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<a href="Martel-module.html">Package Martel</a> ::
<a href="Martel.test-module.html">Package test</a> ::
Module test_RecordReader2
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<h1 class="epydoc">Source Code for <a href="Martel.test.test_RecordReader2-module.html">Module Martel.test.test_RecordReader2</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Still more tests of the RecordReader. This one stresses the ability</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"># to find newlines and pass in lookahead text</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">cStringIO</tt> <tt class="py-keyword">import</tt> <tt class="py-name">StringIO</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">string</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Martel=Martel-module.html"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-0', 'Martel', 'link-0');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt id="link-1" 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-1', 'RecordReader', 'link-1');">RecordReader</a></tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">mx</tt> <tt class="py-keyword">import</tt> <tt class="py-name">TextTools</tt> <tt class="py-keyword">as</tt> <tt class="py-name">TT</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"> </tt>
<a name="count_records"></a><div id="count_records-def"><a name="L9"></a><tt class="py-lineno"> 9</tt> <a class="py-toggle" href="#" id="count_records-toggle" onclick="return toggle('count_records');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.test.test_RecordReader2-module.html#count_records">count_records</a><tt class="py-op">(</tt><tt class="py-param">reader</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="count_records-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="count_records-expanded"><a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"> <tt id="link-2" 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-2', 'i', 'link-2');">i</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"> <tt class="py-comment">#print "Testing new reader", reader</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"> <tt id="link-3" class="py-name" targets="Variable Bio.MarkovModel.x=Bio.MarkovModel-module.html#x,Variable Bio.Statistics.lowess.x=Bio.Statistics.lowess-module.html#x"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-3', 'x', 'link-3');">x</a></tt> <tt class="py-op">=</tt> <tt class="py-name">reader</tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Method Bio.AlignIO.ClustalIO.ClustalIterator.next()=Bio.AlignIO.ClustalIO.ClustalIterator-class.html#next,Method Bio.AlignIO.EmbossIO.EmbossIterator.next()=Bio.AlignIO.EmbossIO.EmbossIterator-class.html#next,Method Bio.AlignIO.FastaIO.FastaM10Iterator.next()=Bio.AlignIO.FastaIO.FastaM10Iterator-class.html#next,Method Bio.AlignIO.Interfaces.AlignmentIterator.next()=Bio.AlignIO.Interfaces.AlignmentIterator-class.html#next,Method Bio.AlignIO.PhylipIO.PhylipIterator.next()=Bio.AlignIO.PhylipIO.PhylipIterator-class.html#next,Method Bio.AlignIO.StockholmIO.StockholmIterator.next()=Bio.AlignIO.StockholmIO.StockholmIterator-class.html#next,Method Bio.Blast.NCBIStandalone.Iterator.next()=Bio.Blast.NCBIStandalone.Iterator-class.html#next,Method Bio.Blast.ParseBlastTable.BlastTableReader.next()=Bio.Blast.ParseBlastTable.BlastTableReader-class.html#next,Method Bio.CDD.Iterator.next()=Bio.CDD.Iterator-class.html#next,Method Bio.Compass.Iterator.next()=Bio.Compass.Iterator-class.html#next,Method Bio.DocSQL.IterationCursor.next()=Bio.DocSQL.IterationCursor-class.html#next,Method Bio.ECell.Iterator.next()=Bio.ECell.Iterator-class.html#next,Method Bio.Enzyme.Iterator.next()=Bio.Enzyme.Iterator-class.html#next,Method Bio.Fasta.Iterator.next()=Bio.Fasta.Iterator-class.html#next,Method Bio.GenBank.Iterator.next()=Bio.GenBank.Iterator-class.html#next,Method Bio.Gobase.Iterator.next()=Bio.Gobase.Iterator-class.html#next,Method Bio.IntelliGenetics.IntelliGeneticsReader.next()=Bio.IntelliGenetics.IntelliGeneticsReader-class.html#next,Method Bio.IntelliGenetics.Iterator.next()=Bio.IntelliGenetics.Iterator-class.html#next,Method Bio.LocusLink.Iterator.next()=Bio.LocusLink.Iterator-class.html#next,Method Bio.Medline.Iterator.next()=Bio.Medline.Iterator-class.html#next,Method Bio.MetaTool.Iterator.next()=Bio.MetaTool.Iterator-class.html#next,Method Bio.NBRF.Iterator.next()=Bio.NBRF.Iterator-class.html#next,Method Bio.Nexus.Nexus.CharBuffer.next()=Bio.Nexus.Nexus.CharBuffer-class.html#next,Method Bio.Prosite.Iterator.next()=Bio.Prosite.Iterator-class.html#next,Method Bio.Prosite.Prodoc.Iterator.next()=Bio.Prosite.Prodoc.Iterator-class.html#next,Method Bio.Rebase.Iterator.next()=Bio.Rebase.Iterator-class.html#next,Method Bio.SCOP.Cla.Iterator.next()=Bio.SCOP.Cla.Iterator-class.html#next,Method Bio.SCOP.Des.Iterator.next()=Bio.SCOP.Des.Iterator-class.html#next,Method Bio.SCOP.Dom.Iterator.next()=Bio.SCOP.Dom.Iterator-class.html#next,Method Bio.SCOP.Hie.Iterator.next()=Bio.SCOP.Hie.Iterator-class.html#next,Method Bio.SCOP.Raf.Iterator.next()=Bio.SCOP.Raf.Iterator-class.html#next,Method Bio.Saf.Iterator.next()=Bio.Saf.Iterator-class.html#next,Method Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next()=Bio.SeqIO.Interfaces.InterlacedSequenceIterator-class.html#next,Method Bio.SeqIO.Interfaces.SequenceIterator.next()=Bio.SeqIO.Interfaces.SequenceIterator-class.html#next,Method Bio.Sequencing.Ace.Iterator.next()=Bio.Sequencing.Ace.Iterator-class.html#next,Method Bio.Sequencing.Phd.Iterator.next()=Bio.Sequencing.Phd.Iterator-class.html#next,Method Bio.SwissProt.SProt.Iterator.next()=Bio.SwissProt.SProt.Iterator-class.html#next,Method Bio.UniGene.Iterator.next()=Bio.UniGene.Iterator-class.html#next,Method Martel.Iterator.EventStream.next()=Martel.Iterator.EventStream-class.html#next,Method Martel.Iterator.HeaderFooterEventStream.next()=Martel.Iterator.HeaderFooterEventStream-class.html#next,Method Martel.Iterator.Iterate.next()=Martel.Iterator.Iterate-class.html#next,Method Martel.Iterator.RecordEventStream.next()=Martel.Iterator.RecordEventStream-class.html#next,Method Martel.RecordReader.CountLines.next()=Martel.RecordReader.CountLines-class.html#next,Method Martel.RecordReader.EndsWith.next()=Martel.RecordReader.EndsWith-class.html#next,Method Martel.RecordReader.Everything.next()=Martel.RecordReader.Everything-class.html#next,Method Martel.RecordReader.Nothing.next()=Martel.RecordReader.Nothing-class.html#next,Method Martel.RecordReader.RecordReader.next()=Martel.RecordReader.RecordReader-class.html#next,Method Martel.RecordReader.StartsWith.next()=Martel.RecordReader.StartsWith-class.html#next,Method Martel.RecordReader.Until.next()=Martel.RecordReader.Until-class.html#next"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-4', 'next', 'link-4');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"> <tt class="py-comment">#print "Read", repr(x)</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt id="link-5" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-5', 'x', 'link-3');">x</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"> <tt id="link-6" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-6', 'i', 'link-2');">i</a></tt> <tt class="py-op">=</tt> <tt id="link-7" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-7', 'i', 'link-2');">i</a></tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-8" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-8', 'i', 'link-2');">i</a></tt> </tt>
</div><a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-comment"># Notice how this omits the final newline?</tt> </tt>
<a name="normalize"></a><div id="normalize-def"><a name="L21"></a><tt class="py-lineno"> 21</tt> <a class="py-toggle" href="#" id="normalize-toggle" onclick="return toggle('normalize');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.test.test_RecordReader2-module.html#normalize">normalize</a><tt class="py-op">(</tt><tt class="py-param">s</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="normalize-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="normalize-expanded"><a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">splitlines</tt><tt class="py-op">(</tt><tt id="link-9" class="py-name" targets="Variable Martel.test.test_swissprot38.s=Martel.test.test_swissprot38-module.html#s"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-9', 's', 'link-9');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">"\n"</tt><tt class="py-op">)</tt> </tt>
</div><a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt id="link-10" class="py-name" targets="Variable Martel.test.test_RecordReader2.data1=Martel.test.test_RecordReader2-module.html#data1"><a title="Martel.test.test_RecordReader2.data1" class="py-name" href="#" onclick="return doclink('link-10', 'data1', 'link-10');">data1</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"""\</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-string">ID Q1234</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-string">DE Some protein</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-string">SQ blah</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-string"> ABCDE FGHIJ</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-string">//</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-string">ID Q2345</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-string">DE ID</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-string">SQ lahb</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-string"> ID just checking</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-string"> BCDEF GHIJA</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-string">//</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-string">ID Q3456</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-string">DE me proteinSo</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-string">SQ ahbl</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"><tt class="py-string"> CDEFG HIJID</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-string">//</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt class="py-string">"""</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt id="link-11" class="py-name"><a title="Martel.test.test_RecordReader2.data1" class="py-name" href="#" onclick="return doclink('link-11', 'data1', 'link-10');">data1</a></tt> <tt class="py-op">=</tt> <tt id="link-12" class="py-name" targets="Class Bio.EUtils.DTDs.LinkOut.normalize=Bio.EUtils.DTDs.LinkOut.normalize-class.html,Method Bio.PDB.Vector'.Vector.normalize()=Bio.PDB.Vector%27.Vector-class.html#normalize,Method Bio.config.FormatRegistry.FormatRegistry.normalize()=Bio.config.FormatRegistry.FormatRegistry-class.html#normalize,Function Martel.test.test_RecordReader2.normalize()=Martel.test.test_RecordReader2-module.html#normalize"><a title="Bio.EUtils.DTDs.LinkOut.normalize
Bio.PDB.Vector'.Vector.normalize
Bio.config.FormatRegistry.FormatRegistry.normalize
Martel.test.test_RecordReader2.normalize" class="py-name" href="#" onclick="return doclink('link-12', 'normalize', 'link-12');">normalize</a></tt><tt class="py-op">(</tt><tt id="link-13" class="py-name"><a title="Martel.test.test_RecordReader2.data1" class="py-name" href="#" onclick="return doclink('link-13', 'data1', 'link-10');">data1</a></tt><tt class="py-op">)</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-comment">### StartsWith</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="test_startswith_generic"></a><div id="test_startswith_generic-def"><a name="L48"></a><tt class="py-lineno"> 48</tt> <a class="py-toggle" href="#" id="test_startswith_generic-toggle" onclick="return toggle('test_startswith_generic');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.test.test_RecordReader2-module.html#test_startswith_generic">test_startswith_generic</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="test_startswith_generic-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="test_startswith_generic-expanded"><a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt class="py-name">to_eol_data</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-string">"A\n"</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="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"AA\n"</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="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"A\nB\n"</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="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"A\nB\nB\n"</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="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"A\nB\nB\nA\n"</tt><tt class="py-op">,</tt> <tt class="py-number">2</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"A\nA\nB\nA\n"</tt><tt class="py-op">,</tt> <tt class="py-number">3</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-op">(</tt><tt class="py-string">"A\n A\nA\n"</tt><tt class="py-op">,</tt> <tt class="py-number">2</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"A A A A A A A A A A A A A A\nB\nA\n"</tt><tt class="py-op">,</tt> <tt class="py-number">2</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-op">)</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-14" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-14', 's', 'link-9');">s</a></tt><tt class="py-op">,</tt> <tt class="py-name">expected</tt> <tt class="py-keyword">in</tt> <tt class="py-name">to_eol_data</tt><tt class="py-op">:</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-name">reader</tt> <tt class="py-op">=</tt> <tt id="link-15" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-15', 'RecordReader', 'link-1');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-16" class="py-name" targets="Class Martel.RecordReader.StartsWith=Martel.RecordReader.StartsWith-class.html"><a title="Martel.RecordReader.StartsWith" class="py-name" href="#" onclick="return doclink('link-16', 'StartsWith', 'link-16');">StartsWith</a></tt><tt class="py-op">(</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt id="link-17" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-17', 's', 'link-9');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">"A"</tt><tt class="py-op">)</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt id="link-18" 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-18', 'count', 'link-18');">count</a></tt> <tt class="py-op">=</tt> <tt id="link-19" class="py-name" targets="Function Martel.test.test_RecordReader2.count_records()=Martel.test.test_RecordReader2-module.html#count_records"><a title="Martel.test.test_RecordReader2.count_records" class="py-name" href="#" onclick="return doclink('link-19', 'count_records', 'link-19');">count_records</a></tt><tt class="py-op">(</tt><tt class="py-name">reader</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">assert</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-18');">count</a></tt> <tt class="py-op">==</tt> <tt class="py-name">expected</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt id="link-21" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-21', 's', 'link-9');">s</a></tt><tt class="py-op">,</tt> <tt class="py-name">expected</tt><tt class="py-op">,</tt> <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-18');">count</a></tt><tt class="py-op">)</tt> <tt class="py-comment"># skips to EOL</tt> </tt>
</div><a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> </tt>
