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<a href="Bio-module.html">Package Bio</a> ::
Module FilteredReader
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<h1 class="epydoc">Source Code for <a href="Bio.FilteredReader-module.html">Module Bio.FilteredReader</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright 2001 by Katharine Lindner. All rights reserved.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">"""Code for more fancy file handles.</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">Classes:</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">Filtered is a decorator for File that allows the user to filter the output</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring">on a line by line basis.</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring">The FilteredReader module reads a file and applies a sequence of filters to the input</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring">The constructor sets a default filter chain, but the user can select another filter by setting</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring">Bio.FilteredReader.filter_chain.</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring">handle = open( "filename" )</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-docstring">filtered_reader = Bio.FilteredReader( handle )</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring">filtered_reader.filter_chain = [ remove_asterisks, replace_dot_with_dash ]</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-docstring">filtered_reasder.read()</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-docstring">All filters in the chain must provide the same interface with a line of text as the single</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-docstring">input parameter and altered text as the return value.</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">os</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">string</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-0" class="py-name" targets="Method Bio.Crystal.Crystal.copy()=Bio.Crystal.Crystal-class.html#copy,Method Bio.GA.Organism.Organism.copy()=Bio.GA.Organism.Organism-class.html#copy,Method Bio.GenBank.NCBIDictionary.copy()=Bio.GenBank.NCBIDictionary-class.html#copy,Method Bio.PDB.Vector'.Vector.copy()=Bio.PDB.Vector%27.Vector-class.html#copy,Method Bio.Prosite.ExPASyDictionary.copy()=Bio.Prosite.ExPASyDictionary-class.html#copy,Method Bio.Prosite.Pattern.PrositeTerm.copy()=Bio.Prosite.Pattern.PrositeTerm-class.html#copy,Method Bio.Prosite.Prodoc.ExPASyDictionary.copy()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#copy,Method Bio.PubMed.Dictionary.copy()=Bio.PubMed.Dictionary-class.html#copy,Method Bio.SwissProt.SProt.ExPASyDictionary.copy()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#copy,Method Martel.Expression.Any.copy()=Martel.Expression.Any-class.html#copy,Method Martel.Expression.AnyEol.copy()=Martel.Expression.AnyEol-class.html#copy,Method Martel.Expression.Assert.copy()=Martel.Expression.Assert-class.html#copy,Method Martel.Expression.AtBeginning.copy()=Martel.Expression.AtBeginning-class.html#copy,Method Martel.Expression.AtEnd.copy()=Martel.Expression.AtEnd-class.html#copy,Method Martel.Expression.Debug.copy()=Martel.Expression.Debug-class.html#copy,Method Martel.Expression.Dot.copy()=Martel.Expression.Dot-class.html#copy,Method Martel.Expression.Expression.copy()=Martel.Expression.Expression-class.html#copy,Method Martel.Expression.ExpressionList.copy()=Martel.Expression.ExpressionList-class.html#copy,Method Martel.Expression.FastFeature.copy()=Martel.Expression.FastFeature-class.html#copy,Method Martel.Expression.Group.copy()=Martel.Expression.Group-class.html#copy,Method Martel.Expression.GroupRef.copy()=Martel.Expression.GroupRef-class.html#copy,Method Martel.Expression.HeaderFooter.copy()=Martel.Expression.HeaderFooter-class.html#copy,Method Martel.Expression.Literal.copy()=Martel.Expression.Literal-class.html#copy,Method Martel.Expression.MaxRepeat.copy()=Martel.Expression.MaxRepeat-class.html#copy,Method Martel.Expression.NullOp.copy()=Martel.Expression.NullOp-class.html#copy,Method Martel.Expression.ParseRecords.copy()=Martel.Expression.ParseRecords-class.html#copy,Method Martel.Expression.PassThrough.copy()=Martel.Expression.PassThrough-class.html#copy,Method Martel.Expression.Str.copy()=Martel.Expression.Str-class.html#copy,Method Martel.IterParser.IterHeaderFooter.copy()=Martel.IterParser.IterHeaderFooter-class.html#copy,Method Martel.IterParser.IterRecords.copy()=Martel.IterParser.IterRecords-class.html#copy,Method Martel.Iterator.IteratorRecords.copy()=Martel.Iterator.IteratorRecords-class.html#copy,Method Martel.Parser.HeaderFooterParser.copy()=Martel.Parser.HeaderFooterParser-class.html#copy,Method Martel.Parser.Parser.copy()=Martel.Parser.Parser-class.html#copy,Method Martel.Parser.RecordParser.copy()=Martel.Parser.RecordParser-class.html#copy"><a title="Bio.Crystal.Crystal.copy
