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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> ::
        Module&nbsp;blocks
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<h1 class="epydoc">Source Code for <a href="Bio.expressions.blocks-module.html">Module Bio.expressions.blocks</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt>  <tt class="py-line"><tt class="py-comment"># This was tested against BLOCKS-12.0, June 2000</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 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="L8"></a><tt class="py-lineno"> 8</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-1" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-1', 'Martel', 'link-0');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name" targets="Module Martel.RecordReader=Martel.RecordReader-module.html,Class Martel.RecordReader.RecordReader=Martel.RecordReader.RecordReader-class.html"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-2', 'RecordReader', 'link-2');">RecordReader</a></tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-3" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-3', 'Bio', 'link-3');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-4" class="py-name" targets="Module Bio.Std=Bio.Std-module.html"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-4', 'Std', 'link-4');">Std</a></tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt>  <tt class="py-line"> </tt>
<a name="L11"></a><tt class="py-lineno">11</tt>  <tt class="py-line"><tt class="py-comment"># Header goes up to the line starting with "ID"</tt> </tt>
<a name="L12"></a><tt class="py-lineno">12</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt id="link-5" class="py-name" targets="Variable Bio.Wise.dnal.Statistics.header=Bio.Wise.dnal.Statistics-class.html#header,Variable Bio.expressions.blast.ncbiblast.header=Bio.expressions.blast.ncbiblast-module.html#header,Variable Bio.expressions.blast.wublast.header=Bio.expressions.blast.wublast-module.html#header,Variable Bio.expressions.blocks.header=Bio.expressions.blocks-module.html#header,Variable Bio.expressions.genbank.header=Bio.expressions.genbank-module.html#header,Variable Bio.expressions.hmmpfam.header=Bio.expressions.hmmpfam-module.html#header"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-5', 'header', 'link-5');">header</a></tt> <tt class="py-op">=</tt> <tt id="link-6" 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-6', 'Rep', 'link-6');">Rep</a></tt><tt class="py-op">(</tt><tt id="link-7" class="py-name" targets="Function Martel.AssertNot()=Martel-module.html#AssertNot"><a title="Martel.AssertNot" class="py-name" href="#" onclick="return doclink('link-7', 'AssertNot', 'link-7');">AssertNot</a></tt><tt class="py-op">(</tt><tt id="link-8" class="py-name" targets="Class Martel.Expression.Str=Martel.Expression.Str-class.html,Function Martel.Str()=Martel-module.html#Str"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-8', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"ID   "</tt><tt class="py-op">)</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-9" class="py-name" targets="Function Martel.ToEol()=Martel-module.html#ToEol"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-9', 'ToEol', 'link-9');">ToEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt>  <tt class="py-line"> </tt>
<a name="L15"></a><tt class="py-lineno">15</tt>  <tt class="py-line"><tt class="py-comment"># ID   kringle; BLOCK</tt> </tt>
<a name="L16"></a><tt class="py-lineno">16</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># ID   14-3-3; BLOCK</tt> </tt>
<a name="L17"></a><tt class="py-lineno">17</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  but not!</tt> </tt>
<a name="L18"></a><tt class="py-lineno">18</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># IDSA_METJA|Q58270  (  46) GGKRIRPYLTV  11</tt> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt id="link-10" class="py-name" targets="Class Bio.EUtils.POM.ID=Bio.EUtils.POM.ID-class.html,Method Bio.UniGene._RecordConsumer.ID()=Bio.UniGene._RecordConsumer-class.html#ID,Variable Bio.expressions.blocks.ID=Bio.expressions.blocks-module.html#ID,Variable Bio.expressions.swissprot.sprot38.ID=Bio.expressions.swissprot.sprot38-module.html#ID,Variable Martel.test.test_swissprot38.ID=Martel.test.test_swissprot38-module.html#ID,Variable Martel.test.testformats.swissprot38.ID=Martel.test.testformats.swissprot38-module.html#ID"><a title="Bio.EUtils.POM.ID