<a name="test_startswith_SP"></a><div id="test_startswith_SP-def"><a name="L64"></a><tt class="py-lineno"> 64</tt> <a class="py-toggle" href="#" id="test_startswith_SP-toggle" onclick="return toggle('test_startswith_SP');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.test.test_RecordReader2-module.html#test_startswith_SP">test_startswith_SP</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="test_startswith_SP-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="test_startswith_SP-expanded"><a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-comment"># Check using a SWISS-PROT-like format</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt id="link-23" class="py-name" targets="Variable Bio.expressions.blast.wublast.ending=Bio.expressions.blast.wublast-module.html#ending"><a title="Bio.expressions.blast.wublast.ending" class="py-name" href="#" onclick="return doclink('link-23', 'ending', 'link-23');">ending</a></tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">"\n"</tt><tt class="py-op">,</tt> <tt class="py-string">"\r"</tt><tt class="py-op">,</tt> <tt class="py-string">"\r\n"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt id="link-24" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-24', 's', 'link-9');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt id="link-25" class="py-name"><a title="Martel.test.test_RecordReader2.data1" class="py-name" href="#" onclick="return doclink('link-25', 'data1', 'link-10');">data1</a></tt><tt class="py-op">,</tt> <tt class="py-string">"\n"</tt><tt class="py-op">,</tt> <tt id="link-26" class="py-name"><a title="Bio.expressions.blast.wublast.ending" class="py-name" href="#" onclick="return doclink('link-26', 'ending', 'link-23');">ending</a></tt><tt class="py-op">)</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">final</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">""</tt><tt class="py-op">,</tt> <tt id="link-27" class="py-name"><a title="Bio.expressions.blast.wublast.ending" class="py-name" href="#" onclick="return doclink('link-27', 'ending', 'link-23');">ending</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt id="link-28" class="py-name" targets="Variable Bio.EUtils.setup.d=Bio.EUtils.setup-module.html#d"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-28', 'd', 'link-28');">d</a></tt> <tt class="py-op">=</tt> <tt id="link-29" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-29', 's', 'link-9');">s</a></tt> <tt class="py-op">+</tt> <tt class="py-name">final</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-30" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-30', 'i', 'link-2');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">5</tt><tt class="py-op">,</tt> <tt class="py-number">20</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-name">infile</tt> <tt class="py-op">=</tt> <tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt id="link-31" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-31', 'd', 'link-28');">d</a></tt><tt class="py-op">)</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-name">reader</tt> <tt class="py-op">=</tt> <tt id="link-32" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-32', 'RecordReader', 'link-1');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-33" class="py-name"><a title="Martel.RecordReader.StartsWith" class="py-name" href="#" onclick="return doclink('link-33', 'StartsWith', 'link-16');">StartsWith</a></tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">,</tt> <tt class="py-string">"ID"</tt><tt class="py-op">,</tt> <tt id="link-34" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-34', 'i', 'link-2');">i</a></tt><tt class="py-op">)</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt id="link-35" 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-35', 'count', 'link-18');">count</a></tt> <tt class="py-op">=</tt> <tt id="link-36" class="py-name"><a title="Martel.test.test_RecordReader2.count_records" class="py-name" href="#" onclick="return doclink('link-36', 'count_records', 'link-19');">count_records</a></tt><tt class="py-op">(</tt><tt class="py-name">reader</tt><tt class="py-op">)</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-37" 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-37', 'count', 'link-18');">count</a></tt> <tt class="py-op">==</tt> <tt class="py-number">3</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt id="link-38" class="py-name"><a title="Bio.expressions.blast.wublast.ending" class="py-name" href="#" onclick="return doclink('link-38', 'ending', 'link-23');">ending</a></tt><tt class="py-op">,</tt> <tt class="py-name">final</tt><tt class="py-op">,</tt> <tt id="link-39" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-39', 'i', 'link-2');">i</a></tt><tt class="py-op">,</tt> <tt id="link-40" 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-40', 'count', 'link-18');">count</a></tt><tt class="py-op">,</tt> <tt id="link-41" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-41', 'd', 'link-28');">d</a></tt><tt class="py-op">)</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-42" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-42', 'i', 'link-2');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">6</tt><tt class="py-op">,</tt> <tt class="py-number">20</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-name">infile</tt> <tt class="py-op">=</tt> <tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt id="link-43" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-43', 'd', 'link-28');">d</a></tt><tt class="py-op">)</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-name">reader</tt> <tt class="py-op">=</tt> <tt id="link-44" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-44', 'RecordReader', 'link-1');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-45" class="py-name"><a title="Martel.RecordReader.StartsWith" class="py-name" href="#" onclick="return doclink('link-45', 'StartsWith', 'link-16');">StartsWith</a></tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">,</tt> <tt class="py-string">"ID "</tt><tt class="py-op">,</tt> <tt id="link-46" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-46', 'i', 'link-2');">i</a></tt><tt class="py-op">)</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt id="link-47" 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-47', 'count', 'link-18');">count</a></tt> <tt class="py-op">=</tt> <tt id="link-48" class="py-name"><a title="Martel.test.test_RecordReader2.count_records" class="py-name" href="#" onclick="return doclink('link-48', 'count_records', 'link-19');">count_records</a></tt><tt class="py-op">(</tt><tt class="py-name">reader</tt><tt class="py-op">)</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-49" 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-49', 'count', 'link-18');">count</a></tt> <tt class="py-op">==</tt> <tt class="py-number">3</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt id="link-50" class="py-name"><a title="Bio.expressions.blast.wublast.ending" class="py-name" href="#" onclick="return doclink('link-50', 'ending', 'link-23');">ending</a></tt><tt class="py-op">,</tt> <tt class="py-name">final</tt><tt class="py-op">,</tt> <tt id="link-51" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-51', 'i', 'link-2');">i</a></tt><tt class="py-op">,</tt> <tt id="link-52" 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-52', 'count', 'link-18');">count</a></tt><tt class="py-op">,</tt> <tt id="link-53" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-53', 'd', 'link-28');">d</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="test_startswith_exhaustive"></a><div id="test_startswith_exhaustive-def"><a name="L83"></a><tt class="py-lineno"> 83</tt> <a class="py-toggle" href="#" id="test_startswith_exhaustive-toggle" onclick="return toggle('test_startswith_exhaustive');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.test.test_RecordReader2-module.html#test_startswith_exhaustive">test_startswith_exhaustive</a><tt class="py-op">(</tt><tt class="py-param">ending</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="test_startswith_exhaustive-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="test_startswith_exhaustive-expanded"><a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-comment"># Exhaustive test of the various combinations. Should catch most</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># edge conditions.</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt class="py-name">base</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">"A"</tt> <tt class="py-op">+</tt> <tt id="link-54" class="py-name"><a title="Bio.expressions.blast.wublast.ending" class="py-name" href="#" onclick="return doclink('link-54', 'ending', 'link-23');">ending</a></tt><tt class="py-op">,</tt> <tt class="py-string">"A"</tt> <tt class="py-op">+</tt> <tt id="link-55" class="py-name"><a title="Bio.expressions.blast.wublast.ending" class="py-name" href="#" onclick="return doclink('link-55', 'ending', 'link-23');">ending</a></tt> <tt class="py-op">+</tt> <tt class="py-string">"BA"</tt> <tt class="py-op">+</tt> <tt id="link-56" class="py-name"><a title="Bio.expressions.blast.wublast.ending" class="py-name" href="#" onclick="return doclink('link-56', 'ending', 'link-23');">ending</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">repeat</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-number">15</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt id="link-57" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-57', 's', 'link-9');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-name">base</tt> <tt class="py-op">*</tt> <tt class="py-name">repeat</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-name">infile</tt> <tt class="py-op">=</tt> <tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt id="link-58" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-58', 's', 'link-9');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-comment">#for marker in ("A", "A\n"): # Don't use; bug when using "\n"</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt class="py-name">marker</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">"A"</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">look</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">5</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-name">lookahead</tt> <tt class="py-op">=</tt> <tt class="py-name">base</tt> <tt class="py-op">*</tt> <tt class="py-name">look</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">readhint</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">4</tt><tt class="py-op">,</tt> <tt class="py-number">10</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">infile</tt><tt class="py-op">.</tt><tt id="link-59" 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-59', 'seek', 'link-59');">seek</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-name">reader</tt> <tt class="py-op">=</tt> <tt id="link-60" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-60', 'RecordReader', 'link-1');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-61" class="py-name"><a title="Martel.RecordReader.StartsWith" class="py-name" href="#" onclick="return doclink('link-61', 'StartsWith', 'link-16');">StartsWith</a></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">infile</tt><tt class="py-op">,</tt> <tt class="py-name">marker</tt><tt class="py-op">,</tt> <tt class="py-name">readhint</tt><tt class="py-op">,</tt> <tt class="py-name">lookahead</tt><tt class="py-op">)</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt id="link-62" 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-62', 'count', 'link-18');">count</a></tt> <tt class="py-op">=</tt> <tt id="link-63" class="py-name"><a title="Martel.test.test_RecordReader2.count_records" class="py-name" href="#" onclick="return doclink('link-63', 'count_records', 'link-19');">count_records</a></tt><tt class="py-op">(</tt><tt class="py-name">reader</tt><tt class="py-op">)</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-64" 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-64', 'count', 'link-18');">count</a></tt> <tt class="py-op">==</tt> <tt class="py-name">repeat</tt> <tt class="py-op">+</tt> <tt class="py-name">look</tt><tt class="py-op">,</tt> \ </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt id="link-65" 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-65', 'count', 'link-18');">count</a></tt><tt class="py-op">,</tt> <tt id="link-66" class="py-name"><a title="Bio.expressions.blast.wublast.ending" class="py-name" href="#" onclick="return doclink('link-66', 'ending', 'link-23');">ending</a></tt><tt class="py-op">,</tt> <tt class="py-name">base</tt><tt class="py-op">,</tt> <tt class="py-name">repeat</tt><tt class="py-op">,</tt> <tt class="py-name">marker</tt><tt class="py-op">,</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-name">look</tt><tt class="py-op">,</tt> <tt class="py-name">readhint</tt><tt class="py-op">)</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-name">infile</tt><tt class="py-op">.</tt><tt id="link-67" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.seek
Bio.File.UndoHandle.seek
Martel.msre_parse.Tokenizer.seek" class="py-name" href="#" onclick="return doclink('link-67', 'seek', 'link-59');">seek</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-name">reader</tt> <tt class="py-op">=</tt> <tt id="link-68" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-68', 'RecordReader', 'link-1');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-69" class="py-name"><a title="Martel.RecordReader.StartsWith" class="py-name" href="#" onclick="return doclink('link-69', 'StartsWith', 'link-16');">StartsWith</a></tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">,</tt> <tt class="py-name">marker</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">lookahead</tt> <tt class="py-op">=</tt> <tt class="py-name">lookahead</tt><tt class="py-op">)</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt id="link-70" 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-70', 'count', 'link-18');">count</a></tt> <tt class="py-op">=</tt> <tt id="link-71" class="py-name"><a title="Martel.test.test_RecordReader2.count_records" class="py-name" href="#" onclick="return doclink('link-71', 'count_records', 'link-19');">count_records</a></tt><tt class="py-op">(</tt><tt class="py-name">reader</tt><tt class="py-op">)</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-72" 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-72', 'count', 'link-18');">count</a></tt> <tt class="py-op">==</tt> <tt class="py-name">repeat</tt> <tt class="py-op">+</tt> <tt class="py-name">look</tt><tt class="py-op">,</tt> \ </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt id="link-73" 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-73', 'count', 'link-18');">count</a></tt><tt class="py-op">,</tt> <tt id="link-74" class="py-name"><a title="Bio.expressions.blast.wublast.ending" class="py-name" href="#" onclick="return doclink('link-74', 'ending', 'link-23');">ending</a></tt><tt class="py-op">,</tt> <tt class="py-name">repeat</tt><tt class="py-op">,</tt> <tt class="py-name">marker</tt><tt class="py-op">,</tt> <tt class="py-name">look</tt><tt class="py-op">)</tt> </tt>
</div><a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> </tt>
<a name="test_startswith_remainder"></a><div id="test_startswith_remainder-def"><a name="L109"></a><tt class="py-lineno">109</tt> <a class="py-toggle" href="#" id="test_startswith_remainder-toggle" onclick="return toggle('test_startswith_remainder');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.test.test_RecordReader2-module.html#test_startswith_remainder">test_startswith_remainder</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="test_startswith_remainder-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="test_startswith_remainder-expanded"><a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-comment"># Make sure the remainder method works</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt class="py-name">repeat</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">20</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-name">vals</tt> <tt class="py-op">=</tt> <tt id="link-75" class="py-name" targets="Method Bio.GFF.FeatureAggregate.map()=Bio.GFF.FeatureAggregate-class.html#map"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-75', 'map', 'link-75');">map</a></tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-76" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-76', 'x', 'link-3');">x</a></tt><tt class="py-op">:</tt> <tt class="py-string">"A\n%d\n"</tt> <tt class="py-op">%</tt> <tt id="link-77" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-77', 'x', 'link-3');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">repeat</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt id="link-78" class="py-name" targets="Variable BioSQL.BioSeq.DBSeq.data=BioSQL.BioSeq.DBSeq-class.html#data"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-78', 'data', 'link-78');">data</a></tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">vals</tt><tt class="py-op">,</tt> <tt class="py-string">""</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">infile</tt> <tt class="py-op">=</tt> <tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt id="link-79" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-79', 'data', 'link-78');">data</a></tt><tt class="py-op">)</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">look</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</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-name">range</tt><tt class="py-op">(</tt><tt class="py-number">10</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-80" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-80', 'data', 'link-78');">data</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-number">5</tt><tt class="py-op">)</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">infile</tt><tt class="py-op">.</tt><tt id="link-81" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.seek
Bio.File.UndoHandle.seek
Martel.msre_parse.Tokenizer.seek" class="py-name" href="#" onclick="return doclink('link-81', 'seek', 'link-59');">seek</a></tt><tt class="py-op">(</tt><tt class="py-name">look</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">lookahead</tt> <tt class="py-op">=</tt> <tt id="link-82" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-82', 'data', 'link-78');">data</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-name">look</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">reader</tt> <tt class="py-op">=</tt> <tt id="link-83" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-83', 'RecordReader', 'link-1');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-84" class="py-name"><a title="Martel.RecordReader.StartsWith" class="py-name" href="#" onclick="return doclink('link-84', 'StartsWith', 'link-16');">StartsWith</a></tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">,</tt> <tt class="py-string">"A"</tt><tt class="py-op">,</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-name">lookahead</tt> <tt class="py-op">=</tt> <tt class="py-name">lookahead</tt><tt class="py-op">)</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-name">all</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt class="py-name">file</tt><tt class="py-op">,</tt> <tt class="py-name">lh</tt> <tt class="py-op">=</tt> <tt class="py-name">reader</tt><tt class="py-op">.</tt><tt id="link-85" class="py-name" targets="Variable Bio.Affy.CelFile.remainder=Bio.Affy.CelFile-module.html#remainder,Variable Bio.LogisticRegression.remainder=Bio.LogisticRegression-module.html#remainder,Variable Bio.MarkovModel.remainder=Bio.MarkovModel-module.html#remainder,Variable Bio.MaxEntropy.remainder=Bio.MaxEntropy-module.html#remainder,Variable Bio.NaiveBayes.remainder=Bio.NaiveBayes-module.html#remainder,Variable Bio.Statistics.lowess.remainder=Bio.Statistics.lowess-module.html#remainder,Variable Bio.distance.remainder=Bio.distance-module.html#remainder,Variable Bio.kNN.remainder=Bio.kNN-module.html#remainder,Method Martel.RecordReader.CountLines.remainder()=Martel.RecordReader.CountLines-class.html#remainder,Method Martel.RecordReader.EndsWith.remainder()=Martel.RecordReader.EndsWith-class.html#remainder,Method Martel.RecordReader.Everything.remainder()=Martel.RecordReader.Everything-class.html#remainder,Method Martel.RecordReader.Nothing.remainder()=Martel.RecordReader.Nothing-class.html#remainder,Method Martel.RecordReader.RecordReader.remainder()=Martel.RecordReader.RecordReader-class.html#remainder,Method Martel.RecordReader.StartsWith.remainder()=Martel.RecordReader.StartsWith-class.html#remainder,Method Martel.RecordReader.Until.remainder()=Martel.RecordReader.Until-class.html#remainder"><a title="Bio.Affy.CelFile.remainder