Bio.GA.Organism.Organism.copy
Bio.GenBank.NCBIDictionary.copy
Bio.PDB.Vector'.Vector.copy
Bio.Prosite.ExPASyDictionary.copy
Bio.Prosite.Pattern.PrositeTerm.copy
Bio.Prosite.Prodoc.ExPASyDictionary.copy
Bio.PubMed.Dictionary.copy
Bio.SwissProt.SProt.ExPASyDictionary.copy
Martel.Expression.Any.copy
Martel.Expression.AnyEol.copy
Martel.Expression.Assert.copy
Martel.Expression.AtBeginning.copy
Martel.Expression.AtEnd.copy
Martel.Expression.Debug.copy
Martel.Expression.Dot.copy
Martel.Expression.Expression.copy
Martel.Expression.ExpressionList.copy
Martel.Expression.FastFeature.copy
Martel.Expression.Group.copy
Martel.Expression.GroupRef.copy
Martel.Expression.HeaderFooter.copy
Martel.Expression.Literal.copy
Martel.Expression.MaxRepeat.copy
Martel.Expression.NullOp.copy
Martel.Expression.ParseRecords.copy
Martel.Expression.PassThrough.copy
Martel.Expression.Str.copy
Martel.IterParser.IterHeaderFooter.copy
Martel.IterParser.IterRecords.copy
Martel.Iterator.IteratorRecords.copy
Martel.Parser.HeaderFooterParser.copy
Martel.Parser.Parser.copy
Martel.Parser.RecordParser.copy" class="py-name" href="#" onclick="return doclink('link-0', 'copy', 'link-0');">copy</a></tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-1" class="py-name" targets="Module Bio.File=Bio.File-module.html"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-1', 'File', 'link-1');">File</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name" targets="Class Bio.File.UndoHandle=Bio.File.UndoHandle-class.html"><a title="Bio.File.UndoHandle" class="py-name" href="#" onclick="return doclink('link-2', 'UndoHandle', 'link-2');">UndoHandle</a></tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-string">"""Used for debugging"""</tt> </tt>
<a name="dump_saved"></a><div id="dump_saved-def"><a name="L34"></a><tt class="py-lineno"> 34</tt> <a class="py-toggle" href="#" id="dump_saved-toggle" onclick="return toggle('dump_saved');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.FilteredReader-module.html#dump_saved">dump_saved</a><tt class="py-op">(</tt> <tt class="py-param">name</tt><tt class="py-op">,</tt> <tt class="py-param">text</tt><tt class="py-op">,</tt> <tt class="py-param">j</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="dump_saved-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="dump_saved-expanded"><a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> <tt class="py-name">dump_file</tt> <tt class="py-op">=</tt> <tt id="link-3" 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-3', 'open', 'link-3');">open</a></tt><tt class="py-op">(</tt> <tt id="link-4" 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-4', 'name', 'link-4');">name</a></tt> <tt class="py-op">+</tt> <tt class="py-string">'%d'</tt> <tt class="py-op">%</tt> <tt class="py-name">j</tt><tt class="py-op">,</tt> <tt class="py-string">"w"</tt> <tt class="py-op">)</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-name">k</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-5" class="py-name" targets="Variable Bio.PDB.Polypeptide.i=Bio.PDB.Polypeptide-module.html#i"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-5', 'i', 'link-5');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt> <tt class="py-op">(</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt> <tt id="link-6" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.text()=Bio.EUtils.POM.ElementNode-class.html#text,Method Bio.Prosite.Prodoc._RecordConsumer.text()=Bio.Prosite.Prodoc._RecordConsumer-class.html#text,Variable Martel.test.test_Iterator.text=Martel.test.test_Iterator-module.html#text,Variable Martel.test.test_ParseRecords.text=Martel.test.test_ParseRecords-module.html#text"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-6', 'text', 'link-6');">text</a></tt> <tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-number">80</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 class="py-name">dump_file</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name" targets="Method Bio.AlignAce.Motif.Motif.write()=Bio.AlignAce.Motif.Motif-class.html#write,Function Bio.AlignIO.write()=Bio.AlignIO-module.html#write,Method Bio.EUtils.sourcegen.SourceFile.write()=Bio.EUtils.sourcegen.SourceFile-class.html#write,Method