Bio.UniGene._RecordConsumer.ID
Bio.expressions.blocks.ID
Bio.expressions.swissprot.sprot38.ID
Martel.test.test_swissprot38.ID
Martel.test.testformats.swissprot38.ID" class="py-name" href="#" onclick="return doclink('link-10', 'ID', 'link-10');">ID</a></tt> <tt class="py-op">=</tt> <tt id="link-11" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-11', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"ID   "</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-12" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-12', 'Std', 'link-4');">Std</a></tt><tt class="py-op">.</tt><tt id="link-13" class="py-name" targets="Function Bio.Std.dbid()=Bio.Std-module.html#dbid"><a title="Bio.Std.dbid" class="py-name" href="#" onclick="return doclink('link-13', 'dbid', 'link-13');">dbid</a></tt><tt class="py-op">(</tt><tt id="link-14" class="py-name" targets="Function Martel.ToSep()=Martel-module.html#ToSep"><a title="Martel.ToSep" class="py-name" href="#" onclick="return doclink('link-14', 'ToSep', 'link-14');">ToSep</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">"type"</tt><tt class="py-op">:</tt> <tt class="py-string">"primary"</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-15" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-15', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">" BLOCK"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-16" 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-16', 'AnyEol', 'link-16');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L21"></a><tt class="py-lineno">21</tt>  <tt class="py-line"> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt>  <tt class="py-line"><tt class="py-comment"># AC   IPB000001A; distance from previous block=(10,266)</tt> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt id="link-17" class="py-name" targets="Variable Bio.expressions.blocks.AC=Bio.expressions.blocks-module.html#AC,Variable Bio.expressions.swissprot.sprot38.AC=Bio.expressions.swissprot.sprot38-module.html#AC,Variable Martel.test.test_swissprot38.AC=Martel.test.test_swissprot38-module.html#AC,Variable Martel.test.testformats.swissprot38.AC=Martel.test.testformats.swissprot38-module.html#AC"><a title="Bio.expressions.blocks.AC
Bio.expressions.swissprot.sprot38.AC
Martel.test.test_swissprot38.AC
Martel.test.testformats.swissprot38.AC" class="py-name" href="#" onclick="return doclink('link-17', 'AC', 'link-17');">AC</a></tt> <tt class="py-op">=</tt> <tt id="link-18" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-18', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"AC   "</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-19" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-19', 'Std', 'link-4');">Std</a></tt><tt class="py-op">.</tt><tt id="link-20" class="py-name"><a title="Bio.Std.dbid" class="py-name" href="#" onclick="return doclink('link-20', 'dbid', 'link-13');">dbid</a></tt><tt class="py-op">(</tt><tt id="link-21" class="py-name"><a title="Martel.ToSep" class="py-name" href="#" onclick="return doclink('link-21', 'ToSep', 'link-14');">ToSep</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">"type"</tt><tt class="py-op">:</tt> <tt class="py-string">"accession"</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-22" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-22', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">" distance from previous block=("</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L25"></a><tt class="py-lineno">25</tt>  <tt class="py-line">     <tt id="link-23" class="py-name" targets="Class Bio.Decode.Integer=Bio.Decode.Integer-class.html,Class Bio.GenBank.LocationParser.Integer=Bio.GenBank.LocationParser.Integer-class.html,Function Martel.Integer()=Martel-module.html#Integer"><a title="Bio.Decode.Integer
Bio.GenBank.LocationParser.Integer
Martel.Integer" class="py-name" href="#" onclick="return doclink('link-23', 'Integer', 'link-23');">Integer</a></tt><tt class="py-op">(</tt><tt class="py-string">"dist1"</tt><tt class="py-op">)</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-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">","</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-25" class="py-name"><a title="Bio.Decode.Integer
Bio.GenBank.LocationParser.Integer