Bio.LogisticRegression.remainder
Bio.MarkovModel.remainder
Bio.MaxEntropy.remainder
Bio.NaiveBayes.remainder
Bio.Statistics.lowess.remainder
Bio.distance.remainder
Bio.kNN.remainder
Martel.RecordReader.CountLines.remainder
Martel.RecordReader.EndsWith.remainder
Martel.RecordReader.Everything.remainder
Martel.RecordReader.Nothing.remainder
Martel.RecordReader.RecordReader.remainder
Martel.RecordReader.StartsWith.remainder
Martel.RecordReader.Until.remainder" class="py-name" href="#" onclick="return doclink('link-85', 'remainder', 'link-85');">remainder</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-name">pos</tt> <tt class="py-op">=</tt> <tt class="py-name">file</tt><tt class="py-op">.</tt><tt id="link-86" class="py-name" targets="Method Bio.EUtils.ReseekFile.ReseekFile.tell()=Bio.EUtils.ReseekFile.ReseekFile-class.html#tell,Method Bio.File.UndoHandle.tell()=Bio.File.UndoHandle-class.html#tell,Method Martel.msre_parse.Tokenizer.tell()=Martel.msre_parse.Tokenizer-class.html#tell"><a title="Bio.EUtils.ReseekFile.ReseekFile.tell
Bio.File.UndoHandle.tell
Martel.msre_parse.Tokenizer.tell" class="py-name" href="#" onclick="return doclink('link-86', 'tell', 'link-86');">tell</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 id="link-87" class="py-name" targets="Method Bio.Nexus.Nexus.CharBuffer.rest()=Bio.Nexus.Nexus.CharBuffer-class.html#rest"><a title="Bio.Nexus.Nexus.CharBuffer.rest" class="py-name" href="#" onclick="return doclink('link-87', 'rest', 'link-87');">rest</a></tt> <tt class="py-op">=</tt> <tt class="py-name">file</tt><tt class="py-op">.</tt><tt id="link-88" 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-88', 'read', 'link-88');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">all</tt> <tt class="py-op">+</tt> <tt class="py-name">lh</tt> <tt class="py-op">+</tt> <tt id="link-89" class="py-name"><a title="Bio.Nexus.Nexus.CharBuffer.rest" class="py-name" href="#" onclick="return doclink('link-89', 'rest', 'link-87');">rest</a></tt> <tt class="py-op">==</tt> <tt id="link-90" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-90', 'data', 'link-78');">data</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">all</tt><tt class="py-op">,</tt> <tt class="py-name">lh</tt><tt class="py-op">,</tt> <tt id="link-91" class="py-name"><a title="Bio.Nexus.Nexus.CharBuffer.rest" class="py-name" href="#" onclick="return doclink('link-91', 'rest', 'link-87');">rest</a></tt><tt class="py-op">,</tt> <tt id="link-92" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-92', 'data', 'link-78');">data</a></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">file</tt><tt class="py-op">.</tt><tt id="link-93" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.seek
Bio.File.UndoHandle.seek
Martel.msre_parse.Tokenizer.seek" class="py-name" href="#" onclick="return doclink('link-93', 'seek', 'link-59');">seek</a></tt><tt class="py-op">(</tt><tt class="py-name">pos</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">assert</tt> <tt id="link-94" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-94', 'data', 'link-78');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-name">all</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt id="link-95" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-95', 'data', 'link-78');">data</a></tt><tt class="py-op">,</tt> <tt class="py-name">all</tt><tt class="py-op">)</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt id="link-96" 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-96', 'record', 'link-96');">record</a></tt> <tt class="py-op">=</tt> <tt class="py-name">reader</tt><tt class="py-op">.</tt><tt id="link-97" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-97', 'next', 'link-4');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-98" 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-98', 'record', 'link-96');">record</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-name">all</tt> <tt class="py-op">=</tt> <tt class="py-name">all</tt> <tt class="py-op">+</tt> <tt id="link-99" 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-99', 'record', 'link-96');">record</a></tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">all</tt> <tt class="py-op">==</tt> <tt id="link-100" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-100', 'data', 'link-78');">data</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">all</tt><tt class="py-op">,</tt> <tt id="link-101" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-101', 'data', 'link-78');">data</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> </tt>
<a name="test_startswith_errors"></a><div id="test_startswith_errors-def"><a name="L135"></a><tt class="py-lineno">135</tt> <a class="py-toggle" href="#" id="test_startswith_errors-toggle" onclick="return toggle('test_startswith_errors');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.test.test_RecordReader2-module.html#test_startswith_errors">test_startswith_errors</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="test_startswith_errors-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="test_startswith_errors-expanded"><a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-comment"># Check the failure cases. Actually, there's only one.</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-comment"># Doesn't start with A</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt id="link-102" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-102', 's', 'link-9');">s</a></tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">"B"</tt><tt class="py-op">,</tt> <tt class="py-string">"B\n"</tt><tt class="py-op">,</tt> <tt class="py-string">" A\n"</tt><tt class="py-op">,</tt> <tt class="py-string">" A"</tt><tt class="py-op">,</tt> <tt class="py-string">"B\nA\n"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-keyword">try</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">infile</tt> <tt class="py-op">=</tt> <tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt id="link-103" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-103', 's', 'link-9');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-comment"># The current implementation will fail here, but the</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># interface spec allows the error to be unreported</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># until reading the record.</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">reader</tt> <tt class="py-op">=</tt> <tt id="link-104" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-104', 'RecordReader', 'link-1');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-105" class="py-name"><a title="Martel.RecordReader.StartsWith" class="py-name" href="#" onclick="return doclink('link-105', 'StartsWith', 'link-16');">StartsWith</a></tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">,</tt> <tt class="py-string">"A"</tt><tt class="py-op">)</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt class="py-name">rec</tt> <tt class="py-op">=</tt> <tt class="py-name">reader</tt><tt class="py-op">.</tt><tt id="link-106" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-106', 'next', 'link-4');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">AssertionError</tt><tt class="py-op">,</tt> <tt class="py-string">"should not allow %r"</tt> <tt class="py-op">%</tt> <tt id="link-107" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-107', 's', 'link-9');">s</a></tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt id="link-108" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-108', 'RecordReader', 'link-1');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-109" class="py-name" targets="Class Martel.RecordReader.ReaderError=Martel.RecordReader.ReaderError-class.html"><a title="Martel.RecordReader.ReaderError" class="py-name" href="#" onclick="return doclink('link-109', 'ReaderError', 'link-109');">ReaderError</a></tt><tt class="py-op">:</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">AssertionError</tt><tt class="py-op">,</tt> <tt class="py-string">"should not get here"</tt> </tt>
</div><a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> </tt>
<a name="test_startswith"></a><div id="test_startswith-def"><a name="L153"></a><tt class="py-lineno">153</tt> <a class="py-toggle" href="#" id="test_startswith-toggle" onclick="return toggle('test_startswith');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.test.test_RecordReader2-module.html#test_startswith">test_startswith</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="test_startswith-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="test_startswith-expanded"><a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"Testing StartsWith"</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">" ... generic"</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt id="link-110" class="py-name" targets="Function Martel.test.test_RecordReader2.test_startswith_generic()=Martel.test.test_RecordReader2-module.html#test_startswith_generic"><a title="Martel.test.test_RecordReader2.test_startswith_generic" class="py-name" href="#" onclick="return doclink('link-110', 'test_startswith_generic', 'link-110');">test_startswith_generic</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">" ... newline variations"</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt id="link-111" class="py-name" targets="Function Martel.test.test_RecordReader2.test_startswith_SP()=Martel.test.test_RecordReader2-module.html#test_startswith_SP"><a title="Martel.test.test_RecordReader2.test_startswith_SP" class="py-name" href="#" onclick="return doclink('link-111', 'test_startswith_SP', 'link-111');">test_startswith_SP</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-112" class="py-name"><a title="Bio.expressions.blast.wublast.ending" class="py-name" href="#" onclick="return doclink('link-112', 'ending', 'link-23');">ending</a></tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">"\n"</tt><tt class="py-op">,</tt> <tt class="py-string">"\r"</tt><tt class="py-op">,</tt> <tt class="py-string">"\r\n"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">" ... exhaustive testing against %r"</tt> <tt class="py-op">%</tt> <tt id="link-113" class="py-name"><a title="Bio.expressions.blast.wublast.ending" class="py-name" href="#" onclick="return doclink('link-113', 'ending', 'link-23');">ending</a></tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt id="link-114" class="py-name" targets="Function Martel.test.test_RecordReader2.test_startswith_exhaustive()=Martel.test.test_RecordReader2-module.html#test_startswith_exhaustive"><a title="Martel.test.test_RecordReader2.test_startswith_exhaustive" class="py-name" href="#" onclick="return doclink('link-114', 'test_startswith_exhaustive', 'link-114');">test_startswith_exhaustive</a></tt><tt class="py-op">(</tt><tt id="link-115" class="py-name"><a title="Bio.expressions.blast.wublast.ending" class="py-name" href="#" onclick="return doclink('link-115', 'ending', 'link-23');">ending</a></tt><tt class="py-op">)</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">" ... remainder"</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt id="link-116" class="py-name" targets="Function Martel.test.test_RecordReader2.test_startswith_remainder()=Martel.test.test_RecordReader2-module.html#test_startswith_remainder"><a title="Martel.test.test_RecordReader2.test_startswith_remainder" class="py-name" href="#" onclick="return doclink('link-116', 'test_startswith_remainder', 'link-116');">test_startswith_remainder</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">" ... format errors"</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt id="link-117" class="py-name" targets="Function Martel.test.test_RecordReader2.test_startswith_errors()=Martel.test.test_RecordReader2-module.html#test_startswith_errors"><a title="Martel.test.test_RecordReader2.test_startswith_errors" class="py-name" href="#" onclick="return doclink('link-117', 'test_startswith_errors', 'link-117');">test_startswith_errors</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"><tt class="py-comment">### EndsWith</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="test_endswith_generic"></a><div id="test_endswith_generic-def"><a name="L174"></a><tt class="py-lineno">174</tt> <a class="py-toggle" href="#" id="test_endswith_generic-toggle" onclick="return toggle('test_endswith_generic');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.test.test_RecordReader2-module.html#test_endswith_generic">test_endswith_generic</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="test_endswith_generic-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="test_endswith_generic-expanded"><a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-name">to_eol_data</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-string">"A\n"</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="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"AA\n"</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="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"B\nA\n"</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="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"B\nB\nA\n"</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="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"A\nA\n"</tt><tt class="py-op">,</tt> <tt class="py-number">2</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"A A\nA\n"</tt><tt class="py-op">,</tt> <tt class="py-number">2</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-comment"># this changes with an "A\n" reader</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"A"</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="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"A\nA A\nA\n"</tt><tt class="py-op">,</tt> <tt class="py-number">3</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-comment"># this changes with an "A\n" reader</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"A\nA A\nA"</tt><tt class="py-op">,</tt> <tt class="py-number">3</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-comment"># this changes with an "A\n" reader</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-118" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-118', 's', 'link-9');">s</a></tt><tt class="py-op">,</tt> <tt class="py-name">expected</tt> <tt class="py-keyword">in</tt> <tt class="py-name">to_eol_data</tt><tt class="py-op">:</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> <tt class="py-name">reader</tt> <tt class="py-op">=</tt> <tt id="link-119" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-119', 'RecordReader', 'link-1');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-120" class="py-name" targets="Class Martel.RecordReader.EndsWith=Martel.RecordReader.EndsWith-class.html"><a title="Martel.RecordReader.EndsWith" class="py-name" href="#" onclick="return doclink('link-120', 'EndsWith', 'link-120');">EndsWith</a></tt><tt class="py-op">(</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt id="link-121" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-121', 's', 'link-9');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">"A"</tt><tt class="py-op">)</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt id="link-122" 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-122', 'count', 'link-18');">count</a></tt> <tt class="py-op">=</tt> <tt id="link-123" class="py-name"><a title="Martel.test.test_RecordReader2.count_records" class="py-name" href="#" onclick="return doclink('link-123', 'count_records', 'link-19');">count_records</a></tt><tt class="py-op">(</tt><tt class="py-name">reader</tt><tt class="py-op">)</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-124" 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-124', 'count', 'link-18');">count</a></tt> <tt class="py-op">==</tt> <tt class="py-name">expected</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt id="link-125" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-125', 's', 'link-9');">s</a></tt><tt class="py-op">,</tt> <tt class="py-name">expected</tt><tt class="py-op">,</tt> <tt id="link-126" 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-126', 'count', 'link-18');">count</a></tt><tt class="py-op">)</tt> <tt class="py-comment"># skips to EOL</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> <tt class="py-name">newline_data</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-string">"A\n"</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="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-comment">#("AA\n", 1), # not legal</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"B\nA\n"</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="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"B\nB\nA\n"</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="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"A\nA\n"</tt><tt class="py-op">,</tt> <tt class="py-number">2</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"A A\nA\n"</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-comment"># this changed with an "A\n" reader</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"A"</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="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"A\nA A\nA\n"</tt><tt class="py-op">,</tt> <tt class="py-number">2</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-comment"># this changed with an "A\n" reader</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"A\nA A\nA"</tt><tt class="py-op">,</tt> <tt class="py-number">2</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-comment"># this changed with an "A\n" reader</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-127" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-127', 's', 'link-9');">s</a></tt><tt class="py-op">,</tt> <tt class="py-name">expected</tt> <tt class="py-keyword">in</tt> <tt class="py-name">newline_data</tt><tt class="py-op">:</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt class="py-name">reader</tt> <tt class="py-op">=</tt> <tt id="link-128" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-128', 'RecordReader', 'link-1');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-129" class="py-name"><a title="Martel.RecordReader.EndsWith" class="py-name" href="#" onclick="return doclink('link-129', 'EndsWith', 'link-120');">EndsWith</a></tt><tt class="py-op">(</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt id="link-130" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-130', 's', 'link-9');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">"A\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt id="link-131" 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-131', 'count', 'link-18');">count</a></tt> <tt class="py-op">=</tt> <tt id="link-132" class="py-name"><a title="Martel.test.test_RecordReader2.count_records" class="py-name" href="#" onclick="return doclink('link-132', 'count_records', 'link-19');">count_records</a></tt><tt class="py-op">(</tt><tt class="py-name">reader</tt><tt class="py-op">)</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-133" 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-133', 'count', 'link-18');">count</a></tt> <tt class="py-op">==</tt> <tt class="py-name">expected</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt id="link-134" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-134', 's', 'link-9');">s</a></tt><tt class="py-op">,</tt> <tt class="py-name">expected</tt><tt class="py-op">,</tt> <tt id="link-135" 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-135', 'count', 'link-18');">count</a></tt><tt class="py-op">)</tt> <tt class="py-comment"># expects newline</tt> </tt>