Bio.EUtils.sourcegen.SourceGen.write()=Bio.EUtils.sourcegen.SourceGen-class.html#write,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.write()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#write,Function Bio.SeqIO.write()=Bio.SeqIO-module.html#write,Method Bio.Writer.Writer.write()=Bio.Writer.Writer-class.html#write,Method Bio.writers.SeqRecord.embl.WriteEmbl.write()=Bio.writers.SeqRecord.embl.WriteEmbl-class.html#write,Method Bio.writers.SeqRecord.fasta.WriteFasta.write()=Bio.writers.SeqRecord.fasta.WriteFasta-class.html#write"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-7', 'write', 'link-7');">write</a></tt><tt class="py-op">(</tt> <tt class="py-string">'%s\n'</tt> <tt class="py-op">%</tt> <tt id="link-8" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-8', 'text', 'link-6');">text</a></tt><tt class="py-op">[</tt> <tt id="link-9" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-9', 'i', 'link-5');">i</a></tt> <tt class="py-op">:</tt> <tt id="link-10" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-10', 'i', 'link-5');">i</a></tt> <tt class="py-op">+</tt> <tt class="py-number">80</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 class="py-name">dump_file</tt><tt class="py-op">.</tt><tt id="link-11" class="py-name" targets="Method Bio.FilteredReader.FilteredReader.close()=Bio.FilteredReader.FilteredReader-class.html#close,Method Bio.Mindy.BerkeleyDB.BerkeleyDB.close()=Bio.Mindy.BerkeleyDB.BerkeleyDB-class.html#close,Method Bio.Mindy.FlatDB.MemoryFlatDB.close()=Bio.Mindy.FlatDB.MemoryFlatDB-class.html#close,Method BioSQL.BioSeqDatabase.Adaptor.close()=BioSQL.BioSeqDatabase.Adaptor-class.html#close,Method Martel.Parser.Parser.close()=Martel.Parser.Parser-class.html#close,Method Martel.Parser.RecordParser.close()=Martel.Parser.RecordParser-class.html#close"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-11', 'close', 'link-11');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> </tt>
<a name="remove_leading_whitespace"></a><div id="remove_leading_whitespace-def"><a name="L41"></a><tt class="py-lineno"> 41</tt> <a class="py-toggle" href="#" id="remove_leading_whitespace-toggle" onclick="return toggle('remove_leading_whitespace');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.FilteredReader-module.html#remove_leading_whitespace">remove_leading_whitespace</a><tt class="py-op">(</tt> <tt class="py-param">line</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="remove_leading_whitespace-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="remove_leading_whitespace-expanded"><a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">lstrip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> </tt>
<a name="remove_empty_line"></a><div id="remove_empty_line-def"><a name="L45"></a><tt class="py-lineno"> 45</tt> <a class="py-toggle" href="#" id="remove_empty_line-toggle" onclick="return toggle('remove_empty_line');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.FilteredReader-module.html#remove_empty_line">remove_empty_line</a><tt class="py-op">(</tt> <tt class="py-param">line</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="remove_empty_line-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="remove_empty_line-expanded"><a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt class="py-name">stripped_line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-12" class="py-name" targets="Class Bio.EUtils.DTDs.LinkOut.strip=Bio.EUtils.DTDs.LinkOut.strip-class.html,Method Bio.File.SGMLStripper.strip()=Bio.File.SGMLStripper-class.html#strip,Method Bio.SGMLExtractor.SGMLExtractor.strip()=Bio.SGMLExtractor.SGMLExtractor-class.html#strip"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-12', 'strip', 'link-12');">strip</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-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">stripped_line</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-keyword">return</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt> <tt class="py-op">:</tt> <tt class="py-op">]</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">''</tt> </tt>
</div><a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> </tt>
