-lineno">50</tt>  <tt class="py-line">    <tt class="py-op">]</tt> </tt>
<a name="L51"></a><tt class="py-lineno">51</tt>  <tt class="py-line"><tt id="link-64" 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-64', 'record', 'link-64');">record</a></tt> <tt class="py-op">=</tt> <tt id="link-65" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-65', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-66" class="py-name" targets="Function Martel.replace_groups()=Martel-module.html#replace_groups"><a title="Martel.replace_groups" class="py-name" href="#" onclick="return doclink('link-66', 'replace_groups', 'link-66');">replace_groups</a></tt><tt class="py-op">(</tt><tt id="link-67" class="py-name"><a title="Bio.expressions.swissprot.sprot38
Bio.formatdefs.swissprot.sprot38" class="py-name" href="#" onclick="return doclink('link-67', 'sprot38', 'link-3');">sprot38</a></tt><tt class="py-op">.</tt><tt id="link-68" 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-68', 'record', 'link-64');">record</a></tt><tt class="py-op">,</tt> <tt id="link-69" class="py-name"><a title="Bio.expressions.swissprot.ipi.replacements
Bio.expressions.swissprot.sprot40.replacements" class="py-name" href="#" onclick="return doclink('link-69', 'replacements', 'link-59');">replacements</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>
<a name="L54"></a><tt class="py-lineno">54</tt>  <tt class="py-line"><tt id="link-70" class="py-name" targets="Variable Bio.expressions.blocks.format_expression=Bio.expressions.blocks-module.html#format_expression,Variable Bio.expressions.embl.embl65.format_expression=Bio.expressions.embl.embl65-module.html#format_expression,Variable Bio.expressions.swissprot.ipi.format_expression=Bio.expressions.swissprot.ipi-module.html#format_expression,Variable Bio.expressions.swissprot.sprot38.format_expression=Bio.expressions.swissprot.sprot38-module.html#format_expression,Variable Bio.expressions.swissprot.sprot40.format_expression=Bio.expressions.swissprot.sprot40-module.html#format_expression,Variable Martel.test.test_swissprot38.format_expression=Martel.test.test_swissprot38-module.html#format_expression,Variable Martel.test.testformats.swissprot38.format_expression=Martel.test.testformats.swissprot38-module.html#format_expression"><a title="Bio.expressions.blocks.format_expression
Bio.expressions.embl.embl65.format_expression
Bio.expressions.swissprot.ipi.format_expression
Bio.expressions.swissprot.sprot38.format_expression
Bio.expressions.swissprot.sprot40.format_expression
Martel.test.test_swissprot38.format_expression
Martel.test.testformats.swissprot38.format_expression" class="py-name" href="#" onclick="return doclink('link-70', 'format_expression', 'link-70');">format_expression</a></tt> <tt class="py-op">=</tt> <tt id="link-71" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-71', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-72" class="py-name"><a title="Martel.replace_groups" class="py-name" href="#" onclick="return doclink('link-72', 'replace_groups', 'link-66');">replace_groups</a></tt><tt class="py-op">(</tt> </tt>
<a name="L55"></a><tt class="py-lineno">55</tt>  <tt class="py-line">    <tt id="link-73" class="py-name"><a title="Bio.expressions.swissprot.sprot38
Bio.formatdefs.swissprot.sprot38" class="py-name" href="#" onclick="return doclink('link-73', 'sprot38', 'link-3');">sprot38</a></tt><tt class="py-op">.</tt><tt id="link-74" class="py-name"><a title="Bio.expressions.blocks.format_expression
Bio.expressions.embl.embl65.format_expression
Bio.expressions.swissprot.ipi.format_expression
Bio.expressions.swissprot.sprot38.format_expression
Bio.expressions.swissprot.sprot40.format_expression
Martel.test.test_swissprot38.format_expression
Martel.test.testformats.swissprot38.format_expression" class="py-name" href="#" onclick="return doclink('link-74', 'format_expression', 'link-70');">format_expression</a></tt><tt class="py-op">,</tt> <tt id="link-75" class="py-name"><a title="Bio.expressions.swissprot.ipi.replacements
Bio.expressions.swissprot.sprot40.replacements" class="py-name" href="#" onclick="return doclink('link-75', 'replacements', 'link-59');">replacements</a></tt><tt class="py-op">)</tt> </tt>
<a name="L56"></a><tt class="py-lineno">56</tt>  <tt class="py-line"> </tt>
<a name="L57"></a><tt class="py-lineno">57</tt>  <tt class="py-line"> </tt>
<a name="L58"></a><tt class="py-lineno">58</tt>  <tt class="py-line"><tt id="link-76" 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-76', 'format', 'link-76');">format</a></tt> <tt class="py-op">=</tt> <tt id="link-77" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-77', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-78" class="py-name"><a title="Martel.replace_groups" class="py-name" href="#" onclick="return doclink('link-78', 'replace_groups', 'link-66');">replace_groups</a></tt><tt class="py-op">(</tt><tt id="link-79" class="py-name"><a title="Bio.expressions.swissprot.sprot38
