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        <a href="Bio-module.html">Package&nbsp;Bio</a> ::
        <a href="Bio.Mindy-module.html">Package&nbsp;Mindy</a> ::
        Module&nbsp;Location
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<h1 class="epydoc">Source Code for <a href="Bio.Mindy.Location-module.html">Module Bio.Mindy.Location</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 id="link-0" class="py-name" targets="Module Bio.Mindy.compression=Bio.Mindy.compression-module.html"><a title="Bio.Mindy.compression" class="py-name" href="#" onclick="return doclink('link-0', 'compression', 'link-0');">compression</a></tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt>  <tt class="py-line"> </tt>
<a name="Location"></a><div id="Location-def"><a name="L3"></a><tt class="py-lineno"> 3</tt> <a class="py-toggle" href="#" id="Location-toggle" onclick="return toggle('Location');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Mindy.Location.Location-class.html">Location</a><tt class="py-op">:</tt> </tt>
</div><div id="Location-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="Location-expanded"><a name="L4"></a><tt class="py-lineno"> 4</tt>  <tt class="py-line">    <tt class="py-docstring">"""Handle for a record (use 'text' to get the record's text)"""</tt> </tt>
<a name="Location.__init__"></a><div id="Location.__init__-def"><a name="L5"></a><tt class="py-lineno"> 5</tt> <a class="py-toggle" href="#" id="Location.__init__-toggle" onclick="return toggle('Location.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.Location.Location-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">namespace</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">,</tt> <tt class="py-param">filename</tt><tt class="py-op">,</tt> <tt class="py-param">startpos</tt><tt class="py-op">,</tt> <tt class="py-param">length</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Location.__init__-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="Location.__init__-expanded"><a name="L6"></a><tt class="py-lineno"> 6</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Variable Bio.Std.namespace=Bio.Std-module.html#namespace,Variable Bio.biblio.namespace=Bio.biblio-module.html#namespace"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-1', 'namespace', 'link-1');">namespace</a></tt> <tt class="py-op">=</tt> <tt id="link-2" class="py-name"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-2', 'namespace', 'link-1');">namespace</a></tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-3" 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-3', 'name', 'link-3');">name</a></tt> <tt class="py-op">=</tt> <tt id="link-4" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-4', 'name', 'link-3');">name</a></tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">filename</tt> <tt class="py-op">=</tt> <tt class="py-name">filename</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">startpos</tt> <tt class="py-op">=</tt> <tt class="py-name">startpos</tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Method Bio.Blast.NCBIStandalone._AlignmentConsumer.length()=Bio.Blast.NCBIStandalone._AlignmentConsumer-class.html#length,Method Bio.GFF.easy.Location.length()=Bio.GFF.easy.Location-class.html#length"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-5', 'length', 'link-5');">length</a></tt> <tt class="py-op">=</tt> <tt id="link-6" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-6', 'length', 'link-5');">length</a></tt> </tt>
</div><a name="Location.__repr__"></a><div id="Location.__repr__-def"><a name="L11"></a><tt class="py-lineno">11</tt> <a class="py-toggle" href="#" id="Location.__repr__-toggle" onclick="return toggle('Location.__repr__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.Location.Location-class.html#__repr__">__repr__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Location.__repr__-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="Location.__repr__-expanded"><a name="L12"></a><tt class="py-lineno">12</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-string">"Location(namespace = %r, name = %r, filename = %r, startpos = %r, length = %r)"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-7', 'namespace', 'link-1');">namespace</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-8" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-8', 'name', 'link-3');">name</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">filename</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">startpos</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-9', 'length', 'link-5');">length</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="Location.__str__"></a><div id="Location.__str__-def"><a name="L13"></a><tt class="py-lineno">13</tt> <a class="py-toggle" href="#" id="Location.__str__-toggle" onclick="return toggle('Location.__str__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.Location.Location-class.html#__str__">__str__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Location.__str__-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="Location.__str__-expanded"><a name="L14"></a><tt class="py-lineno">14</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-string">"Location(%s:%s at %s: %s, %s)"</tt> <tt class="py-op">%</tt> \ </tt>
<a name="L15"></a><tt class="py-lineno">15</tt>  <tt class="py-line">               <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-10" class="py-name"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-10', 'namespace', 'link-1');">namespace</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-11" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-11', 'name', 'link-3');">name</a></tt><tt class="py-op">,</tt> </tt>