<a name="remove_useless_dot"></a><div id="remove_useless_dot-def"><a name="L52"></a><tt class="py-lineno"> 52</tt> <a class="py-toggle" href="#" id="remove_useless_dot-toggle" onclick="return toggle('remove_useless_dot');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.FilteredReader-module.html#remove_useless_dot">remove_useless_dot</a><tt class="py-op">(</tt> <tt class="py-param">line</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="remove_useless_dot-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="remove_useless_dot-expanded"><a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-name">before</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-keyword">while</tt><tt class="py-op">(</tt> <tt class="py-number">1</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 class="py-name">after</tt> <tt class="py-op">=</tt> <tt class="py-name">before</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt> <tt class="py-string">"\t.\t"</tt><tt class="py-op">,</tt> <tt class="py-string">"\t\t"</tt> <tt class="py-op">)</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt> <tt class="py-name">before</tt> <tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt> <tt class="py-name">after</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 class="py-keyword">break</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt class="py-name">before</tt> <tt class="py-op">=</tt> <tt class="py-name">after</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">after</tt><tt class="py-op">.</tt><tt class="py-name">endswith</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="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-name">after</tt> <tt class="py-op">=</tt> <tt class="py-name">after</tt><tt class="py-op">[</tt> <tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt> <tt class="py-op">]</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">after</tt> </tt>
</div><a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> </tt>
<a name="fix_punctuation"></a><div id="fix_punctuation-def"><a name="L63"></a><tt class="py-lineno"> 63</tt> <a class="py-toggle" href="#" id="fix_punctuation-toggle" onclick="return toggle('fix_punctuation');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.FilteredReader-module.html#fix_punctuation">fix_punctuation</a><tt class="py-op">(</tt> <tt class="py-param">line</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="fix_punctuation-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="fix_punctuation-expanded"><a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt> <tt class="py-string">"'"</tt><tt class="py-op">,</tt> <tt class="py-string">''</tt> <tt class="py-op">)</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt> <tt class="py-string">'"'</tt><tt class="py-op">,</tt> <tt class="py-string">''</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">line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt> <tt class="py-string">';'</tt><tt class="py-op">,</tt> <tt class="py-string">'\t'</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">line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt> <tt class="py-string">'entryname'</tt><tt class="py-op">,</tt> <tt class="py-string">'id'</tt> <tt class="py-op">)</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"><tt class="py-comment"># line = line.lower( )</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">line</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt> <tt class="py-op">:</tt> <tt class="py-op">]</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">''</tt> </tt>
</div><a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> </tt>
<a name="FilteredReader"></a><div id="FilteredReader-def"><a name="L76"></a><tt class="py-lineno"> 76</tt> <a class="py-toggle" href="#" id="FilteredReader-toggle" onclick="return toggle('FilteredReader');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.FilteredReader.FilteredReader-class.html">FilteredReader</a><tt class="py-op">:</tt> </tt>
</div><div id="FilteredReader-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="FilteredReader-expanded"><a name="FilteredReader.__init__"></a><div id="FilteredReader.__init__-def"><a name="L77"></a><tt class="py-lineno"> 77</tt> <a class="py-toggle" href="#" id="FilteredReader.__init__-toggle" onclick="return toggle('FilteredReader.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.FilteredReader.FilteredReader-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">handle</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FilteredReader.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FilteredReader.