Martel.Integer" class="py-name" href="#" onclick="return doclink('link-25', 'Integer', 'link-23');">Integer</a></tt><tt class="py-op">(</tt><tt class="py-string">"dist2"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L26"></a><tt class="py-lineno">26</tt>  <tt class="py-line">     <tt id="link-26" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-26', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">")"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-27" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-27', 'AnyEol', 'link-16');">AnyEol</a></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>
<a name="L28"></a><tt class="py-lineno">28</tt>  <tt class="py-line"> </tt>
<a name="L29"></a><tt class="py-lineno">29</tt>  <tt class="py-line"><tt class="py-comment"># DE   Kringle domain</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">#  If the DE line is long, it doen't fold .. it's all on one line</tt> </tt>
<a name="L31"></a><tt class="py-lineno">31</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt id="link-28" class="py-name" targets="Variable Bio.expressions.blocks.DE=Bio.expressions.blocks-module.html#DE,Variable Bio.expressions.swissprot.sprot38.DE=Bio.expressions.swissprot.sprot38-module.html#DE,Variable Martel.test.test_swissprot38.DE=Martel.test.test_swissprot38-module.html#DE,Variable Martel.test.testformats.swissprot38.DE=Martel.test.testformats.swissprot38-module.html#DE"><a title="Bio.expressions.blocks.DE
Bio.expressions.swissprot.sprot38.DE
Martel.test.test_swissprot38.DE
Martel.test.testformats.swissprot38.DE" class="py-name" href="#" onclick="return doclink('link-28', 'DE', 'link-28');">DE</a></tt> <tt class="py-op">=</tt> <tt id="link-29" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-29', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"DE   "</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-30" class="py-name"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-30', 'ToEol', 'link-9');">ToEol</a></tt><tt class="py-op">(</tt><tt class="py-string">"description"</tt><tt class="py-op">)</tt> </tt>
<a name="L32"></a><tt class="py-lineno">32</tt>  <tt class="py-line"> </tt>
<a name="L33"></a><tt class="py-lineno">33</tt>  <tt class="py-line"> </tt>
<a name="L34"></a><tt class="py-lineno">34</tt>  <tt class="py-line"><tt class="py-comment"># BL   CCY;  width=14; seqs=44; 99.5%=717; strength=1059</tt> </tt>
<a name="L35"></a><tt class="py-lineno">35</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt id="link-31" class="py-name" targets="Variable Bio.expressions.blocks.BL=Bio.expressions.blocks-module.html#BL"><a title="Bio.expressions.blocks.BL" class="py-name" href="#" onclick="return doclink('link-31', 'BL', 'link-31');">BL</a></tt> <tt class="py-op">=</tt> <tt id="link-32" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-32', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"BL   "</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-33" class="py-name"><a title="Martel.ToSep" class="py-name" href="#" onclick="return doclink('link-33', 'ToSep', 'link-14');">ToSep</a></tt><tt class="py-op">(</tt><tt class="py-string">"protomat_id"</tt><tt class="py-op">,</tt> <tt class="py-string">";"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L36"></a><tt class="py-lineno">36</tt>  <tt class="py-line">     <tt id="link-34" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-34', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"  width="</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-35" class="py-name" targets="Function Martel.Digits()=Martel-module.html#Digits"><a title="Martel.Digits" class="py-name" href="#" onclick="return doclink('link-35', 'Digits', 'link-35');">Digits</a></tt><tt class="py-op">(</tt><tt class="py-string">"width"</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-36" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-36', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"; seqs="</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-37" class="py-name"><a title="Martel.Digits" class="py-name" href="#" onclick="return doclink('link-37', 'Digits', 'link-35');">Digits</a></tt><tt class="py-op">(</tt><tt class="py-string">"numseqs"</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 id="link-38" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-38', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"; 99.5%="</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-39" class="py-name"><a title="Martel.Digits" class="py-name" href="#" onclick="return doclink('link-39', 'Digits', 'link-35');">Digits</a></tt><tt class="py-op">(</tt><tt