<a name="L16"></a><tt class="py-lineno">16</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">filename</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">startpos</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-12" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-12', 'length', 'link-5');">length</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="Location.__getattr__"></a><div id="Location.__getattr__-def"><a name="L17"></a><tt class="py-lineno">17</tt> <a class="py-toggle" href="#" id="Location.__getattr__-toggle" onclick="return toggle('Location.__getattr__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.Location.Location-class.html#__getattr__">__getattr__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">key</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Location.__getattr__-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="Location.__getattr__-expanded"><a name="L18"></a><tt class="py-lineno">18</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt id="link-13" class="py-name" targets="Variable Bio.Translate.key=Bio.Translate-module.html#key"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-13', 'key', 'link-13');">key</a></tt> <tt class="py-op">==</tt> <tt class="py-string">"text"</tt><tt class="py-op">:</tt> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt>  <tt class="py-line">            <tt class="py-name">infile</tt> <tt class="py-op">=</tt> <tt id="link-14" class="py-name"><a title="Bio.Mindy.compression" class="py-name" href="#" onclick="return doclink('link-14', 'compression', 'link-0');">compression</a></tt><tt class="py-op">.</tt><tt id="link-15" class="py-name" targets="Function Bio.Mindy.compression.open_file()=Bio.Mindy.compression-module.html#open_file"><a title="Bio.Mindy.compression.open_file" class="py-name" href="#" onclick="return doclink('link-15', 'open_file', 'link-15');">open_file</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
<a name="L20"></a><tt class="py-lineno">20</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">hasattr</tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">,</tt> <tt class="py-string">"seek"</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 class="py-name">infile</tt><tt class="py-op">.</tt><tt id="link-16" 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-16', 'seek', 'link-16');">seek</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">startpos</tt><tt class="py-op">)</tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt>  <tt class="py-line">                <tt class="py-keyword">return</tt> <tt class="py-name">infile</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name" targets="Method Bio.AlignAce.Motif.Motif.read()=Bio.AlignAce.Motif.Motif-class.html#read,Function Bio.AlignIO.read()=Bio.AlignIO-module.html#read,Function Bio.Cluster.read()=Bio.Cluster-module.html#read,Method Bio.EUtils.ReseekFile.ReseekFile.read()=Bio.EUtils.ReseekFile.ReseekFile-class.html#read,Function Bio.Entrez.read()=Bio.Entrez-module.html#read,Method Bio.File.SGMLHandle.read()=Bio.File.SGMLHandle-class.html#read,Method Bio.File.UndoHandle.read()=Bio.File.UndoHandle-class.html#read,Method Bio.FilteredReader.FilteredReader.read()=Bio.FilteredReader.FilteredReader-class.html#read,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.read()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#read,Method Bio.Nexus.Nexus.Nexus.read()=Bio.Nexus.Nexus.Nexus-class.html#read,Function Bio.Prosite.Prodoc.read()=Bio.Prosite.Prodoc-module.html#read,Function Bio.Prosite.read()=Bio.Prosite-module.html#read,Method Bio.SGMLExtractor.SGMLExtractorHandle.read()=Bio.SGMLExtractor.SGMLExtractorHandle-class.html#read,Function Bio.SeqIO.read()=Bio.SeqIO-module.html#read,Function Bio.SwissProt.read()=Bio.SwissProt-module.html#read"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-17', 'read', 'link-17');">read</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-18', 'length', 'link-5');">length</a></tt><tt class="py-op">)</tt> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt>  <tt class="py-line">            <tt class="py-comment"># read 1MB chunks at a time</tt> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-name">CHUNKSIZE</tt> <tt class="py-op">=</tt> <tt class="py-number">1000000</tt> </tt>
<a name="L25"></a><tt class="py-lineno">25</tt>  <tt class="py-line">            <tt id="link-19" class="py-name" targets="Method Bio.Crystal.Chain.count()=Bio.Crystal.Chain-class.html#count,Method Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count()=Bio.NeuralNetwork.Gene.Pattern.PatternRepository-class.html#count,Method Bio.Seq.MutableSeq.count()=Bio.Seq.MutableSeq-class.html#count,Method Bio.Seq.Seq.count()=Bio.Seq.Seq-class.html#count,Function Bio.listfns.count()=Bio.listfns-module.html#count"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-19', 'count', 'link-19');">count</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L26"></a><tt class="py-lineno">26</tt>  <tt class="py-line">            <tt class="py-keyword">while</tt> <tt id="link-20" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-20', 'count', 'link-19');">count</a></tt> <tt class="py-op">+</tt> <tt class="py-name">CHUNKSIZE</tt> <tt class="py-op">&lt;</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">startpos</tt><tt class="py-op">:</tt> </tt>
<a name="L27"></a><tt class="py-lineno">27</tt>  <tt class="py-line">                <tt class="py-name">infile</tt><tt class="py-op">.</tt><tt id="link-21" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-21', 'read', 'link-17');">read</a></tt><tt class="py-op">(</tt><tt class="py-name">CHUNKSIZE</tt><tt class="py-op">)</tt> </tt>
<a name="L28"></a><tt class="py-lineno">28</tt>  <tt class="py-line">                <tt id="link-22" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-22', 'count', 'link-19');">count</a></tt> <tt class="py-op">+=</tt> <tt class="py-name">CHUNKSIZE</tt> </tt>
<a name="L29"></a><tt class="py-lineno">29</tt>  <tt class="py-line">            <tt class="py-name">infile</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-23', 'read', 'link-17');">read</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">startpos</tt> <tt class="py-op">-</tt> <tt id="link-24" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-24', 'count', 'link-19');">count</a></tt><tt class="py-op">)</tt> </tt>
<a name="L30"></a><tt class="py-lineno">30</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-name">infile</tt><tt class="py-op">.</tt><tt id="link-25" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-25', 'read', 'link-17');">read</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-26', 'length', 'link-5');">length</a></tt><tt class="py-op">)</tt> </tt>
<a name="L31"></a><tt class="py-lineno">31</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt id="link-27" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-27', 'key', 'link-13');">key</a></tt> <tt class="py-op">==</tt> <tt class="py-string">"__members__"</tt><tt class="py-op">:</tt> </tt>
<a name="L32"></a><tt class="py-lineno">32</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-op">[</tt><tt class="py-string">"text"</tt><tt class="py-op">]</tt> </tt>
<a name="L33"></a><tt class="py-lineno">33</tt>  <tt class="py-line">        <tt class="py-keyword">raise</tt> <tt class="py-name">AttributeError</tt><tt class="py-op">(</tt><tt id="link-28" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-28', 'key', 'link-13');">key</a></tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L34"></a><tt class="py-lineno">34</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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