__init__-expanded"><a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_handle</tt> <tt class="py-op">=</tt> <tt id="link-13" class="py-name" targets="Variable Bio.LocusLink.web_parse.handle=Bio.LocusLink.web_parse-module.html#handle,Variable Bio.Ndb.handle=Bio.Ndb-module.html#handle"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-13', 'handle', 'link-13');">handle</a></tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_start_line</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_debug_count</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">filter_chain</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> <tt id="link-14" class="py-name" targets="Function Bio.FilteredReader.remove_empty_line()=Bio.FilteredReader-module.html#remove_empty_line"><a title="Bio.FilteredReader.remove_empty_line" class="py-name" href="#" onclick="return doclink('link-14', 'remove_empty_line', 'link-14');">remove_empty_line</a></tt><tt class="py-op">,</tt> <tt id="link-15" class="py-name" targets="Function Bio.FilteredReader.remove_useless_dot()=Bio.FilteredReader-module.html#remove_useless_dot"><a title="Bio.FilteredReader.remove_useless_dot" class="py-name" href="#" onclick="return doclink('link-15', 'remove_useless_dot', 'link-15');">remove_useless_dot</a></tt><tt class="py-op">,</tt> <tt id="link-16" class="py-name" targets="Function Bio.FilteredReader.fix_punctuation()=Bio.FilteredReader-module.html#fix_punctuation"><a title="Bio.FilteredReader.fix_punctuation" class="py-name" href="#" onclick="return doclink('link-16', 'fix_punctuation', 'link-16');">fix_punctuation</a></tt> <tt class="py-op">]</tt> </tt>
</div><a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> </tt>
<a name="FilteredReader.__getattr__"></a><div id="FilteredReader.__getattr__-def"><a name="L83"></a><tt class="py-lineno"> 83</tt> <a class="py-toggle" href="#" id="FilteredReader.__getattr__-toggle" onclick="return toggle('FilteredReader.__getattr__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.FilteredReader.FilteredReader-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">attr</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FilteredReader.__getattr__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FilteredReader.__getattr__-expanded"><a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">getattr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_handle</tt><tt class="py-op">,</tt> <tt class="py-name">attr</tt><tt class="py-op">)</tt> </tt>
</div><a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> </tt>
<a name="FilteredReader.close"></a><div id="FilteredReader.close-def"><a name="L88"></a><tt class="py-lineno"> 88</tt> <a class="py-toggle" href="#" id="FilteredReader.close-toggle" onclick="return toggle('FilteredReader.close');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.FilteredReader.FilteredReader-class.html#close">close</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-op">*</tt><tt class="py-param">args</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-param">keywds</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FilteredReader.close-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FilteredReader.close-expanded"><a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_handle</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-17', 'close', 'link-11');">close</a></tt><tt class="py-op">(</tt> <tt class="py-op">*</tt><tt class="py-name">args</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-name">keywds</tt><tt class="py-op">)</tt> </tt>
</div><a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> </tt>
<a name="FilteredReader.read"></a><div id="FilteredReader.read-def"><a name="L91"></a><tt class="py-lineno"> 91</tt> <a class="py-toggle" href="#" id="FilteredReader.read-toggle" onclick="return toggle('FilteredReader.read');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.FilteredReader.FilteredReader-class.html#read">read</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-op">*</tt><tt class="py-param">args</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-param">keywds</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FilteredReader.read-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FilteredReader.read-expanded"><a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-name">len_expected</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name" targets="Method Bio.FilteredReader.FilteredReader._get_len_expected()=Bio.FilteredReader.FilteredReader-class.html#_get_len_expected"><a title="Bio.FilteredReader.FilteredReader._get_len_expected" class="py-name" href="#" onclick="return doclink('link-18', '_get_len_expected', 'link-18');">_get_len_expected</a></tt><tt class="py-op">(</tt> <tt class="py-name">args</tt><tt class="py-op">,</tt> <tt class="py-name">keywds</tt> <tt class="py-op">)</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">len_expected</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-name">filtered_text</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name" targets="Method