class="py-string">"protomat_count"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L39"></a><tt class="py-lineno">39</tt>  <tt class="py-line">     <tt id="link-40" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-40', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"; strength="</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-41" class="py-name"><a title="Martel.Digits" class="py-name" href="#" onclick="return doclink('link-41', 'Digits', 'link-35');">Digits</a></tt><tt class="py-op">(</tt><tt class="py-string">"strength"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L40"></a><tt class="py-lineno">40</tt>  <tt class="py-line">     <tt id="link-42" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-42', 'AnyEol', 'link-16');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L41"></a><tt class="py-lineno">41</tt>  <tt class="py-line"> </tt>
<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"># PLMN_BOVIN|P06868  (  60) CEEETDFVCRAFQY  26</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"># ^^^^^^^^^^^^^^^^^</tt> </tt>
<a name="L45"></a><tt class="py-lineno">45</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#                     ^^^^-- number of segments</tt> </tt>
<a name="L46"></a><tt class="py-lineno">46</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#                           ^^^^^^^^^^^^^^-- matching sequence</tt> </tt>
<a name="L47"></a><tt class="py-lineno">47</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#                                           ^^-- weight</tt> </tt>
<a name="L48"></a><tt class="py-lineno">48</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L49"></a><tt class="py-lineno">49</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt id="link-43" class="py-name" targets="Variable Bio.expressions.blocks.identifier=Bio.expressions.blocks-module.html#identifier"><a title="Bio.expressions.blocks.identifier" class="py-name" href="#" onclick="return doclink('link-43', 'identifier', 'link-43');">identifier</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-44" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-44', 'Std', 'link-4');">Std</a></tt><tt class="py-op">.</tt><tt id="link-45" 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-45', 'dbxref_dbid', 'link-45');">dbxref_dbid</a></tt><tt class="py-op">(</tt><tt id="link-46" class="py-name" targets="Function Martel.UntilSep()=Martel-module.html#UntilSep"><a title="Martel.UntilSep" class="py-name" href="#" onclick="return doclink('link-46', 'UntilSep', 'link-46');">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="L50"></a><tt class="py-lineno">50</tt>  <tt class="py-line">                          <tt class="py-op">{</tt><tt class="py-string">"dbname"</tt><tt class="py-op">:</tt> <tt class="py-string">"swissprot"</tt><tt class="py-op">,</tt> <tt class="py-string">"type"</tt><tt class="py-op">:</tt> <tt class="py-string">"primary"</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L51"></a><tt class="py-lineno">51</tt>  <tt class="py-line">              <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-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"|"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L52"></a><tt class="py-lineno">52</tt>  <tt class="py-line">              <tt id="link-48" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-48', 'Std', 'link-4');">Std</a></tt><tt class="py-op">.</tt><tt id="link-49" class="py-name"><a title="Bio.Std.dbxref_dbid" class="py-name" href="#" onclick="return doclink('link-49', 'dbxref_dbid', 'link-45');">dbxref_dbid</a></tt><tt class="py-op">(</tt><tt id="link-50" class="py-name"><a title="Martel.UntilSep" class="py-name" href="#" onclick="return doclink('link-50', 'UntilSep', 'link-46');">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="L53"></a><tt class="py-lineno">53</tt>  <tt class="py-line">                              <tt class="py-op">{</tt><tt class="py-string">"dbname"</tt><tt class="py-op">:</tt> <tt class="py-string">"swissprot"</tt><tt class="py-op">,</tt> <tt class="py-string">"type"</tt><tt class="py-op">:</tt> <tt class="py-string">"accession"</tt><tt class="py-op">}</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">|</tt>\ </tt>