Bio.formatdefs.swissprot.sprot38" class="py-name" href="#" onclick="return doclink('link-79', 'sprot38', 'link-3');">sprot38</a></tt><tt class="py-op">.</tt><tt id="link-80" class="py-name"><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-80', 'format', 'link-76');">format</a></tt><tt class="py-op">,</tt> <tt id="link-81" class="py-name"><a title="Bio.expressions.swissprot.ipi.replacements
Bio.expressions.swissprot.sprot40.replacements" class="py-name" href="#" onclick="return doclink('link-81', 'replacements', 'link-59');">replacements</a></tt><tt class="py-op">)</tt> </tt>
<a name="L59"></a><tt class="py-lineno">59</tt>  <tt class="py-line"> </tt>
<a name="L60"></a><tt class="py-lineno">60</tt>  <tt class="py-line"><tt class="py-keyword">if</tt> <tt class="py-name">__name__</tt> <tt class="py-op">==</tt> <tt class="py-string">"__main__"</tt><tt class="py-op">:</tt> </tt>
<a name="L61"></a><tt class="py-lineno">61</tt>  <tt class="py-line">    <tt class="py-name">parser</tt> <tt class="py-op">=</tt> <tt id="link-82" class="py-name"><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-82', 'format', 'link-76');">format</a></tt><tt class="py-op">.</tt><tt id="link-83" class="py-name" targets="Method Bio.config.FormatRegistry.FormatObject.make_parser()=Bio.config.FormatRegistry.FormatObject-class.html#make_parser,Method Bio.config._support.make_cached_expression.make_parser()=Bio.config._support.make_cached_expression-class.html#make_parser,Method Martel.Expression.Expression.make_parser()=Martel.Expression.Expression-class.html#make_parser,Method Martel.Expression.HeaderFooter.make_parser()=Martel.Expression.HeaderFooter-class.html#make_parser,Method Martel.Expression.ParseRecords.make_parser()=Martel.Expression.ParseRecords-class.html#make_parser"><a title="Bio.config.FormatRegistry.FormatObject.make_parser
Bio.config._support.make_cached_expression.make_parser
Martel.Expression.Expression.make_parser
Martel.Expression.HeaderFooter.make_parser
Martel.Expression.ParseRecords.make_parser" class="py-name" href="#" onclick="return doclink('link-83', 'make_parser', 'link-83');">make_parser</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L62"></a><tt class="py-lineno">62</tt>  <tt class="py-line">    <tt class="py-name">filename</tt> <tt class="py-op">=</tt> <tt class="py-string">"/home/dalke/ftps/databases/swiss-prot/release_compressed/sprot40.dat"</tt> </tt>
<a name="L63"></a><tt class="py-lineno">63</tt>  <tt class="py-line"><tt class="py-comment">##    import os</tt> </tt>
<a name="L64"></a><tt class="py-lineno">64</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">##    infile = os.popen("zcat " + filename)</tt> </tt>
<a name="L65"></a><tt class="py-lineno">65</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-name">infile</tt> <tt class="py-op">=</tt> <tt id="link-84" class="py-name" targets="Function Bio.Mindy.FlatDB.open()=Bio.Mindy.FlatDB-module.html#open,Function Bio.Mindy.open()=Bio.Mindy-module.html#open"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-84', 'open', 'link-84');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
<a name="L66"></a><tt class="py-lineno">66</tt>  <tt class="py-line">    <tt class="py-name">infile</tt><tt class="py-op">.</tt><tt id="link-85" class="py-name" targets="Method Bio.EUtils.ReseekFile.ReseekFile.seek()=Bio.EUtils.ReseekFile.ReseekFile-class.html#seek,Method Bio.File.UndoHandle.seek()=Bio.File.UndoHandle-class.html#seek,Method Martel.msre_parse.Tokenizer.seek()=Martel.msre_parse.Tokenizer-class.html#seek"><a title="Bio.EUtils.ReseekFile.ReseekFile.seek
Bio.File.UndoHandle.seek
Martel.msre_parse.Tokenizer.seek" class="py-name" href="#" onclick="return doclink('link-85', 'seek', 'link-85');">seek</a></tt><tt class="py-op">(</tt><tt class="py-number">107976062</tt><tt class="py-op">)</tt> </tt>
<a name="L67"></a><tt class="py-lineno">67</tt>  <tt class="py-line">    <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt id="link-86" class="py-name" targets="Method Bio.EUtils.POM.POMDocument.parseFile()=Bio.EUtils.POM.POMDocument-class.html#parseFile,Method Martel.Parser.HeaderFooterParser.parseFile()=Martel.Parser.HeaderFooterParser-class.html#parseFile,Method Martel.Parser.Parser.parseFile()=Martel.Parser.Parser-class.html#parseFile,Method Martel.Parser.RecordParser.parseFile()=Martel.Parser.RecordParser-class.html#parseFile"><a title="Bio.EUtils.POM.POMDocument.parseFile
Martel.Parser.HeaderFooterParser.parseFile
Martel.Parser.Parser.parseFile
Martel.Parser.RecordParser.parseFile" class="py-name" href="#" onclick="return doclink('link-86', 'parseFile', 'link-86');">parseFile</a></tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">)</tt> </tt>
<a name="L68"></a><tt class="py-lineno">68</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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