Bio.FilteredReader.FilteredReader.read_block()=Bio.FilteredReader.FilteredReader-class.html#read_block"><a title="Bio.FilteredReader.FilteredReader.read_block" class="py-name" href="#" onclick="return doclink('link-19', 'read_block', 'link-19');">read_block</a></tt><tt class="py-op">(</tt> <tt class="py-name">len_expected</tt> <tt class="py-op">)</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-name">filtered_text</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name" targets="Method Bio.FilteredReader.FilteredReader.read_to_end()=Bio.FilteredReader.FilteredReader-class.html#read_to_end"><a title="Bio.FilteredReader.FilteredReader.read_to_end" class="py-name" href="#" onclick="return doclink('link-20', 'read_to_end', 'link-20');">read_to_end</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">filtered_text</tt> </tt>
</div><a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> </tt>
<a name="FilteredReader.read_block"></a><div id="FilteredReader.read_block-def"><a name="L100"></a><tt class="py-lineno">100</tt> <a class="py-toggle" href="#" id="FilteredReader.read_block-toggle" onclick="return toggle('FilteredReader.read_block');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.FilteredReader.FilteredReader-class.html#read_block">read_block</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">len_expected</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FilteredReader.read_block-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FilteredReader.read_block-expanded"><a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-name">len_filtered</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-name">len_adjusted</tt> <tt class="py-op">=</tt> <tt class="py-name">len_expected</tt> <tt class="py-op">-</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_start_line</tt> <tt class="py-op">)</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-name">filtered_text</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-keyword">while</tt><tt class="py-op">(</tt> <tt class="py-name">len_filtered</tt> <tt class="py-op"><</tt> <tt class="py-name">len_expected</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-name">text_read</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_handle</tt><tt class="py-op">.</tt><tt id="link-21" 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-21', 'read', 'link-21');">read</a></tt><tt class="py-op">(</tt> <tt class="py-name">len_adjusted</tt> <tt class="py-op">)</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-name">full_text</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_start_line</tt> <tt class="py-op">+</tt> <tt class="py-name">text_read</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-name">lines</tt> <tt class="py-op">=</tt> <tt class="py-name">full_text</tt><tt class="py-op">.</tt><tt class="py-name">splitlines</tt><tt class="py-op">(</tt> <tt class="py-number">1</tt> <tt class="py-op">)</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">text_read</tt> <tt class="py-op">==</tt> <tt class="py-string">''</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-name">filtered_text</tt> <tt class="py-op">=</tt> <tt class="py-name">filtered_text</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name" targets="Function Bio.FSSP.FSSPTools.filter()=Bio.FSSP.FSSPTools-module.html#filter,Method Bio.FilteredReader.FilteredReader.filter()=Bio.FilteredReader.FilteredReader-class.html#filter,Variable Bio.expressions.swissprot.filter=Bio.expressions.swissprot-module.html#filter"><a title="Bio.FSSP.FSSPTools.filter
Bio.FilteredReader.FilteredReader.filter
Bio.expressions.swissprot.filter" class="py-name" href="#" onclick="return doclink('link-22', 'filter', 'link-22');">filter</a></tt><tt class="py-op">(</tt> <tt class="py-name">lines</tt> <tt class="py-op">)</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-name">all_but_last_line</tt> <tt class="py-op">=</tt> <tt class="py-name">lines</tt><tt class="py-op">[</tt> <tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt> <tt class="py-op">]</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_start_line</tt> <tt class="py-op">=</tt> <tt class="py-name">lines</tt><tt class="py-op">[</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt> <tt class="py-op">]</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-name">filtered_text</tt> <tt class="py-op">=</tt> <tt class="py-name">filtered_text</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name"><a title="Bio.FSSP.FSSPTools.filter
Bio.FilteredReader.FilteredReader.filter