</div><a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> </tt>
<a name="test_endswith_SP"></a><div id="test_endswith_SP-def"><a name="L207"></a><tt class="py-lineno">207</tt> <a class="py-toggle" href="#" id="test_endswith_SP-toggle" onclick="return toggle('test_endswith_SP');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.test.test_RecordReader2-module.html#test_endswith_SP">test_endswith_SP</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="test_endswith_SP-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="test_endswith_SP-expanded"><a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> <tt class="py-comment"># Check using a SWISS-PROT-like format</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt id="link-136" class="py-name"><a title="Bio.expressions.blast.wublast.ending" class="py-name" href="#" onclick="return doclink('link-136', 'ending', 'link-23');">ending</a></tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">"\n"</tt><tt class="py-op">,</tt> <tt class="py-string">"\r"</tt><tt class="py-op">,</tt> <tt class="py-string">"\r\n"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> <tt id="link-137" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-137', 's', 'link-9');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt id="link-138" class="py-name"><a title="Martel.test.test_RecordReader2.data1" class="py-name" href="#" onclick="return doclink('link-138', 'data1', 'link-10');">data1</a></tt><tt class="py-op">,</tt> <tt class="py-string">"\n"</tt><tt class="py-op">,</tt> <tt id="link-139" class="py-name"><a title="Bio.expressions.blast.wublast.ending" class="py-name" href="#" onclick="return doclink('link-139', 'ending', 'link-23');">ending</a></tt><tt class="py-op">)</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">final</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">""</tt><tt class="py-op">,</tt> <tt id="link-140" class="py-name"><a title="Bio.expressions.blast.wublast.ending" class="py-name" href="#" onclick="return doclink('link-140', 'ending', 'link-23');">ending</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> <tt id="link-141" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-141', 'd', 'link-28');">d</a></tt> <tt class="py-op">=</tt> <tt id="link-142" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-142', 's', 'link-9');">s</a></tt> <tt class="py-op">+</tt> <tt class="py-name">final</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt class="py-name">loop</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-143" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-143', 'i', 'link-2');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">5</tt><tt class="py-op">,</tt> <tt class="py-number">20</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt class="py-name">infile</tt> <tt class="py-op">=</tt> <tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt id="link-144" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-144', 'd', 'link-28');">d</a></tt><tt class="py-op">)</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt class="py-name">reader</tt> <tt class="py-op">=</tt> <tt id="link-145" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-145', 'RecordReader', 'link-1');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-146" class="py-name"><a title="Martel.RecordReader.EndsWith" class="py-name" href="#" onclick="return doclink('link-146', 'EndsWith', 'link-120');">EndsWith</a></tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">,</tt> <tt class="py-string">"//"</tt><tt class="py-op">,</tt> <tt id="link-147" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-147', 'i', 'link-2');">i</a></tt><tt class="py-op">)</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt id="link-148" 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-148', 'count', 'link-18');">count</a></tt> <tt class="py-op">=</tt> <tt id="link-149" class="py-name"><a title="Martel.test.test_RecordReader2.count_records" class="py-name" href="#" onclick="return doclink('link-149', 'count_records', 'link-19');">count_records</a></tt><tt class="py-op">(</tt><tt class="py-name">reader</tt><tt class="py-op">)</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-150" 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-150', 'count', 'link-18');">count</a></tt> <tt class="py-op">==</tt> <tt class="py-number">3</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt id="link-151" class="py-name"><a title="Bio.expressions.blast.wublast.ending" class="py-name" href="#" onclick="return doclink('link-151', 'ending', 'link-23');">ending</a></tt><tt class="py-op">,</tt> <tt class="py-name">final</tt><tt class="py-op">,</tt> <tt id="link-152" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-152', 'i', 'link-2');">i</a></tt><tt class="py-op">,</tt> <tt id="link-153" 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-153', 'count', 'link-18');">count</a></tt><tt class="py-op">,</tt> <tt id="link-154" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-154', 'd', 'link-28');">d</a></tt><tt class="py-op">)</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-155" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-155', 'i', 'link-2');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">5</tt><tt class="py-op">,</tt> <tt class="py-number">20</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt class="py-name">infile</tt> <tt class="py-op">=</tt> <tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt id="link-156" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-156', 'd', 'link-28');">d</a></tt><tt class="py-op">)</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt class="py-name">reader</tt> <tt class="py-op">=</tt> <tt id="link-157" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-157', 'RecordReader', 'link-1');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-158" class="py-name"><a title="Martel.RecordReader.EndsWith" class="py-name" href="#" onclick="return doclink('link-158', 'EndsWith', 'link-120');">EndsWith</a></tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">,</tt> <tt class="py-string">"//\n"</tt><tt class="py-op">,</tt> <tt id="link-159" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-159', 'i', 'link-2');">i</a></tt><tt class="py-op">)</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> <tt id="link-160" 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-160', 'count', 'link-18');">count</a></tt> <tt class="py-op">=</tt> <tt id="link-161" class="py-name"><a title="Martel.test.test_RecordReader2.count_records" class="py-name" href="#" onclick="return doclink('link-161', 'count_records', 'link-19');">count_records</a></tt><tt class="py-op">(</tt><tt class="py-name">reader</tt><tt class="py-op">)</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-162" 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-162', 'count', 'link-18');">count</a></tt> <tt class="py-op">==</tt> <tt class="py-number">3</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt id="link-163" class="py-name"><a title="Bio.expressions.blast.wublast.ending" class="py-name" href="#" onclick="return doclink('link-163', 'ending', 'link-23');">ending</a></tt><tt class="py-op">,</tt> <tt class="py-name">final</tt><tt class="py-op">,</tt> <tt id="link-164" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-164', 'i', 'link-2');">i</a></tt><tt class="py-op">,</tt> <tt id="link-165" 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-165', 'count', 'link-18');">count</a></tt><tt class="py-op">,</tt> <tt id="link-166" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-166', 'd', 'link-28');">d</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> </tt>
<a name="test_endswith_exhaustive"></a><div id="test_endswith_exhaustive-def"><a name="L228"></a><tt class="py-lineno">228</tt> <a class="py-toggle" href="#" id="test_endswith_exhaustive-toggle" onclick="return toggle('test_endswith_exhaustive');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.test.test_RecordReader2-module.html#test_endswith_exhaustive">test_endswith_exhaustive</a><tt class="py-op">(</tt><tt class="py-param">ending</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="test_endswith_exhaustive-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="test_endswith_exhaustive-expanded"><a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> <tt class="py-comment"># Exhaustive test of the various combinations. Should catch most</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># edge conditions.</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt class="py-name">base</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">"A"</tt> <tt class="py-op">+</tt> <tt id="link-167" class="py-name"><a title="Bio.expressions.blast.wublast.ending" class="py-name" href="#" onclick="return doclink('link-167', 'ending', 'link-23');">ending</a></tt><tt class="py-op">,</tt> <tt class="py-string">"BA"</tt> <tt class="py-op">+</tt> <tt id="link-168" class="py-name"><a title="Bio.expressions.blast.wublast.ending" class="py-name" href="#" onclick="return doclink('link-168', 'ending', 'link-23');">ending</a></tt> <tt class="py-op">+</tt> <tt class="py-string">"A"</tt> <tt class="py-op">+</tt> <tt id="link-169" class="py-name"><a title="Bio.expressions.blast.wublast.ending" class="py-name" href="#" onclick="return doclink('link-169', 'ending', 'link-23');">ending</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">repeat</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-number">15</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> <tt id="link-170" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-170', 's', 'link-9');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-name">base</tt> <tt class="py-op">*</tt> <tt class="py-name">repeat</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"> <tt class="py-name">infile</tt> <tt class="py-op">=</tt> <tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt id="link-171" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-171', 's', 'link-9');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">marker</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">"A"</tt><tt class="py-op">,</tt> <tt class="py-string">"A\n"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">look</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">5</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> <tt class="py-name">lookahead</tt> <tt class="py-op">=</tt> <tt class="py-name">base</tt> <tt class="py-op">*</tt> <tt class="py-name">look</tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">readhint</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">4</tt><tt class="py-op">,</tt> <tt class="py-number">10</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> <tt class="py-name">infile</tt><tt class="py-op">.</tt><tt id="link-172" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.seek
Bio.File.UndoHandle.seek
Martel.msre_parse.Tokenizer.seek" class="py-name" href="#" onclick="return doclink('link-172', 'seek', 'link-59');">seek</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> <tt class="py-name">reader</tt> <tt class="py-op">=</tt> <tt id="link-173" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-173', 'RecordReader', 'link-1');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-174" class="py-name"><a title="Martel.RecordReader.EndsWith" class="py-name" href="#" onclick="return doclink('link-174', 'EndsWith', 'link-120');">EndsWith</a></tt><tt class="py-op">(</tt>\ </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt class="py-name">infile</tt><tt class="py-op">,</tt> <tt class="py-name">marker</tt><tt class="py-op">,</tt> <tt class="py-name">readhint</tt><tt class="py-op">,</tt> <tt class="py-name">lookahead</tt><tt class="py-op">)</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> <tt id="link-175" 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-175', 'count', 'link-18');">count</a></tt> <tt class="py-op">=</tt> <tt id="link-176" class="py-name"><a title="Martel.test.test_RecordReader2.count_records" class="py-name" href="#" onclick="return doclink('link-176', 'count_records', 'link-19');">count_records</a></tt><tt class="py-op">(</tt><tt class="py-name">reader</tt><tt class="py-op">)</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-177" 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-177', 'count', 'link-18');">count</a></tt> <tt class="py-op">==</tt> <tt class="py-name">repeat</tt> <tt class="py-op">+</tt> <tt class="py-name">look</tt><tt class="py-op">,</tt> \ </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt id="link-178" 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-178', 'count', 'link-18');">count</a></tt><tt class="py-op">,</tt> <tt id="link-179" class="py-name"><a title="Bio.expressions.blast.wublast.ending" class="py-name" href="#" onclick="return doclink('link-179', 'ending', 'link-23');">ending</a></tt><tt class="py-op">,</tt> <tt class="py-name">base</tt><tt class="py-op">,</tt> <tt class="py-name">repeat</tt><tt class="py-op">,</tt> <tt class="py-name">marker</tt><tt class="py-op">,</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> <tt class="py-name">look</tt><tt class="py-op">,</tt> <tt class="py-name">readhint</tt><tt class="py-op">)</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> <tt class="py-name">infile</tt><tt class="py-op">.</tt><tt id="link-180" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.seek
Bio.File.UndoHandle.seek
Martel.msre_parse.Tokenizer.seek" class="py-name" href="#" onclick="return doclink('link-180', 'seek', 'link-59');">seek</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"> <tt class="py-name">reader</tt> <tt class="py-op">=</tt> <tt id="link-181" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-181', 'RecordReader', 'link-1');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-182" class="py-name"><a title="Martel.RecordReader.EndsWith" class="py-name" href="#" onclick="return doclink('link-182', 'EndsWith', 'link-120');">EndsWith</a></tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">,</tt> <tt class="py-name">marker</tt><tt class="py-op">,</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> <tt class="py-name">lookahead</tt> <tt class="py-op">=</tt> <tt class="py-name">lookahead</tt><tt class="py-op">)</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> <tt id="link-183" 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-183', 'count', 'link-18');">count</a></tt> <tt class="py-op">=</tt> <tt id="link-184" class="py-name"><a title="Martel.test.test_RecordReader2.count_records" class="py-name" href="#" onclick="return doclink('link-184', 'count_records', 'link-19');">count_records</a></tt><tt class="py-op">(</tt><tt class="py-name">reader</tt><tt class="py-op">)</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-185" 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-185', 'count', 'link-18');">count</a></tt> <tt class="py-op">==</tt> <tt class="py-name">repeat</tt> <tt class="py-op">+</tt> <tt class="py-name">look</tt><tt class="py-op">,</tt> \ </tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt id="link-186" 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-186', 'count', 'link-18');">count</a></tt><tt class="py-op">,</tt> <tt id="link-187" class="py-name"><a title="Bio.expressions.blast.wublast.ending" class="py-name" href="#" onclick="return doclink('link-187', 'ending', 'link-23');">ending</a></tt><tt class="py-op">,</tt> <tt class="py-name">repeat</tt><tt class="py-op">,</tt> <tt class="py-name">marker</tt><tt class="py-op">,</tt> <tt class="py-name">look</tt><tt class="py-op">)</tt> </tt>
</div><a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> </tt>