<a name="L54"></a><tt class="py-lineno">54</tt>  <tt class="py-line">              <tt id="link-51" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-51', 'Std', 'link-4');">Std</a></tt><tt class="py-op">.</tt><tt id="link-52" class="py-name"><a title="Bio.Std.dbxref_dbid" class="py-name" href="#" onclick="return doclink('link-52', 'dbxref_dbid', 'link-45');">dbxref_dbid</a></tt><tt class="py-op">(</tt><tt id="link-53" class="py-name"><a title="Martel.UntilSep" class="py-name" href="#" onclick="return doclink('link-53', 'UntilSep', 'link-46');">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="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 id="link-54" class="py-name" targets="Method Bio.GFF.Connection.segment()=Bio.GFF.Connection-class.html#segment,Method Bio.GenBank._FeatureConsumer.segment()=Bio.GenBank._FeatureConsumer-class.html#segment,Method Bio.GenBank._RecordConsumer.segment()=Bio.GenBank._RecordConsumer-class.html#segment,Variable Bio.expressions.blocks.segment=Bio.expressions.blocks-module.html#segment,Variable Bio.expressions.genbank.segment=Bio.expressions.genbank-module.html#segment"><a title="Bio.GFF.Connection.segment
Bio.GenBank._FeatureConsumer.segment
Bio.GenBank._RecordConsumer.segment
Bio.expressions.blocks.segment
Bio.expressions.genbank.segment" class="py-name" href="#" onclick="return doclink('link-54', 'segment', 'link-54');">segment</a></tt> <tt class="py-op">=</tt> <tt id="link-55" class="py-name"><a title="Martel.AssertNot" class="py-name" href="#" onclick="return doclink('link-55', 'AssertNot', 'link-7');">AssertNot</a></tt><tt class="py-op">(</tt><tt id="link-56" class="py-name" targets="Function Martel.Re()=Martel-module.html#Re"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-56', 'Re', 'link-56');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">r".. "</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L57"></a><tt class="py-lineno">57</tt>  <tt class="py-line">          <tt id="link-57" class="py-name"><a title="Bio.expressions.blocks.identifier" class="py-name" href="#" onclick="return doclink('link-57', 'identifier', 'link-43');">identifier</a></tt> <tt class="py-op">+</tt> \ </tt>
<a name="L58"></a><tt class="py-lineno">58</tt>  <tt class="py-line">          <tt id="link-58" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-58', 'Re', 'link-56');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">r" *\( *"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L59"></a><tt class="py-lineno">59</tt>  <tt class="py-line">          <tt id="link-59" class="py-name"><a title="Bio.Decode.Integer
Bio.GenBank.LocationParser.Integer
Martel.Integer" class="py-name" href="#" onclick="return doclink('link-59', 'Integer', 'link-23');">Integer</a></tt><tt class="py-op">(</tt><tt class="py-string">"position"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L60"></a><tt class="py-lineno">60</tt>  <tt class="py-line">          <tt id="link-60" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-60', 'Re', 'link-56');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">r"\) *"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L61"></a><tt class="py-lineno">61</tt>  <tt class="py-line">          <tt id="link-61" class="py-name" targets="Function Martel.Word()=Martel-module.html#Word"><a title="Martel.Word" class="py-name" href="#" onclick="return doclink('link-61', 'Word', 'link-61');">Word</a></tt><tt class="py-op">(</tt><tt class="py-string">"matching_sequence"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-62" class="py-name" targets="Function Martel.Spaces()=Martel-module.html#Spaces"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-62', 'Spaces', 'link-62');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L62"></a><tt class="py-lineno">62</tt>  <tt class="py-line">          <tt id="link-63" class="py-name"><a title="Martel.Digits" class="py-name" href="#" onclick="return doclink('link-63', 'Digits', 'link-35');">Digits</a></tt><tt class="py-op">(</tt><tt class="py-string">"weight"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-64" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-64', 'AnyEol', 'link-16');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L63"></a><tt class="py-lineno">63</tt>  <tt class="py-line"> </tt>
<a name="L64"></a><tt class="py-lineno">64</tt>  <tt class="py-line"><tt id="link-65" class="py-name" targets="Variable Bio.expressions.blocks.segment_block=Bio.expressions.blocks-module.html#segment_block"><a title="Bio.expressions.blocks.segment_block" class="py-name" href="#" onclick="return doclink('link-65', 'segment_block', 'link-65');">segment_block</a></tt> <tt class="py-op">=</tt> <tt id="link-66" class="py-name" targets="Function Martel.Rep1()=Martel-module.html#Rep1"><a title="Martel.Rep1" class="py-name" href="#" onclick="return doclink('link-66', 'Rep1', 'link-66');">Rep1</a></tt><tt class="py-op">(</tt><tt id="link-67" class="py-name"><a title="Bio.GFF.Connection.segment