Bio.expressions.swissprot.filter" class="py-name" href="#" onclick="return doclink('link-23', 'filter', 'link-22');">filter</a></tt><tt class="py-op">(</tt> <tt class="py-name">all_but_last_line</tt> <tt class="py-op">)</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt class="py-name">len_filtered_text</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt> <tt class="py-name">filtered_text</tt> <tt class="py-op">)</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-name">len_adjusted</tt> <tt class="py-op">=</tt> <tt class="py-name">len_adjusted</tt> <tt class="py-op">-</tt> <tt class="py-name">len_filtered_text</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">filtered_text</tt><tt class="py-op">[</tt> <tt class="py-op">:</tt> <tt class="py-op">]</tt> </tt>
</div><a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> </tt>
<a name="FilteredReader.read_to_end"></a><div id="FilteredReader.read_to_end-def"><a name="L121"></a><tt class="py-lineno">121</tt> <a class="py-toggle" href="#" id="FilteredReader.read_to_end-toggle" onclick="return toggle('FilteredReader.read_to_end');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.FilteredReader.FilteredReader-class.html#read_to_end">read_to_end</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="FilteredReader.read_to_end-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FilteredReader.read_to_end-expanded"><a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt class="py-name">filtered_text</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-name">text_read</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_handle</tt><tt class="py-op">.</tt><tt id="link-24" 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-24', 'read', 'link-21');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-name">full_text</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_start_line</tt> <tt class="py-op">+</tt> <tt class="py-name">text_read</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-name">lines</tt> <tt class="py-op">=</tt> <tt class="py-name">full_text</tt><tt class="py-op">.</tt><tt class="py-name">splitlines</tt><tt class="py-op">(</tt> <tt class="py-number">1</tt> <tt class="py-op">)</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt class="py-name">filtered_text</tt> <tt class="py-op">=</tt> <tt class="py-name">filtered_text</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-25" class="py-name"><a title="Bio.FSSP.FSSPTools.filter
Bio.FilteredReader.FilteredReader.filter
Bio.expressions.swissprot.filter" class="py-name" href="#" onclick="return doclink('link-25', 'filter', 'link-22');">filter</a></tt><tt class="py-op">(</tt> <tt class="py-name">lines</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> <tt class="py-op">)</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">filtered_text</tt><tt class="py-op">[</tt> <tt class="py-op">:</tt> <tt class="py-op">]</tt> </tt>
</div><a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> </tt>
<a name="FilteredReader._get_len_expected"></a><div id="FilteredReader._get_len_expected-def"><a name="L134"></a><tt class="py-lineno">134</tt> <a class="py-toggle" href="#" id="FilteredReader._get_len_expected-toggle" onclick="return toggle('FilteredReader._get_len_expected');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.FilteredReader.FilteredReader-class.html#_get_len_expected">_get_len_expected</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">args</tt><tt class="py-op">,</tt> <tt class="py-param">keywds</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FilteredReader._get_len_expected-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FilteredReader._get_len_expected-expanded"><a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt> <tt class="py-name">args</tt><tt class="py-op">)</tt> <tt class="py-op">></tt> <tt class="py-number">0</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-name">len_expected</tt> <tt class="py-op">=</tt> <tt class="py-name">args</tt><tt class="py-op">[</tt> <tt class="py-number">0</tt> <tt class="py-op">]</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">len_expected</tt> <tt class="py-op"><</tt> <tt class="py-number">0</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-name">len_expected</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt><tt class="py-op">(</tt> <tt class="py-name">keywds</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name" targets="Method Bio.Crystal.Crystal.has_key()=Bio.Crystal.Crystal-class.html#has_key,Method Bio.EUtils.POM.ElementNode.has_key()=Bio.EUtils.POM.ElementNode-class.html#has_key,Method