<a name="test_endswith_remainder"></a><div id="test_endswith_remainder-def"><a name="L253"></a><tt class="py-lineno">253</tt> <a class="py-toggle" href="#" id="test_endswith_remainder-toggle" onclick="return toggle('test_endswith_remainder');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.test.test_RecordReader2-module.html#test_endswith_remainder">test_endswith_remainder</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="test_endswith_remainder-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="test_endswith_remainder-expanded"><a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"> <tt class="py-comment"># Make sure the remainder method works</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt class="py-name">repeat</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">20</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> <tt class="py-name">vals</tt> <tt class="py-op">=</tt> <tt id="link-188" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-188', 'map', 'link-75');">map</a></tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-189" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-189', 'x', 'link-3');">x</a></tt><tt class="py-op">:</tt> <tt class="py-string">"%d\nA\n"</tt> <tt class="py-op">%</tt> <tt id="link-190" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-190', 'x', 'link-3');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">repeat</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"> <tt id="link-191" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-191', 'data', 'link-78');">data</a></tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">vals</tt><tt class="py-op">,</tt> <tt class="py-string">""</tt><tt class="py-op">)</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> <tt class="py-name">infile</tt> <tt class="py-op">=</tt> <tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt id="link-192" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-192', 'data', 'link-78');">data</a></tt><tt class="py-op">)</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">look</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</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-name">range</tt><tt class="py-op">(</tt><tt class="py-number">10</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-193" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-193', 'data', 'link-78');">data</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-number">5</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"> <tt class="py-name">infile</tt><tt class="py-op">.</tt><tt id="link-194" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.seek
Bio.File.UndoHandle.seek
Martel.msre_parse.Tokenizer.seek" class="py-name" href="#" onclick="return doclink('link-194', 'seek', 'link-59');">seek</a></tt><tt class="py-op">(</tt><tt class="py-name">look</tt><tt class="py-op">)</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> <tt class="py-name">lookahead</tt> <tt class="py-op">=</tt> <tt id="link-195" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-195', 'data', 'link-78');">data</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-name">look</tt><tt class="py-op">]</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> <tt class="py-name">reader</tt> <tt class="py-op">=</tt> <tt id="link-196" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-196', 'RecordReader', 'link-1');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-197" class="py-name"><a title="Martel.RecordReader.EndsWith" class="py-name" href="#" onclick="return doclink('link-197', 'EndsWith', 'link-120');">EndsWith</a></tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">,</tt> <tt class="py-string">"A"</tt><tt class="py-op">,</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"> <tt class="py-name">lookahead</tt> <tt class="py-op">=</tt> <tt class="py-name">lookahead</tt><tt class="py-op">)</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> <tt class="py-name">all</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> <tt class="py-name">file</tt><tt class="py-op">,</tt> <tt class="py-name">lh</tt> <tt class="py-op">=</tt> <tt class="py-name">reader</tt><tt class="py-op">.</tt><tt id="link-198" class="py-name"><a title="Bio.Affy.CelFile.remainder
Bio.LogisticRegression.remainder
Bio.MarkovModel.remainder
Bio.MaxEntropy.remainder
Bio.NaiveBayes.remainder
Bio.Statistics.lowess.remainder
Bio.distance.remainder
Bio.kNN.remainder
Martel.RecordReader.CountLines.remainder
Martel.RecordReader.EndsWith.remainder
Martel.RecordReader.Everything.remainder
Martel.RecordReader.Nothing.remainder
Martel.RecordReader.RecordReader.remainder
Martel.RecordReader.StartsWith.remainder
Martel.RecordReader.Until.remainder" class="py-name" href="#" onclick="return doclink('link-198', 'remainder', 'link-85');">remainder</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> <tt class="py-name">pos</tt> <tt class="py-op">=</tt> <tt class="py-name">file</tt><tt class="py-op">.</tt><tt id="link-199" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.tell
Bio.File.UndoHandle.tell
Martel.msre_parse.Tokenizer.tell" class="py-name" href="#" onclick="return doclink('link-199', 'tell', 'link-86');">tell</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"> <tt id="link-200" class="py-name"><a title="Bio.Nexus.Nexus.CharBuffer.rest" class="py-name" href="#" onclick="return doclink('link-200', 'rest', 'link-87');">rest</a></tt> <tt class="py-op">=</tt> <tt class="py-name">file</tt><tt class="py-op">.</tt><tt id="link-201" 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-201', 'read', 'link-88');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">all</tt> <tt class="py-op">+</tt> <tt class="py-name">lh</tt> <tt class="py-op">+</tt> <tt id="link-202" class="py-name"><a title="Bio.Nexus.Nexus.CharBuffer.rest" class="py-name" href="#" onclick="return doclink('link-202', 'rest', 'link-87');">rest</a></tt> <tt class="py-op">==</tt> <tt id="link-203" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-203', 'data', 'link-78');">data</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">all</tt><tt class="py-op">,</tt> <tt class="py-name">lh</tt><tt class="py-op">,</tt> <tt id="link-204" class="py-name"><a title="Bio.Nexus.Nexus.CharBuffer.rest" class="py-name" href="#" onclick="return doclink('link-204', 'rest', 'link-87');">rest</a></tt><tt class="py-op">,</tt> <tt id="link-205" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-205', 'data', 'link-78');">data</a></tt><tt class="py-op">)</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"> <tt class="py-name">file</tt><tt class="py-op">.</tt><tt id="link-206" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.seek
Bio.File.UndoHandle.seek
Martel.msre_parse.Tokenizer.seek" class="py-name" href="#" onclick="return doclink('link-206', 'seek', 'link-59');">seek</a></tt><tt class="py-op">(</tt><tt class="py-name">pos</tt><tt class="py-op">)</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-207" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-207', 'data', 'link-78');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-name">all</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt id="link-208" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-208', 'data', 'link-78');">data</a></tt><tt class="py-op">,</tt> <tt class="py-name">all</tt><tt class="py-op">)</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> <tt id="link-209" 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-209', 'record', 'link-96');">record</a></tt> <tt class="py-op">=</tt> <tt class="py-name">reader</tt><tt class="py-op">.</tt><tt id="link-210" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-210', 'next', 'link-4');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-211" 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-211', 'record', 'link-96');">record</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"> <tt class="py-name">all</tt> <tt class="py-op">=</tt> <tt class="py-name">all</tt> <tt class="py-op">+</tt> <tt id="link-212" 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-212', 'record', 'link-96');">record</a></tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">all</tt> <tt class="py-op">==</tt> <tt id="link-213" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-213', 'data', 'link-78');">data</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">all</tt><tt class="py-op">,</tt> <tt id="link-214" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-214', 'data', 'link-78');">data</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"> </tt>
<a name="test_endswith_errors"></a><div id="test_endswith_errors-def"><a name="L278"></a><tt class="py-lineno">278</tt> <a class="py-toggle" href="#" id="test_endswith_errors-toggle" onclick="return toggle('test_endswith_errors');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.test.test_RecordReader2-module.html#test_endswith_errors">test_endswith_errors</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="test_endswith_errors-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="test_endswith_errors-expanded"><a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"> <tt class="py-comment"># Check the failure cases.</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"> <tt class="py-comment"># Could no record at all</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Could be some records followed by an incomplete record</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Could be a line which partially matches the data</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt id="link-215" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-215', 's', 'link-9');">s</a></tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">"B"</tt><tt class="py-op">,</tt> <tt class="py-string">"B\n"</tt><tt class="py-op">,</tt> <tt class="py-string">"A\nB\n"</tt><tt class="py-op">,</tt> <tt class="py-string">"A\nB\nA\nB\n"</tt><tt class="py-op">,</tt> <tt class="py-string">"A\nB\nA\n "</tt><tt class="py-op">,</tt> <tt class="py-string">"AA"</tt><tt class="py-op">,</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"> <tt class="py-string">"AA\n"</tt><tt class="py-op">,</tt> <tt class="py-string">"A\nB\nA X\n"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"> <tt class="py-name">has_error</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"> <tt class="py-name">infile</tt> <tt class="py-op">=</tt> <tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt id="link-216" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-216', 's', 'link-9');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"> <tt class="py-name">reader</tt> <tt class="py-op">=</tt> <tt id="link-217" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-217', 'RecordReader', 'link-1');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-218" class="py-name"><a title="Martel.RecordReader.EndsWith" class="py-name" href="#" onclick="return doclink('link-218', 'EndsWith', 'link-120');">EndsWith</a></tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">,</tt> <tt class="py-string">"A\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt id="link-219" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-219', 'RecordReader', 'link-1');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-220" class="py-name"><a title="Martel.RecordReader.ReaderError" class="py-name" href="#" onclick="return doclink('link-220', 'ReaderError', 'link-109');">ReaderError</a></tt><tt class="py-op">:</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"> <tt class="py-name">has_error</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">has_error</tt><tt class="py-op">:</tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-keyword">not</tt> <tt class="py-name">has_error</tt><tt class="py-op">:</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"> <tt class="py-name">rec</tt> <tt class="py-op">=</tt> <tt class="py-name">reader</tt><tt class="py-op">.</tt><tt id="link-221" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-221', 'next', 'link-4');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt id="link-222" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-222', 'RecordReader', 'link-1');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-223" class="py-name"><a title="Martel.RecordReader.ReaderError" class="py-name" href="#" onclick="return doclink('link-223', 'ReaderError', 'link-109');">ReaderError</a></tt><tt class="py-op">:</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"> <tt class="py-name">has_error</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">has_error</tt> <tt class="py-keyword">and</tt> <tt class="py-name">rec</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">has_error</tt><tt class="py-op">:</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">AssertionError</tt><tt class="py-op">,</tt> <tt class="py-string">"should not get here with %r"</tt> <tt class="py-op">%</tt> <tt id="link-224" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-224', 's', 'link-9');">s</a></tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"> <tt class="py-comment"># Could no record at all</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Could be some records followed by an incomplete record</tt> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># *Allowed* to read rest of line</tt> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt id="link-225" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-225', 's', 'link-9');">s</a></tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">"B"</tt><tt class="py-op">,</tt> <tt class="py-string">"B\n"</tt><tt class="py-op">,</tt> <tt class="py-string">"A\nB\n"</tt><tt class="py-op">,</tt> <tt class="py-string">"A\nB\nA\nB\n"</tt><tt class="py-op">,</tt> <tt class="py-string">"A\nB\nA\n "</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"> <tt class="py-name">has_error</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"> <tt class="py-name">infile</tt> <tt class="py-op">=</tt> <tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt id="link-226" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-226', 's', 'link-9');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"> <tt class="py-name">reader</tt> <tt class="py-op">=</tt> <tt id="link-227" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-227', 'RecordReader', 'link-1');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-228" class="py-name"><a title="Martel.RecordReader.EndsWith" class="py-name" href="#" onclick="return doclink('link-228', 'EndsWith', 'link-120');">EndsWith</a></tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">,</tt> <tt class="py-string">"A"</tt><tt class="py-op">)</tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt id="link-229" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-229', 'RecordReader', 'link-1');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-230" class="py-name"><a title="Martel.RecordReader.ReaderError" class="py-name" href="#" onclick="return doclink('link-230', 'ReaderError', 'link-109');">ReaderError</a></tt><tt class="py-op">:</tt> </tt>
<a name="L313"></a><tt class="py-lineno">313</tt> <tt class="py-line"> <tt class="py-name">has_error</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">has_error</tt><tt class="py-op">:</tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-keyword">not</tt> <tt class="py-name">has_error</tt><tt class="py-op">:</tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"> <tt class="py-name">rec</tt> <tt class="py-op">=</tt> <tt class="py-name">reader</tt><tt class="py-op">.</tt><tt id="link-231" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-231', 'next', 'link-4');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt id="link-232" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-232', 'RecordReader', 'link-1');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-233" class="py-name"><a title="Martel.RecordReader.ReaderError" class="py-name" href="#" onclick="return doclink('link-233', 'ReaderError', 'link-109');">ReaderError</a></tt><tt class="py-op">:</tt> </tt>
<a name="L320"></a><tt class="py-lineno">320</tt> <tt class="py-line"> <tt class="py-name">has_error</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">has_error</tt> <tt class="py-keyword">and</tt> <tt class="py-name">rec</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">has_error</tt><tt class="py-op">:</tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">AssertionError</tt><tt class="py-op">,</tt> <tt class="py-string">"should not get here with %r"</tt> <tt class="py-op">%</tt> <tt id="link-234" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-234', 's', 'link-9');">s</a></tt> </tt>
</div><a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"> </tt>
