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<a href="Martel-module.html">Package Martel</a> ::
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Module delimiter
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<h1 class="epydoc">Source Code for <a href="Martel.test.testformats.delimiter-module.html">Module Martel.test.testformats.delimiter</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-docstring">"""Example of using Martel on a simple delimited file</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-0" class="py-name" targets="Package Martel=Martel-module.html"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-0', 'Martel', 'link-0');">Martel</a></tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</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="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"> </tt>
<a name="delimiter"></a><div id="delimiter-def"><a name="L7"></a><tt class="py-lineno"> 7</tt> <a class="py-toggle" href="#" id="delimiter-toggle" onclick="return toggle('delimiter');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.test.testformats.delimiter-module.html#delimiter">delimiter</a><tt class="py-op">(</tt><tt class="py-param">delim</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="delimiter-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="delimiter-expanded"><a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">delim</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="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"> <tt class="py-string">"delimiter can only be a single character long, not %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt class="py-name">delim</tt><tt class="py-op">)</tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">delim</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-string">"\n\r"</tt><tt class="py-op">,</tt> <tt class="py-string">"Cannot use %s as a delimiter"</tt> <tt class="py-op">%</tt> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt class="py-name">delim</tt><tt class="py-op">)</tt> </tt>
<a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"> </tt>
<a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"> <tt class="py-name">field</tt> <tt class="py-op">=</tt> <tt id="link-3" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-3', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-4" 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-4', 'Group', 'link-4');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"field"</tt><tt class="py-op">,</tt> <tt id="link-5" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-5', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-6" class="py-name" targets="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"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-7', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-8" class="py-name" targets="Function Martel.AnyBut()=Martel-module.html#AnyBut"><a title="Martel.AnyBut" class="py-name" href="#" onclick="return doclink('link-8', 'AnyBut', 'link-8');">AnyBut</a></tt><tt class="py-op">(</tt><tt class="py-name">delim</tt> <tt class="py-op">+</tt> <tt class="py-string">"\r\n"</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>
<a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">field</tt> <tt class="py-op">+</tt> <tt id="link-9" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-9', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-10" class="py-name"><a title="Bio.Pathway.Rep
Martel.Rep" class="py-name" href="#" onclick="return doclink('link-10', 'Rep', 'link-6');">Rep</a></tt><tt class="py-op">(</tt><tt id="link-11" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-11', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-12" 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-12', 'Str', 'link-12');">Str</a></tt><tt class="py-op">(</tt><tt class="py-name">delim</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-name">field</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-13" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-13', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-14" 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-14', 'AnyEol', 'link-14');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"> <tt id="link-15" 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-15', 'record', 'link-15');">record</a></tt> <tt class="py-op">=</tt> <tt id="link-16" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-16', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-17" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-17', 'Group', 'link-4');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"record"</tt><tt class="py-op">,</tt> <tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"> </tt>
<a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"> <tt id="link-18" 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-18', 'format', 'link-18');">format</a></tt> <tt class="py-op">=</tt> <tt id="link-19" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-19', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-20" class="py-name" targets="Class Martel.Expression.ParseRecords=Martel.Expression.ParseRecords-class.html"><a title="Martel.Expression.ParseRecords" class="py-name" href="#" onclick="return doclink('link-20', 'ParseRecords', 'link-20');">ParseRecords</a></tt><tt class="py-op">(</tt><tt class="py-string">"delimited"</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">,</tt> <tt id="link-21" 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-21', 'record', 'link-15');">record</a></tt><tt class="py-op">,</tt> </tt>