Bio.GenBank.NCBIDictionary.has_key()=Bio.GenBank.NCBIDictionary-class.html#has_key,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#has_key,Method Bio.PDB.FragmentMapper'.FragmentMapper.has_key()=Bio.PDB.FragmentMapper%27.FragmentMapper-class.html#has_key,Method Bio.Prosite.ExPASyDictionary.has_key()=Bio.Prosite.ExPASyDictionary-class.html#has_key,Method Bio.Prosite.Prodoc.ExPASyDictionary.has_key()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#has_key,Method Bio.PubMed.Dictionary.has_key()=Bio.PubMed.Dictionary-class.html#has_key,Method Bio.SwissProt.SProt.ExPASyDictionary.has_key()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#has_key,Method Martel.Parser.MartelAttributeList.has_key()=Martel.Parser.MartelAttributeList-class.html#has_key"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-26', 'has_key', 'link-26');">has_key</a></tt><tt class="py-op">(</tt> <tt class="py-string">'size'</tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-name">len_expected</tt> <tt class="py-op">=</tt> <tt class="py-name">keywds</tt><tt class="py-op">[</tt> <tt class="py-string">'size'</tt> <tt class="py-op">]</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt class="py-name">len_expected</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">len_expected</tt> </tt>
</div><a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> </tt>
<a name="FilteredReader.filter"></a><div id="FilteredReader.filter-def"><a name="L146"></a><tt class="py-lineno">146</tt> <a class="py-toggle" href="#" id="FilteredReader.filter-toggle" onclick="return toggle('FilteredReader.filter');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.FilteredReader.FilteredReader-class.html#filter">filter</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">lines</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FilteredReader.filter-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FilteredReader.filter-expanded"><a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-name">filter_chain</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">filter_chain</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt class="py-name">filtered_text</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt class="py-name">lines</tt><tt class="py-op">:</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-27" class="py-name"><a title="Bio.FSSP.FSSPTools.filter
Bio.FilteredReader.FilteredReader.filter
Bio.expressions.swissprot.filter" class="py-name" href="#" onclick="return doclink('link-27', 'filter', 'link-22');">filter</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">filter_chain</tt><tt class="py-op">:</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt id="link-28" class="py-name"><a title="Bio.FSSP.FSSPTools.filter
Bio.FilteredReader.FilteredReader.filter
Bio.expressions.swissprot.filter" class="py-name" href="#" onclick="return doclink('link-28', 'filter', 'link-22');">filter</a></tt><tt class="py-op">(</tt> <tt class="py-op">*</tt><tt class="py-op">(</tt> <tt class="py-name">line</tt><tt class="py-op">,</tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-name">filtered_text</tt> <tt class="py-op">=</tt> <tt class="py-name">filtered_text</tt> <tt class="py-op">+</tt> <tt class="py-name">line</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">filtered_text</tt> </tt>
</div></div><a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> </tt>
<a name="has_trailing_linefeed"></a><div id="has_trailing_linefeed-def"><a name="L156"></a><tt class="py-lineno">156</tt> <a class="py-toggle" href="#" id="has_trailing_linefeed-toggle" onclick="return toggle('has_trailing_linefeed');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.FilteredReader-module.html#has_trailing_linefeed">has_trailing_linefeed</a><tt class="py-op">(</tt> <tt class="py-param">line</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="has_trailing_linefeed-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="has_trailing_linefeed-expanded"><a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">endswith</tt><tt class="py-op">(</tt> <tt class="py-name">chr</tt><tt class="py-op">(</tt> <tt class="py-number">13</tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt> <tt class="py-keyword">or</tt> \ </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">endswith</tt><tt class="py-op">(</tt> <tt class="py-name">chr</tt><tt class="py-op">(</tt> <tt class="py-number">10</tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
</div><a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> </tt><script type="text/javascript">
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