Bio.GenBank._FeatureConsumer.segment
Bio.GenBank._RecordConsumer.segment
Bio.expressions.blocks.segment
Bio.expressions.genbank.segment" class="py-name" href="#" onclick="return doclink('link-67', 'segment', 'link-54');">segment</a></tt> <tt class="py-op">|</tt> <tt id="link-68" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-68', 'AnyEol', 'link-16');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L65"></a><tt class="py-lineno">65</tt>  <tt class="py-line"> </tt>
<a name="L66"></a><tt class="py-lineno">66</tt>  <tt class="py-line"><tt id="link-69" class="py-name" targets="Method Bio.GFF.easy.Location.end()=Bio.GFF.easy.Location-class.html#end,Method Bio.Prosite.Pattern.PrositeMatch.end()=Bio.Prosite.Pattern.PrositeMatch-class.html#end,Variable Bio.expressions.blocks.end=Bio.expressions.blocks-module.html#end,Variable Bio.expressions.embl.embl65.end=Bio.expressions.embl.embl65-module.html#end,Variable Bio.expressions.swissprot.sprot38.end=Bio.expressions.swissprot.sprot38-module.html#end,Method Martel.LAX.LAX.end()=Martel.LAX.LAX-class.html#end,Variable Martel.test.test_swissprot38.end=Martel.test.test_swissprot38-module.html#end,Variable Martel.test.testformats.swissprot38.end=Martel.test.testformats.swissprot38-module.html#end"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-69', 'end', 'link-69');">end</a></tt> <tt class="py-op">=</tt> <tt id="link-70" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-70', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"//"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-71" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-71', 'AnyEol', 'link-16');">AnyEol</a></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 id="link-72" 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-72', 'record', 'link-72');">record</a></tt> <tt class="py-op">=</tt> <tt id="link-73" class="py-name" targets="Class Martel.Expression.Group=Martel.Expression.Group-class.html,Function Martel.Group()=Martel-module.html#Group"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-73', 'Group', 'link-73');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"record"</tt><tt class="py-op">,</tt> </tt>
<a name="L69"></a><tt class="py-lineno">69</tt>  <tt class="py-line">               <tt id="link-74" class="py-name"><a title="Bio.EUtils.POM.ID
Bio.UniGene._RecordConsumer.ID
Bio.expressions.blocks.ID
Bio.expressions.swissprot.sprot38.ID
Martel.test.test_swissprot38.ID
Martel.test.testformats.swissprot38.ID" class="py-name" href="#" onclick="return doclink('link-74', 'ID', 'link-10');">ID</a></tt> <tt class="py-op">+</tt> <tt id="link-75" class="py-name"><a title="Bio.expressions.blocks.AC
Bio.expressions.swissprot.sprot38.AC
Martel.test.test_swissprot38.AC
Martel.test.testformats.swissprot38.AC" class="py-name" href="#" onclick="return doclink('link-75', 'AC', 'link-17');">AC</a></tt> <tt class="py-op">+</tt> <tt id="link-76" class="py-name"><a title="Bio.expressions.blocks.DE
Bio.expressions.swissprot.sprot38.DE
Martel.test.test_swissprot38.DE
Martel.test.testformats.swissprot38.DE" class="py-name" href="#" onclick="return doclink('link-76', 'DE', 'link-28');">DE</a></tt> <tt class="py-op">+</tt> <tt id="link-77" class="py-name"><a title="Bio.expressions.blocks.BL" class="py-name" href="#" onclick="return doclink('link-77', 'BL', 'link-31');">BL</a></tt> <tt class="py-op">+</tt> <tt id="link-78" class="py-name"><a title="Bio.expressions.blocks.segment_block" class="py-name" href="#" onclick="return doclink('link-78', 'segment_block', 'link-65');">segment_block</a></tt> <tt class="py-op">+</tt> <tt id="link-79" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-79', 'end', 'link-69');">end</a></tt><tt class="py-op">)</tt> </tt>
<a name="L70"></a><tt class="py-lineno">70</tt>  <tt class="py-line"> </tt>
<a name="L71"></a><tt class="py-lineno">71</tt>  <tt class="py-line"><tt id="link-80" 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-80', 'format_expression', 'link-80');">format_expression</a></tt> <tt class="py-op">=</tt> <tt id="link-81" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-81', 'header', 'link-5');">header</a></tt> <tt class="py-op">+</tt> <tt id="link-82" class="py-name"><a title="Martel.Rep1" class="py-name" href="#" onclick="return doclink('link-82', 'Rep1', 'link-66');">Rep1</a></tt><tt class="py-op">(</tt><tt id="link-83" 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-83', 'record', 'link-72');">record</a></tt><tt class="py-op">)</tt> </tt>