<a name="test_endswith"></a><div id="test_endswith-def"><a name="L328"></a><tt class="py-lineno">328</tt> <a class="py-toggle" href="#" id="test_endswith-toggle" onclick="return toggle('test_endswith');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.test.test_RecordReader2-module.html#test_endswith">test_endswith</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="test_endswith-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="test_endswith-expanded"><a name="L329"></a><tt class="py-lineno">329</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"Testing EndsWith"</tt> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">" ... generic"</tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"> <tt id="link-235" class="py-name" targets="Function Martel.test.test_RecordReader2.test_endswith_generic()=Martel.test.test_RecordReader2-module.html#test_endswith_generic"><a title="Martel.test.test_RecordReader2.test_endswith_generic" class="py-name" href="#" onclick="return doclink('link-235', 'test_endswith_generic', 'link-235');">test_endswith_generic</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">" ... newline variations"</tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"> <tt id="link-236" class="py-name" targets="Function Martel.test.test_RecordReader2.test_endswith_SP()=Martel.test.test_RecordReader2-module.html#test_endswith_SP"><a title="Martel.test.test_RecordReader2.test_endswith_SP" class="py-name" href="#" onclick="return doclink('link-236', 'test_endswith_SP', 'link-236');">test_endswith_SP</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-237" class="py-name"><a title="Bio.expressions.blast.wublast.ending" class="py-name" href="#" onclick="return doclink('link-237', 'ending', 'link-23');">ending</a></tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">"\n"</tt><tt class="py-op">,</tt> <tt class="py-string">"\r"</tt><tt class="py-op">,</tt> <tt class="py-string">"\r\n"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">" ... exhaustive testing against %r"</tt> <tt class="py-op">%</tt> <tt id="link-238" class="py-name"><a title="Bio.expressions.blast.wublast.ending" class="py-name" href="#" onclick="return doclink('link-238', 'ending', 'link-23');">ending</a></tt> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt> <tt class="py-line"> <tt id="link-239" class="py-name" targets="Function Martel.test.test_RecordReader2.test_endswith_exhaustive()=Martel.test.test_RecordReader2-module.html#test_endswith_exhaustive"><a title="Martel.test.test_RecordReader2.test_endswith_exhaustive" class="py-name" href="#" onclick="return doclink('link-239', 'test_endswith_exhaustive', 'link-239');">test_endswith_exhaustive</a></tt><tt class="py-op">(</tt><tt id="link-240" class="py-name"><a title="Bio.expressions.blast.wublast.ending" class="py-name" href="#" onclick="return doclink('link-240', 'ending', 'link-23');">ending</a></tt><tt class="py-op">)</tt> </tt>
<a name="L340"></a><tt class="py-lineno">340</tt> <tt class="py-line"> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">" ... remainder"</tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt> <tt class="py-line"> <tt id="link-241" class="py-name" targets="Function Martel.test.test_RecordReader2.test_endswith_remainder()=Martel.test.test_RecordReader2-module.html#test_endswith_remainder"><a title="Martel.test.test_RecordReader2.test_endswith_remainder" class="py-name" href="#" onclick="return doclink('link-241', 'test_endswith_remainder', 'link-241');">test_endswith_remainder</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt> <tt class="py-line"> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">" ... format errors"</tt> </tt>
<a name="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"> <tt id="link-242" class="py-name" targets="Function Martel.test.test_RecordReader2.test_endswith_errors()=Martel.test.test_RecordReader2-module.html#test_endswith_errors"><a title="Martel.test.test_RecordReader2.test_endswith_errors" class="py-name" href="#" onclick="return doclink('link-242', 'test_endswith_errors', 'link-242');">test_endswith_errors</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L346"></a><tt class="py-lineno">346</tt> <tt class="py-line"> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt> <tt class="py-line"><tt class="py-comment">### Until</tt> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt> <tt class="py-line"><tt class="py-comment"># Don't need to do that much testing since the code is built on</tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># top of the StartsWith reader, which has already been tested.</tt> </tt>
<a name="test_until"></a><div id="test_until-def"><a name="L351"></a><tt class="py-lineno">351</tt> <a class="py-toggle" href="#" id="test_until-toggle" onclick="return toggle('test_until');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.test.test_RecordReader2-module.html#test_until">test_until</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="test_until-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="test_until-expanded"><a name="L352"></a><tt class="py-lineno">352</tt> <tt class="py-line"> <tt class="py-comment"># Can only read at most one record</tt> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">print</tt> <tt class="py-string">"Testing Until"</tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt> <tt class="py-line"> <tt class="py-name">test_data</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-string">"A"</tt><tt class="py-op">,</tt> </tt>
<a name="L355"></a><tt class="py-lineno">355</tt> <tt class="py-line"> <tt class="py-string">"A\n"</tt><tt class="py-op">,</tt> </tt>
<a name="L356"></a><tt class="py-lineno">356</tt> <tt class="py-line"> <tt class="py-string">"A\nB"</tt><tt class="py-op">,</tt> </tt>
<a name="L357"></a><tt class="py-lineno">357</tt> <tt class="py-line"> <tt class="py-string">"A\nB\n"</tt><tt class="py-op">,</tt> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt> <tt class="py-line"> <tt class="py-string">"A\nBCDE\nQWE\nTRYU\nA\n"</tt><tt class="py-op">,</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt> <tt class="py-line"> <tt class="py-string">"A\nA\nA\nA\nA\nA\nA\n"</tt><tt class="py-op">,</tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt> <tt class="py-line"> <tt class="py-string">"AB"</tt><tt class="py-op">,</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt> <tt class="py-line"> <tt class="py-string">"AB\n"</tt><tt class="py-op">,</tt> </tt>
<a name="L362"></a><tt class="py-lineno">362</tt> <tt class="py-line"> <tt class="py-string">"AB\nAC"</tt><tt class="py-op">,</tt> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt> <tt class="py-line"> <tt class="py-string">"AB\nAC\n"</tt><tt class="py-op">,</tt> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt> <tt class="py-line"> </tt>
<a name="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-243" class="py-name"><a title="Bio.expressions.blast.wublast.ending" class="py-name" href="#" onclick="return doclink('link-243', 'ending', 'link-23');">ending</a></tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">"\n"</tt><tt class="py-op">,</tt> <tt class="py-string">"\r"</tt><tt class="py-op">,</tt> <tt class="py-string">"\r\n"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">pre</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">""</tt><tt class="py-op">,</tt> <tt class="py-string">"B\n"</tt><tt class="py-op">,</tt> <tt class="py-string">"BA\n"</tt><tt class="py-op">,</tt> <tt class="py-string">"CA\nBA\n"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt> <tt class="py-line"> <tt class="py-name">pre_nl</tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-name">pre</tt><tt class="py-op">,</tt> <tt class="py-string">"\n"</tt><tt class="py-op">,</tt> <tt id="link-244" class="py-name"><a title="Bio.expressions.blast.wublast.ending" class="py-name" href="#" onclick="return doclink('link-244', 'ending', 'link-23');">ending</a></tt><tt class="py-op">)</tt> </tt>
<a name="L369"></a><tt class="py-lineno">369</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">look</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-number">3</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L370"></a><tt class="py-lineno">370</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-245" 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-245', 'text', 'link-245');">text</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">test_data</tt><tt class="py-op">:</tt> </tt>
<a name="L371"></a><tt class="py-lineno">371</tt> <tt class="py-line"> <tt class="py-name">text_nl</tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt id="link-246" 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-246', 'text', 'link-245');">text</a></tt><tt class="py-op">,</tt> <tt class="py-string">"\n"</tt><tt class="py-op">,</tt> <tt id="link-247" class="py-name"><a title="Bio.expressions.blast.wublast.ending" class="py-name" href="#" onclick="return doclink('link-247', 'ending', 'link-23');">ending</a></tt><tt class="py-op">)</tt> </tt>
<a name="L372"></a><tt class="py-lineno">372</tt> <tt class="py-line"> <tt id="link-248" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-248', 's', 'link-9');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-name">pre_nl</tt> <tt class="py-op">+</tt> <tt class="py-name">text_nl</tt> </tt>
<a name="L373"></a><tt class="py-lineno">373</tt> <tt class="py-line"> <tt class="py-name">reader</tt> <tt class="py-op">=</tt> <tt id="link-249" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-249', 'RecordReader', 'link-1');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-250" class="py-name" targets="Class Martel.RecordReader.Until=Martel.RecordReader.Until-class.html"><a title="Martel.RecordReader.Until" class="py-name" href="#" onclick="return doclink('link-250', 'Until', 'link-250');">Until</a></tt><tt class="py-op">(</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt id="link-251" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-251', 's', 'link-9');">s</a></tt><tt class="py-op">[</tt><tt class="py-name">look</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L374"></a><tt class="py-lineno">374</tt> <tt class="py-line"> <tt class="py-string">"A"</tt><tt class="py-op">,</tt> </tt>
<a name="L375"></a><tt class="py-lineno">375</tt> <tt class="py-line"> <tt class="py-name">lookahead</tt> <tt class="py-op">=</tt> <tt id="link-252" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-252', 's', 'link-9');">s</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-name">look</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L376"></a><tt class="py-lineno">376</tt> <tt class="py-line"> <tt class="py-name">sizehint</tt> <tt class="py-op">=</tt> <tt class="py-number">4</tt><tt class="py-op">)</tt> </tt>
<a name="L377"></a><tt class="py-lineno">377</tt> <tt class="py-line"> <tt class="py-name">found_record</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L378"></a><tt class="py-lineno">378</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L379"></a><tt class="py-lineno">379</tt> <tt class="py-line"> <tt class="py-name">rec</tt> <tt class="py-op">=</tt> <tt class="py-name">reader</tt><tt class="py-op">.</tt><tt id="link-253" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-253', 'next', 'link-4');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L380"></a><tt class="py-lineno">380</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">rec</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L381"></a><tt class="py-lineno">381</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L382"></a><tt class="py-lineno">382</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-keyword">not</tt> <tt class="py-name">found_record</tt><tt class="py-op">,</tt> \ </tt>
<a name="L383"></a><tt class="py-lineno">383</tt> <tt class="py-line"> <tt class="py-string">"Already found %r but also found %r in %r"</tt> <tt class="py-op">%</tt> \ </tt>
<a name="L384"></a><tt class="py-lineno">384</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">found_record</tt><tt class="py-op">,</tt> <tt class="py-name">rec</tt><tt class="py-op">,</tt> <tt id="link-254" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-254', 's', 'link-9');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L385"></a><tt class="py-lineno">385</tt> <tt class="py-line"> <tt class="py-name">found_record</tt> <tt class="py-op">=</tt> <tt class="py-name">rec</tt> </tt>
<a name="L386"></a><tt class="py-lineno">386</tt> <tt class="py-line"> </tt>
<a name="L387"></a><tt class="py-lineno">387</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">found_record</tt> <tt class="py-op">==</tt> <tt class="py-name">pre_nl</tt><tt class="py-op">,</tt> \ </tt>
<a name="L388"></a><tt class="py-lineno">388</tt> <tt class="py-line"> <tt class="py-string">"Expecting record %r, found %r in %r"</tt> <tt class="py-op">%</tt> \ </tt>
<a name="L389"></a><tt class="py-lineno">389</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">pre_nl</tt><tt class="py-op">,</tt> <tt class="py-name">found_record</tt><tt class="py-op">,</tt> <tt id="link-255" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-255', 's', 'link-9');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L390"></a><tt class="py-lineno">390</tt> <tt class="py-line"> <tt class="py-name">infile</tt><tt class="py-op">,</tt> <tt id="link-256" class="py-name"><a title="Bio.Affy.CelFile.remainder
Bio.LogisticRegression.remainder
Bio.MarkovModel.remainder
Bio.MaxEntropy.remainder
Bio.NaiveBayes.remainder
Bio.Statistics.lowess.remainder
Bio.distance.remainder
Bio.kNN.remainder
Martel.RecordReader.CountLines.remainder
Martel.RecordReader.EndsWith.remainder
Martel.RecordReader.Everything.remainder
Martel.RecordReader.Nothing.remainder
Martel.RecordReader.RecordReader.remainder
Martel.RecordReader.StartsWith.remainder
Martel.RecordReader.Until.remainder" class="py-name" href="#" onclick="return doclink('link-256', 'remainder', 'link-85');">remainder</a></tt> <tt class="py-op">=</tt> <tt class="py-name">reader</tt><tt class="py-op">.</tt><tt id="link-257" class="py-name"><a title="Bio.Affy.CelFile.remainder
Bio.LogisticRegression.remainder
Bio.MarkovModel.remainder
Bio.MaxEntropy.remainder
Bio.NaiveBayes.remainder
Bio.Statistics.lowess.remainder
Bio.distance.remainder
Bio.kNN.remainder
Martel.RecordReader.CountLines.remainder
Martel.RecordReader.EndsWith.remainder
Martel.RecordReader.Everything.remainder
Martel.RecordReader.Nothing.remainder
Martel.RecordReader.RecordReader.remainder
Martel.RecordReader.StartsWith.remainder
Martel.RecordReader.Until.remainder" class="py-name" href="#" onclick="return doclink('link-257', 'remainder', 'link-85');">remainder</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L391"></a><tt class="py-lineno">391</tt> <tt class="py-line"> <tt id="link-258" class="py-name"><a title="Bio.Affy.CelFile.remainder
Bio.LogisticRegression.remainder
Bio.MarkovModel.remainder
Bio.MaxEntropy.remainder
Bio.NaiveBayes.remainder
Bio.Statistics.lowess.remainder
Bio.distance.remainder
Bio.kNN.remainder
Martel.RecordReader.CountLines.remainder
Martel.RecordReader.EndsWith.remainder
Martel.RecordReader.Everything.remainder
Martel.RecordReader.Nothing.remainder
Martel.RecordReader.RecordReader.remainder
Martel.RecordReader.StartsWith.remainder
Martel.RecordReader.Until.remainder" class="py-name" href="#" onclick="return doclink('link-258', 'remainder', 'link-85');">remainder</a></tt> <tt class="py-op">=</tt> <tt id="link-259" class="py-name"><a title="Bio.Affy.CelFile.remainder
Bio.LogisticRegression.remainder
Bio.MarkovModel.remainder
Bio.MaxEntropy.remainder
Bio.NaiveBayes.remainder
Bio.Statistics.lowess.remainder
Bio.distance.remainder
Bio.kNN.remainder
Martel.RecordReader.CountLines.remainder
Martel.RecordReader.EndsWith.remainder
Martel.RecordReader.Everything.remainder
Martel.RecordReader.Nothing.remainder
Martel.RecordReader.RecordReader.remainder
Martel.RecordReader.StartsWith.remainder
Martel.RecordReader.Until.remainder" class="py-name" href="#" onclick="return doclink('link-259', 'remainder', 'link-85');">remainder</a></tt> <tt class="py-op">+</tt> <tt class="py-name">infile</tt><tt class="py-op">.</tt><tt id="link-260" 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-260', 'read', 'link-88');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L392"></a><tt class="py-lineno">392</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-261" class="py-name"><a title="Bio.Affy.CelFile.remainder
Bio.LogisticRegression.remainder
Bio.MarkovModel.remainder
Bio.MaxEntropy.remainder
Bio.NaiveBayes.remainder
Bio.Statistics.lowess.remainder
Bio.distance.remainder
Bio.kNN.remainder
Martel.RecordReader.CountLines.remainder
Martel.RecordReader.EndsWith.remainder
Martel.RecordReader.Everything.remainder
Martel.RecordReader.Nothing.remainder
Martel.RecordReader.RecordReader.remainder
Martel.RecordReader.StartsWith.remainder
Martel.RecordReader.Until.remainder" class="py-name" href="#" onclick="return doclink('link-261', 'remainder', 'link-85');">remainder</a></tt> <tt class="py-op">==</tt> <tt class="py-name">text_nl</tt><tt class="py-op">,</tt> \ </tt>
<a name="L393"></a><tt class="py-lineno">393</tt> <tt class="py-line"> <tt class="py-string">"Expecting remainder %r, found %r in %r"</tt> <tt class="py-op">%</tt> \ </tt>
<a name="L394"></a><tt class="py-lineno">394</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">text_nl</tt><tt class="py-op">,</tt> <tt id="link-262" class="py-name"><a title="Bio.Affy.CelFile.remainder
Bio.LogisticRegression.remainder
Bio.MarkovModel.remainder
Bio.MaxEntropy.remainder
Bio.NaiveBayes.remainder
Bio.Statistics.lowess.remainder
Bio.distance.remainder
Bio.kNN.remainder
Martel.RecordReader.CountLines.remainder
Martel.RecordReader.EndsWith.remainder
Martel.RecordReader.Everything.remainder
Martel.RecordReader.Nothing.remainder
Martel.RecordReader.RecordReader.remainder
Martel.RecordReader.StartsWith.remainder
Martel.RecordReader.Until.remainder" class="py-name" href="#" onclick="return doclink('link-262', 'remainder', 'link-85');">remainder</a></tt><tt class="py-op">,</tt> <tt id="link-263" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-263', 's', 'link-9');">s</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L395"></a><tt class="py-lineno">395</tt> <tt class="py-line"> </tt>
<a name="L396"></a><tt class="py-lineno">396</tt> <tt class="py-line"><tt class="py-comment">### CountLines</tt> </tt>
<a name="L397"></a><tt class="py-lineno">397</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="test_count_lines"></a><div id="test_count_lines-def"><a name="L398"></a><tt class="py-lineno">398</tt> <a class="py-toggle" href="#" id="test_count_lines-toggle" onclick="return toggle('test_count_lines');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.test.test_RecordReader2-module.html#test_count_lines">test_count_lines</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="test_count_lines-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="test_count_lines-expanded"><a name="L399"></a><tt class="py-lineno">399</tt> <tt class="py-line"> <tt class="py-comment"># Create a set of 'i' lines and read 'count' lines at a time.</tt> </tt>
<a name="L400"></a><tt class="py-lineno">400</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Either count divides i or it doesn't. If it does, the reader</tt> </tt>