<a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"> <tt id="link-22" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-22', 'RecordReader', 'link-2');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-23" class="py-name" targets="Class Martel.RecordReader.CountLines=Martel.RecordReader.CountLines-class.html"><a title="Martel.RecordReader.CountLines" class="py-name" href="#" onclick="return doclink('link-23', 'CountLines', 'link-23');">CountLines</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-24" 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-24', 'format', 'link-18');">format</a></tt> </tt>
</div><a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"> </tt>
<a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"><tt id="link-25" class="py-name" targets="Variable Martel.test.testformats.delimiter.tabformat=Martel.test.testformats.delimiter-module.html#tabformat"><a title="Martel.test.testformats.delimiter.tabformat" class="py-name" href="#" onclick="return doclink('link-25', 'tabformat', 'link-25');">tabformat</a></tt> <tt class="py-op">=</tt> <tt id="link-26" class="py-name" targets="Module Martel.test.testformats.delimiter=Martel.test.testformats.delimiter-module.html,Function Martel.test.testformats.delimiter.delimiter()=Martel.test.testformats.delimiter-module.html#delimiter"><a title="Martel.test.testformats.delimiter
Martel.test.testformats.delimiter.delimiter" class="py-name" href="#" onclick="return doclink('link-26', 'delimiter', 'link-26');">delimiter</a></tt><tt class="py-op">(</tt><tt class="py-string">"\t"</tt><tt class="py-op">)</tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"><tt id="link-27" class="py-name" targets="Variable Martel.test.testformats.delimiter.spaceformat=Martel.test.testformats.delimiter-module.html#spaceformat"><a title="Martel.test.testformats.delimiter.spaceformat" class="py-name" href="#" onclick="return doclink('link-27', 'spaceformat', 'link-27');">spaceformat</a></tt> <tt class="py-op">=</tt> <tt id="link-28" class="py-name"><a title="Martel.test.testformats.delimiter
Martel.test.testformats.delimiter.delimiter" class="py-name" href="#" onclick="return doclink('link-28', 'delimiter', 'link-26');">delimiter</a></tt><tt class="py-op">(</tt><tt class="py-string">" "</tt><tt class="py-op">)</tt> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"><tt id="link-29" class="py-name" targets="Variable Martel.test.testformats.delimiter.colonformat=Martel.test.testformats.delimiter-module.html#colonformat"><a title="Martel.test.testformats.delimiter.colonformat" class="py-name" href="#" onclick="return doclink('link-29', 'colonformat', 'link-29');">colonformat</a></tt> <tt class="py-op">=</tt> <tt id="link-30" class="py-name"><a title="Martel.test.testformats.delimiter
Martel.test.testformats.delimiter.delimiter" class="py-name" href="#" onclick="return doclink('link-30', 'delimiter', 'link-26');">delimiter</a></tt><tt class="py-op">(</tt><tt class="py-string">":"</tt><tt class="py-op">)</tt> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"><tt id="link-31" class="py-name" targets="Variable Martel.test.testformats.delimiter.commaformat=Martel.test.testformats.delimiter-module.html#commaformat"><a title="Martel.test.testformats.delimiter.commaformat" class="py-name" href="#" onclick="return doclink('link-31', 'commaformat', 'link-31');">commaformat</a></tt> <tt class="py-op">=</tt> <tt id="link-32" class="py-name"><a title="Martel.test.testformats.delimiter
Martel.test.testformats.delimiter.delimiter" class="py-name" href="#" onclick="return doclink('link-32', 'delimiter', 'link-26');">delimiter</a></tt><tt class="py-op">(</tt><tt class="py-string">","</tt><tt class="py-op">)</tt> </tt>
<a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"> </tt>
<a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"><tt 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="L27"></a><tt class="py-lineno">27</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="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"> <tt class="py-name">parser</tt> <tt class="py-op">=</tt> <tt id="link-33" class="py-name"><a title="Martel.test.testformats.delimiter.colonformat" class="py-name" href="#" onclick="return doclink('link-33', 'colonformat', 'link-29');">colonformat</a></tt><tt class="py-op">.</tt><tt id="link-34" 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-34', 'make_parser', 'link-34');">make_parser</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L29"></a><tt class="py-lineno">29</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="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"> <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt id="link-35" 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-35', 'parseFile', 'link-35');">parseFile</a></tt><tt class="py-op">(</tt><tt id="link-36" 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-36', 'open', 'link-36');">open</a></tt><tt class="py-op">(</tt><tt class="py-string">"/etc/passwd"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"> </tt><script type="text/javascript">
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