<a name="L72"></a><tt class="py-lineno">72</tt>  <tt class="py-line"><tt id="link-84" 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-84', 'format', 'link-84');">format</a></tt> <tt class="py-op">=</tt> <tt id="link-85" 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-85', 'HeaderFooter', 'link-85');">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">"blocks/12"</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-86" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-86', 'header', 'link-5');">header</a></tt><tt class="py-op">,</tt> <tt id="link-87" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-87', 'RecordReader', 'link-2');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-88" 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-88', 'Until', 'link-88');">Until</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-string">"ID "</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L74"></a><tt class="py-lineno">74</tt>  <tt class="py-line">                      <tt id="link-89" 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-89', 'record', 'link-72');">record</a></tt><tt class="py-op">,</tt> <tt id="link-90" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-90', 'RecordReader', 'link-2');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-91" class="py-name" targets="Class Martel.RecordReader.EndsWith=Martel.RecordReader.EndsWith-class.html"><a title="Martel.RecordReader.EndsWith" class="py-name" href="#" onclick="return doclink('link-91', 'EndsWith', 'link-91');">EndsWith</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-string">"//\n"</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L75"></a><tt class="py-lineno">75</tt>  <tt class="py-line">                      <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
<a name="L76"></a><tt class="py-lineno">76</tt>  <tt class="py-line"> </tt>
<a name="L77"></a><tt class="py-lineno">77</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="L78"></a><tt class="py-lineno">78</tt>  <tt class="py-line">    <tt class="py-keyword">import</tt> <tt class="py-name">os</tt> </tt>
<a name="L79"></a><tt class="py-lineno">79</tt>  <tt class="py-line">    <tt class="py-keyword">from</tt> <tt class="py-name">xml</tt><tt class="py-op">.</tt><tt class="py-name">sax</tt> <tt class="py-keyword">import</tt> <tt class="py-name">saxutils</tt> </tt>
<a name="L80"></a><tt class="py-lineno">80</tt>  <tt class="py-line">    <tt class="py-name">filename</tt> <tt class="py-op">=</tt> <tt class="py-string">"/home/dalke/ftps/databases/blocks/unix/blocks-12.0/blocks.dat.Z"</tt> </tt>
<a name="L81"></a><tt class="py-lineno">81</tt>  <tt class="py-line">    <tt class="py-name">infile</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">popen</tt><tt class="py-op">(</tt><tt class="py-string">"zcat "</tt> <tt class="py-op">+</tt> <tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
<a name="L82"></a><tt class="py-lineno">82</tt>  <tt class="py-line">    <tt class="py-name">parser</tt> <tt class="py-op">=</tt> <tt id="link-92" 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-92', 'format', 'link-84');">format</a></tt><tt class="py-op">.</tt><tt id="link-93" 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-93', 'make_parser', 'link-93');">make_parser</a></tt><tt class="py-op">(</tt><tt class="py-name">debug_level</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L83"></a><tt class="py-lineno">83</tt>  <tt class="py-line">    <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt class="py-name">setContentHandler</tt><tt class="py-op">(</tt><tt class="py-name">saxutils</tt><tt class="py-op">.</tt><tt class="py-name">XMLGenerator</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L84"></a><tt class="py-lineno">84</tt>  <tt class="py-line">    <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt id="link-94" 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-94', 'parseFile', 'link-94');">parseFile</a></tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">)</tt> </tt>
<a name="L85"></a><tt class="py-lineno">85</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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</pre>
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