<a name="L401"></a><tt class="py-lineno">401</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># should go to completion. If it does not, the reader should</tt> </tt>
<a name="L402"></a><tt class="py-lineno">402</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># have a remainder whose size can be verified.</tt> </tt>
<a name="L403"></a><tt class="py-lineno">403</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L404"></a><tt class="py-lineno">404</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"Testing CountLines"</tt> </tt>
<a name="L405"></a><tt class="py-lineno">405</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-264" class="py-name"><a title="Bio.expressions.blast.wublast.ending" class="py-name" href="#" onclick="return doclink('link-264', 'ending', 'link-23');">ending</a></tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">"\n"</tt><tt class="py-op">,</tt> <tt class="py-string">"\r"</tt><tt class="py-op">,</tt> <tt class="py-string">"\r\n"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L406"></a><tt class="py-lineno">406</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">" ... exhaustive testing against %r"</tt> <tt class="py-op">%</tt> <tt id="link-265" class="py-name"><a title="Bio.expressions.blast.wublast.ending" class="py-name" href="#" onclick="return doclink('link-265', 'ending', 'link-23');">ending</a></tt> </tt>
<a name="L407"></a><tt class="py-lineno">407</tt> <tt class="py-line"> <tt id="link-266" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-266', 's', 'link-9');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L408"></a><tt class="py-lineno">408</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-267" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-267', 'i', 'link-2');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">25</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L409"></a><tt class="py-lineno">409</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-268" 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-268', 'count', 'link-18');">count</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt id="link-269" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-269', 'i', 'link-2');">i</a></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="L410"></a><tt class="py-lineno">410</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">look</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">2</tt><tt class="py-op">,</tt> <tt class="py-number">5</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L411"></a><tt class="py-lineno">411</tt> <tt class="py-line"> <tt class="py-name">rep</tt><tt class="py-op">,</tt> <tt class="py-name">final</tt> <tt class="py-op">=</tt> <tt class="py-name">divmod</tt><tt class="py-op">(</tt><tt id="link-270" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-270', 'i', 'link-2');">i</a></tt><tt class="py-op">,</tt> <tt id="link-271" 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-271', 'count', 'link-18');">count</a></tt><tt class="py-op">)</tt> </tt>
<a name="L412"></a><tt class="py-lineno">412</tt> <tt class="py-line"> <tt class="py-name">reader</tt> <tt class="py-op">=</tt> <tt id="link-272" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-272', 'RecordReader', 'link-1');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-273" 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-273', 'CountLines', 'link-273');">CountLines</a></tt><tt class="py-op">(</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt id="link-274" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-274', 's', 'link-9');">s</a></tt><tt class="py-op">[</tt><tt class="py-name">look</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L413"></a><tt class="py-lineno">413</tt> <tt class="py-line"> <tt id="link-275" 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-275', 'count', 'link-18');">count</a></tt><tt class="py-op">,</tt> </tt>
<a name="L414"></a><tt class="py-lineno">414</tt> <tt class="py-line"> <tt class="py-name">lookahead</tt> <tt class="py-op">=</tt> <tt id="link-276" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-276', 's', 'link-9');">s</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-name">look</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L415"></a><tt class="py-lineno">415</tt> <tt class="py-line"> <tt class="py-name">sizehint</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L416"></a><tt class="py-lineno">416</tt> <tt class="py-line"> <tt class="py-name">all</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L417"></a><tt class="py-lineno">417</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-name">rep</tt> <tt class="py-op">></tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L418"></a><tt class="py-lineno">418</tt> <tt class="py-line"> <tt class="py-name">rec</tt> <tt class="py-op">=</tt> <tt class="py-name">reader</tt><tt class="py-op">.</tt><tt id="link-277" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-277', 'next', 'link-4');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L419"></a><tt class="py-lineno">419</tt> <tt class="py-line"> <tt class="py-name">lines</tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt id="link-278" class="py-name" targets="Method Bio.Nexus.Trees.Tree.split()=Bio.Nexus.Trees.Tree-class.html#split,Method Bio.Restriction.Restriction.RestrictionBatch.split()=Bio.Restriction.Restriction.RestrictionBatch-class.html#split"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-278', 'split', 'link-278');">split</a></tt><tt class="py-op">(</tt><tt class="py-name">rec</tt><tt class="py-op">,</tt> <tt id="link-279" class="py-name"><a title="Bio.expressions.blast.wublast.ending" class="py-name" href="#" onclick="return doclink('link-279', 'ending', 'link-23');">ending</a></tt><tt class="py-op">)</tt> </tt>
<a name="L420"></a><tt class="py-lineno">420</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">lines</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-number">1</tt> <tt class="py-op">==</tt> <tt id="link-280" 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-280', 'count', 'link-18');">count</a></tt><tt class="py-op">,</tt> \ </tt>
<a name="L421"></a><tt class="py-lineno">421</tt> <tt class="py-line"> <tt class="py-string">"Expecting %d lines, got %d in %r using %r"</tt> <tt class="py-op">%</tt> \ </tt>
<a name="L422"></a><tt class="py-lineno">422</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt id="link-281" 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-281', 'count', 'link-18');">count</a></tt><tt class="py-op">,</tt> <tt class="py-name">len</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 class="py-name">rec</tt><tt class="py-op">,</tt> <tt id="link-282" class="py-name"><a title="Bio.expressions.blast.wublast.ending" class="py-name" href="#" onclick="return doclink('link-282', 'ending', 'link-23');">ending</a></tt><tt class="py-op">)</tt> </tt>
<a name="L423"></a><tt class="py-lineno">423</tt> <tt class="py-line"> <tt class="py-name">all</tt> <tt class="py-op">=</tt> <tt class="py-name">all</tt> <tt class="py-op">+</tt> <tt class="py-name">rec</tt> </tt>
<a name="L424"></a><tt class="py-lineno">424</tt> <tt class="py-line"> <tt class="py-name">rep</tt> <tt class="py-op">=</tt> <tt class="py-name">rep</tt> <tt class="py-op">-</tt> <tt class="py-number">1</tt> </tt>
<a name="L425"></a><tt class="py-lineno">425</tt> <tt class="py-line"> </tt>
<a name="L426"></a><tt class="py-lineno">426</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">final</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L427"></a><tt class="py-lineno">427</tt> <tt class="py-line"> <tt class="py-comment"># Reader should be at the end of input</tt> </tt>
<a name="L428"></a><tt class="py-lineno">428</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">rec</tt> <tt class="py-op">=</tt> <tt class="py-name">reader</tt><tt class="py-op">.</tt><tt id="link-283" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-283', 'next', 'link-4');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L429"></a><tt class="py-lineno">429</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">rec</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> \ </tt>
<a name="L430"></a><tt class="py-lineno">430</tt> <tt class="py-line"> <tt class="py-string">"Should be at end of reader, got %r"</tt> <tt class="py-op">%</tt> <tt class="py-name">rec</tt> </tt>
<a name="L431"></a><tt class="py-lineno">431</tt> <tt class="py-line"> <tt class="py-name">rec</tt> <tt class="py-op">=</tt> <tt class="py-name">reader</tt><tt class="py-op">.</tt><tt id="link-284" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-284', 'next', 'link-4');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L432"></a><tt class="py-lineno">432</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">rec</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> \ </tt>
<a name="L433"></a><tt class="py-lineno">433</tt> <tt class="py-line"> <tt class="py-string">"data after end of reader, got %r"</tt> <tt class="py-op">%</tt> <tt class="py-name">rec</tt> </tt>
<a name="L434"></a><tt class="py-lineno">434</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L435"></a><tt class="py-lineno">435</tt> <tt class="py-line"> <tt class="py-comment"># There should be a remainder of size i % count lines</tt> </tt>
<a name="L436"></a><tt class="py-lineno">436</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">infile</tt><tt class="py-op">,</tt> <tt id="link-285" class="py-name"><a title="Bio.Affy.CelFile.remainder
Bio.LogisticRegression.remainder
Bio.MarkovModel.remainder
Bio.MaxEntropy.remainder
Bio.NaiveBayes.remainder
Bio.Statistics.lowess.remainder
Bio.distance.remainder
Bio.kNN.remainder
Martel.RecordReader.CountLines.remainder
Martel.RecordReader.EndsWith.remainder
Martel.RecordReader.Everything.remainder
Martel.RecordReader.Nothing.remainder
Martel.RecordReader.RecordReader.remainder
Martel.RecordReader.StartsWith.remainder
Martel.RecordReader.Until.remainder" class="py-name" href="#" onclick="return doclink('link-285', 'remainder', 'link-85');">remainder</a></tt> <tt class="py-op">=</tt> <tt class="py-name">reader</tt><tt class="py-op">.</tt><tt id="link-286" class="py-name"><a title="Bio.Affy.CelFile.remainder
Bio.LogisticRegression.remainder
Bio.MarkovModel.remainder
Bio.MaxEntropy.remainder
Bio.NaiveBayes.remainder
Bio.Statistics.lowess.remainder
Bio.distance.remainder
Bio.kNN.remainder
Martel.RecordReader.CountLines.remainder
Martel.RecordReader.EndsWith.remainder
Martel.RecordReader.Everything.remainder
Martel.RecordReader.Nothing.remainder
Martel.RecordReader.RecordReader.remainder
Martel.RecordReader.StartsWith.remainder
Martel.RecordReader.Until.remainder" class="py-name" href="#" onclick="return doclink('link-286', 'remainder', 'link-85');">remainder</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L437"></a><tt class="py-lineno">437</tt> <tt class="py-line"> <tt id="link-287" 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-287', 'text', 'link-245');">text</a></tt> <tt class="py-op">=</tt> <tt id="link-288" class="py-name"><a title="Bio.Affy.CelFile.remainder
Bio.LogisticRegression.remainder
Bio.MarkovModel.remainder
Bio.MaxEntropy.remainder
Bio.NaiveBayes.remainder
Bio.Statistics.lowess.remainder
Bio.distance.remainder
Bio.kNN.remainder
Martel.RecordReader.CountLines.remainder
Martel.RecordReader.EndsWith.remainder
Martel.RecordReader.Everything.remainder
Martel.RecordReader.Nothing.remainder
Martel.RecordReader.RecordReader.remainder
Martel.RecordReader.StartsWith.remainder
Martel.RecordReader.Until.remainder" class="py-name" href="#" onclick="return doclink('link-288', 'remainder', 'link-85');">remainder</a></tt> <tt class="py-op">+</tt> <tt class="py-name">infile</tt><tt class="py-op">.</tt><tt id="link-289" 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-289', 'read', 'link-88');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L438"></a><tt class="py-lineno">438</tt> <tt class="py-line"> <tt class="py-name">all</tt> <tt class="py-op">=</tt> <tt class="py-name">all</tt> <tt class="py-op">+</tt> <tt id="link-290" 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-290', 'text', 'link-245');">text</a></tt> </tt>
<a name="L439"></a><tt class="py-lineno">439</tt> <tt class="py-line"> <tt class="py-name">lines</tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt id="link-291" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-291', 'split', 'link-278');">split</a></tt><tt class="py-op">(</tt><tt id="link-292" 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-292', 'text', 'link-245');">text</a></tt><tt class="py-op">,</tt> <tt id="link-293" class="py-name"><a title="Bio.expressions.blast.wublast.ending" class="py-name" href="#" onclick="return doclink('link-293', 'ending', 'link-23');">ending</a></tt><tt class="py-op">)</tt> </tt>
<a name="L440"></a><tt class="py-lineno">440</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">lines</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-name">final</tt><tt class="py-op">,</tt> \ </tt>
<a name="L441"></a><tt class="py-lineno">441</tt> <tt class="py-line"> <tt class="py-string">"Expecting %d final lines, got %d"</tt> <tt class="py-op">%</tt> \ </tt>
<a name="L442"></a><tt class="py-lineno">442</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">final</tt><tt class="py-op">,</tt> <tt class="py-name">len</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="L443"></a><tt class="py-lineno">443</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L444"></a><tt class="py-lineno">444</tt> <tt class="py-line"> <tt class="py-name">rec</tt> <tt class="py-op">=</tt> <tt class="py-name">reader</tt><tt class="py-op">.</tt><tt id="link-294" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-294', 'next', 'link-4');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L445"></a><tt class="py-lineno">445</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">AssertionError</tt><tt class="py-op">,</tt> \ </tt>
<a name="L446"></a><tt class="py-lineno">446</tt> <tt class="py-line"> <tt class="py-string">"Got unexpected final record, %r"</tt> <tt class="py-op">%</tt> <tt class="py-name">rec</tt> </tt>
<a name="L447"></a><tt class="py-lineno">447</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt id="link-295" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-295', 'RecordReader', 'link-1');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-296" class="py-name"><a title="Martel.RecordReader.ReaderError" class="py-name" href="#" onclick="return doclink('link-296', 'ReaderError', 'link-109');">ReaderError</a></tt><tt class="py-op">:</tt> </tt>
<a name="L448"></a><tt class="py-lineno">448</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L449"></a><tt class="py-lineno">449</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">all</tt> <tt class="py-op">==</tt> <tt id="link-297" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-297', 's', 'link-9');">s</a></tt><tt class="py-op">,</tt> \ </tt>
<a name="L450"></a><tt class="py-lineno">450</tt> <tt class="py-line"> <tt class="py-string">"record data %r doesn't rebuild input %r"</tt> <tt class="py-op">%</tt> \ </tt>
<a name="L451"></a><tt class="py-lineno">451</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">all</tt><tt class="py-op">,</tt> <tt id="link-298" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-298', 's', 'link-9');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L452"></a><tt class="py-lineno">452</tt> <tt class="py-line"> <tt id="link-299" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-299', 's', 'link-9');">s</a></tt> <tt class="py-op">=</tt> <tt id="link-300" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-300', 's', 'link-9');">s</a></tt> <tt class="py-op">+</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-301" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-301', 'i', 'link-2');">i</a></tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-302" class="py-name"><a title="Bio.expressions.blast.wublast.ending" class="py-name" href="#" onclick="return doclink('link-302', 'ending', 'link-23');">ending</a></tt> </tt>
</div><a name="L453"></a><tt class="py-lineno">453</tt> <tt class="py-line"> </tt>
<a name="L454"></a><tt class="py-lineno">454</tt> <tt class="py-line"><tt class="py-comment">### Nothing</tt> </tt>
<a name="L455"></a><tt class="py-lineno">455</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="test_nothing"></a><div id="test_nothing-def"><a name="L456"></a><tt class="py-lineno">456</tt> <a class="py-toggle" href="#" id="test_nothing-toggle" onclick="return toggle('test_nothing');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.test.test_RecordReader2-module.html#test_nothing">test_nothing</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="test_nothing-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="test_nothing-expanded"><a name="L457"></a><tt class="py-lineno">457</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"Testing Nothing"</tt> </tt>
<a name="L458"></a><tt class="py-lineno">458</tt> <tt class="py-line"> </tt>
<a name="L459"></a><tt class="py-lineno">459</tt> <tt class="py-line"> <tt id="link-303" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-303', 's', 'link-9');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"This is a test.\nThis is only a test.\nHad this been an actual...\n"</tt> </tt>
<a name="L460"></a><tt class="py-lineno">460</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-304" class="py-name"><a title="Bio.expressions.blast.wublast.ending" class="py-name" href="#" onclick="return doclink('link-304', 'ending', 'link-23');">ending</a></tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">"\n"</tt><tt class="py-op">,</tt> <tt class="py-string">"\r"</tt><tt class="py-op">,</tt> <tt class="py-string">"\r\n"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L461"></a><tt class="py-lineno">461</tt> <tt class="py-line"> <tt id="link-305" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-305', 'data', 'link-78');">data</a></tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt id="link-306" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-306', 's', 'link-9');">s</a></tt><tt class="py-op">,</tt> <tt class="py-string">"\n"</tt><tt class="py-op">,</tt> <tt id="link-307" class="py-name"><a title="Bio.expressions.blast.wublast.ending" class="py-name" href="#" onclick="return doclink('link-307', 'ending', 'link-23');">ending</a></tt><tt class="py-op">)</tt> </tt>
<a name="L462"></a><tt class="py-lineno">462</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">look</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-number">2</tt><tt class="py-op">,</tt> <tt class="py-number">5</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L463"></a><tt class="py-lineno">463</tt> <tt class="py-line"> <tt class="py-name">reader</tt> <tt class="py-op">=</tt> <tt id="link-308" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-308', 'RecordReader', 'link-1');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-309" class="py-name" targets="Class Martel.RecordReader.Nothing=Martel.RecordReader.Nothing-class.html"><a title="Martel.RecordReader.Nothing" class="py-name" href="#" onclick="return doclink('link-309', 'Nothing', 'link-309');">Nothing</a></tt><tt class="py-op">(</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt id="link-310" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-310', 'data', 'link-78');">data</a></tt><tt class="py-op">[</tt><tt class="py-name">look</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L464"></a><tt class="py-lineno">464</tt> <tt class="py-line"> <tt class="py-name">sizehint</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> </tt>
<a name="L465"></a><tt class="py-lineno">465</tt> <tt class="py-line"> <tt class="py-name">lookahead</tt> <tt class="py-op">=</tt> <tt id="link-311" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-311', 'data', 'link-78');">data</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-name">look</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L466"></a><tt class="py-lineno">466</tt> <tt class="py-line"> <tt class="py-name">rec</tt> <tt class="py-op">=</tt> <tt class="py-name">reader</tt><tt class="py-op">.</tt><tt id="link-312" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-312', 'next', 'link-4');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L467"></a><tt class="py-lineno">467</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">rec</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-string">"should be empty, not %r"</tt> <tt class="py-op">%</tt> <tt class="py-name">rec</tt> </tt>
<a name="L468"></a><tt class="py-lineno">468</tt> <tt class="py-line"> <tt class="py-name">rec</tt> <tt class="py-op">=</tt> <tt class="py-name">reader</tt><tt class="py-op">.</tt><tt id="link-313" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-313', 'next', 'link-4');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L469"></a><tt class="py-lineno">469</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">rec</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-string">"2nd time should also be empty, not %r"</tt> <tt class="py-op">%</tt> <tt class="py-name">rec</tt> </tt>
<a name="L470"></a><tt class="py-lineno">470</tt> <tt class="py-line"> </tt>
<a name="L471"></a><tt class="py-lineno">471</tt> <tt class="py-line"> <tt class="py-name">infile</tt><tt class="py-op">,</tt> <tt id="link-314" class="py-name"><a title="Bio.Affy.CelFile.remainder
Bio.LogisticRegression.remainder
Bio.MarkovModel.remainder
Bio.MaxEntropy.remainder
Bio.NaiveBayes.remainder
Bio.Statistics.lowess.remainder
Bio.distance.remainder
Bio.kNN.remainder
Martel.RecordReader.CountLines.remainder
Martel.RecordReader.EndsWith.remainder
Martel.RecordReader.Everything.remainder
Martel.RecordReader.Nothing.remainder
Martel.RecordReader.RecordReader.remainder
Martel.RecordReader.StartsWith.remainder
Martel.RecordReader.Until.remainder" class="py-name" href="#" onclick="return doclink('link-314', 'remainder', 'link-85');">remainder</a></tt> <tt class="py-op">=</tt> <tt class="py-name">reader</tt><tt class="py-op">.</tt><tt id="link-315" class="py-name"><a title="Bio.Affy.CelFile.remainder
Bio.LogisticRegression.remainder
Bio.MarkovModel.remainder
Bio.MaxEntropy.remainder
Bio.NaiveBayes.remainder
Bio.Statistics.lowess.remainder
Bio.distance.remainder
Bio.kNN.remainder
Martel.RecordReader.CountLines.remainder
Martel.RecordReader.EndsWith.remainder
Martel.RecordReader.Everything.remainder
Martel.RecordReader.Nothing.remainder
Martel.RecordReader.RecordReader.remainder
Martel.RecordReader.StartsWith.remainder
Martel.RecordReader.Until.remainder" class="py-name" href="#" onclick="return doclink('link-315', 'remainder', 'link-85');">remainder</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L472"></a><tt class="py-lineno">472</tt> <tt class="py-line"> <tt id="link-316" class="py-name"><a title="Bio.Affy.CelFile.remainder
Bio.LogisticRegression.remainder
Bio.MarkovModel.remainder
Bio.MaxEntropy.remainder
Bio.NaiveBayes.remainder
Bio.Statistics.lowess.remainder
Bio.distance.remainder
Bio.kNN.remainder
Martel.RecordReader.CountLines.remainder
Martel.RecordReader.EndsWith.remainder
Martel.RecordReader.Everything.remainder
Martel.RecordReader.Nothing.remainder
Martel.RecordReader.RecordReader.remainder
Martel.RecordReader.StartsWith.remainder
Martel.RecordReader.Until.remainder" class="py-name" href="#" onclick="return doclink('link-316', 'remainder', 'link-85');">remainder</a></tt> <tt class="py-op">=</tt> <tt id="link-317" class="py-name"><a title="Bio.Affy.CelFile.remainder
Bio.LogisticRegression.remainder
Bio.MarkovModel.remainder
Bio.MaxEntropy.remainder
Bio.NaiveBayes.remainder
Bio.Statistics.lowess.remainder
Bio.distance.remainder
Bio.kNN.remainder
Martel.RecordReader.CountLines.remainder
Martel.RecordReader.EndsWith.remainder
Martel.RecordReader.Everything.remainder
Martel.RecordReader.Nothing.remainder
Martel.RecordReader.RecordReader.remainder
Martel.RecordReader.StartsWith.remainder
Martel.RecordReader.Until.remainder" class="py-name" href="#" onclick="return doclink('link-317', 'remainder', 'link-85');">remainder</a></tt> <tt class="py-op">+</tt> <tt class="py-name">infile</tt><tt class="py-op">.</tt><tt id="link-318" 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-318', 'read', 'link-88');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L473"></a><tt class="py-lineno">473</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-319" class="py-name"><a title="Bio.Affy.CelFile.remainder
Bio.LogisticRegression.remainder
Bio.MarkovModel.remainder
Bio.MaxEntropy.remainder
Bio.NaiveBayes.remainder
Bio.Statistics.lowess.remainder
Bio.distance.remainder
Bio.kNN.remainder
Martel.RecordReader.CountLines.remainder
Martel.RecordReader.EndsWith.remainder
Martel.RecordReader.Everything.remainder
Martel.RecordReader.Nothing.remainder
Martel.RecordReader.RecordReader.remainder
Martel.RecordReader.StartsWith.remainder
Martel.RecordReader.Until.remainder" class="py-name" href="#" onclick="return doclink('link-319', 'remainder', 'link-85');">remainder</a></tt> <tt class="py-op">==</tt> <tt id="link-320" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-320', 'data', 'link-78');">data</a></tt><tt class="py-op">,</tt> <tt class="py-string">"Why %r when input was %r?"</tt> <tt class="py-op">%</tt> \ </tt>
<a name="L474"></a><tt class="py-lineno">474</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt id="link-321" class="py-name"><a title="Bio.Affy.CelFile.remainder
Bio.LogisticRegression.remainder
Bio.MarkovModel.remainder
Bio.MaxEntropy.remainder
Bio.NaiveBayes.remainder
Bio.Statistics.lowess.remainder
Bio.distance.remainder
Bio.kNN.remainder
Martel.RecordReader.CountLines.remainder
Martel.RecordReader.EndsWith.remainder
Martel.RecordReader.Everything.remainder
Martel.RecordReader.Nothing.remainder
Martel.RecordReader.RecordReader.remainder
Martel.RecordReader.StartsWith.remainder
Martel.RecordReader.Until.remainder" class="py-name" href="#" onclick="return doclink('link-321', 'remainder', 'link-85');">remainder</a></tt><tt class="py-op">,</tt> <tt id="link-322" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-322', 'data', 'link-78');">data</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L475"></a><tt class="py-lineno">475</tt> <tt class="py-line"> </tt>
<a name="L476"></a><tt class="py-lineno">476</tt> <tt class="py-line"><tt class="py-comment">### Everything</tt> </tt>
<a name="L477"></a><tt class="py-lineno">477</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="test_everything"></a><div id="test_everything-def"><a name="L478"></a><tt class="py-lineno">478</tt> <a class="py-toggle" href="#" id="test_everything-toggle" onclick="return toggle('test_everything');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.test.test_RecordReader2-module.html#test_everything">test_everything</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="test_everything-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="test_everything-expanded"><a name="L479"></a><tt class="py-lineno">479</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"Testing Everything"</tt> </tt>
<a name="L480"></a><tt class="py-lineno">480</tt> <tt class="py-line"> </tt>
<a name="L481"></a><tt class="py-lineno">481</tt> <tt class="py-line"> <tt id="link-323" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-323', 's', 'link-9');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"This is a test.\nThis is only a test.\nHad this been an actual...\n"</tt> </tt>
<a name="L482"></a><tt class="py-lineno">482</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-324" class="py-name"><a title="Bio.expressions.blast.wublast.ending" class="py-name" href="#" onclick="return doclink('link-324', 'ending', 'link-23');">ending</a></tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">"\n"</tt><tt class="py-op">,</tt> <tt class="py-string">"\r"</tt><tt class="py-op">,</tt> <tt class="py-string">"\r\n"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L483"></a><tt class="py-lineno">483</tt> <tt class="py-line"> <tt id="link-325" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-325', 'data', 'link-78');">data</a></tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt id="link-326" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-326', 's', 'link-9');">s</a></tt><tt class="py-op">,</tt> <tt class="py-string">"\n"</tt><tt class="py-op">,</tt> <tt id="link-327" class="py-name"><a title="Bio.expressions.blast.wublast.ending" class="py-name" href="#" onclick="return doclink('link-327', 'ending', 'link-23');">ending</a></tt><tt class="py-op">)</tt> </tt>
<a name="L484"></a><tt class="py-lineno">484</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">look</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-number">2</tt><tt class="py-op">,</tt> <tt class="py-number">5</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L485"></a><tt class="py-lineno">485</tt> <tt class="py-line"> <tt class="py-name">reader</tt> <tt class="py-op">=</tt> <tt id="link-328" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-328', 'RecordReader', 'link-1');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-329" class="py-name" targets="Class Martel.RecordReader.Everything=Martel.RecordReader.Everything-class.html"><a title="Martel.RecordReader.Everything" class="py-name" href="#" onclick="return doclink('link-329', 'Everything', 'link-329');">Everything</a></tt><tt class="py-op">(</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt id="link-330" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-330', 'data', 'link-78');">data</a></tt><tt class="py-op">[</tt><tt class="py-name">look</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L486"></a><tt class="py-lineno">486</tt> <tt class="py-line"> <tt class="py-name">sizehint</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> </tt>
<a name="L487"></a><tt class="py-lineno">487</tt> <tt class="py-line"> <tt class="py-name">lookahead</tt> <tt class="py-op">=</tt> <tt id="link-331" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-331', 'data', 'link-78');">data</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-name">look</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L488"></a><tt class="py-lineno">488</tt> <tt class="py-line"> <tt class="py-name">rec</tt> <tt class="py-op">=</tt> <tt class="py-name">reader</tt><tt class="py-op">.</tt><tt id="link-332" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-332', 'next', 'link-4');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L489"></a><tt class="py-lineno">489</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">rec</tt> <tt class="py-op">==</tt> <tt id="link-333" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-333', 'data', 'link-78');">data</a></tt><tt class="py-op">,</tt> <tt class="py-string">"Record %r is not same as input %r"</tt> <tt class="py-op">%</tt> \ </tt>
<a name="L490"></a><tt class="py-lineno">490</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">rec</tt><tt class="py-op">,</tt> <tt id="link-334" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-334', 'data', 'link-78');">data</a></tt><tt class="py-op">)</tt> </tt>
<a name="L491"></a><tt class="py-lineno">491</tt> <tt class="py-line"> <tt class="py-name">infile</tt><tt class="py-op">,</tt> <tt id="link-335" class="py-name"><a title="Bio.Affy.CelFile.remainder
Bio.LogisticRegression.remainder
Bio.MarkovModel.remainder
Bio.MaxEntropy.remainder
Bio.NaiveBayes.remainder
Bio.Statistics.lowess.remainder
Bio.distance.remainder
Bio.kNN.remainder
Martel.RecordReader.CountLines.remainder
Martel.RecordReader.EndsWith.remainder
Martel.RecordReader.Everything.remainder
Martel.RecordReader.Nothing.remainder
Martel.RecordReader.RecordReader.remainder
Martel.RecordReader.StartsWith.remainder
Martel.RecordReader.Until.remainder" class="py-name" href="#" onclick="return doclink('link-335', 'remainder', 'link-85');">remainder</a></tt> <tt class="py-op">=</tt> <tt class="py-name">reader</tt><tt class="py-op">.</tt><tt id="link-336" class="py-name"><a title="Bio.Affy.CelFile.remainder
Bio.LogisticRegression.remainder
Bio.MarkovModel.remainder
Bio.MaxEntropy.remainder
Bio.NaiveBayes.remainder
Bio.Statistics.lowess.remainder
Bio.distance.remainder
Bio.kNN.remainder
Martel.RecordReader.CountLines.remainder
Martel.RecordReader.EndsWith.remainder
Martel.RecordReader.Everything.remainder
Martel.RecordReader.Nothing.remainder
Martel.RecordReader.RecordReader.remainder
Martel.RecordReader.StartsWith.remainder
Martel.RecordReader.Until.remainder" class="py-name" href="#" onclick="return doclink('link-336', 'remainder', 'link-85');">remainder</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L492"></a><tt class="py-lineno">492</tt> <tt class="py-line"> <tt id="link-337" class="py-name"><a title="Bio.Affy.CelFile.remainder
Bio.LogisticRegression.remainder
Bio.MarkovModel.remainder
Bio.MaxEntropy.remainder
Bio.NaiveBayes.remainder
Bio.Statistics.lowess.remainder
Bio.distance.remainder
Bio.kNN.remainder
Martel.RecordReader.CountLines.remainder
Martel.RecordReader.EndsWith.remainder
Martel.RecordReader.Everything.remainder
Martel.RecordReader.Nothing.remainder
Martel.RecordReader.RecordReader.remainder
Martel.RecordReader.StartsWith.remainder
Martel.RecordReader.Until.remainder" class="py-name" href="#" onclick="return doclink('link-337', 'remainder', 'link-85');">remainder</a></tt> <tt class="py-op">=</tt> <tt id="link-338" class="py-name"><a title="Bio.Affy.CelFile.remainder
Bio.LogisticRegression.remainder
Bio.MarkovModel.remainder
Bio.MaxEntropy.remainder
Bio.NaiveBayes.remainder
Bio.Statistics.lowess.remainder
Bio.distance.remainder
Bio.kNN.remainder
Martel.RecordReader.CountLines.remainder
Martel.RecordReader.EndsWith.remainder
Martel.RecordReader.Everything.remainder
Martel.RecordReader.Nothing.remainder
Martel.RecordReader.RecordReader.remainder
Martel.RecordReader.StartsWith.remainder
Martel.RecordReader.Until.remainder" class="py-name" href="#" onclick="return doclink('link-338', 'remainder', 'link-85');">remainder</a></tt> <tt class="py-op">+</tt> <tt class="py-name">infile</tt><tt class="py-op">.</tt><tt id="link-339" 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-339', 'read', 'link-88');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L493"></a><tt class="py-lineno">493</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-keyword">not</tt> <tt id="link-340" class="py-name"><a title="Bio.Affy.CelFile.remainder
Bio.LogisticRegression.remainder
Bio.MarkovModel.remainder
Bio.MaxEntropy.remainder
Bio.NaiveBayes.remainder
Bio.Statistics.lowess.remainder
Bio.distance.remainder
Bio.kNN.remainder
Martel.RecordReader.CountLines.remainder
Martel.RecordReader.EndsWith.remainder
Martel.RecordReader.Everything.remainder
Martel.RecordReader.Nothing.remainder
Martel.RecordReader.RecordReader.remainder
Martel.RecordReader.StartsWith.remainder
Martel.RecordReader.Until.remainder" class="py-name" href="#" onclick="return doclink('link-340', 'remainder', 'link-85');">remainder</a></tt><tt class="py-op">,</tt> <tt class="py-string">"Why is there a remainder of %r?"</tt> <tt class="py-op">%</tt> \ </tt>
<a name="L494"></a><tt class="py-lineno">494</tt> <tt class="py-line"> <tt id="link-341" class="py-name"><a title="Bio.Affy.CelFile.remainder
Bio.LogisticRegression.remainder
Bio.MarkovModel.remainder
Bio.MaxEntropy.remainder
Bio.NaiveBayes.remainder
Bio.Statistics.lowess.remainder
Bio.distance.remainder
Bio.kNN.remainder
Martel.RecordReader.CountLines.remainder
Martel.RecordReader.EndsWith.remainder
Martel.RecordReader.Everything.remainder
Martel.RecordReader.Nothing.remainder
Martel.RecordReader.RecordReader.remainder
Martel.RecordReader.StartsWith.remainder
Martel.RecordReader.Until.remainder" class="py-name" href="#" onclick="return doclink('link-341', 'remainder', 'link-85');">remainder</a></tt> </tt>
<a name="L495"></a><tt class="py-lineno">495</tt> <tt class="py-line"> </tt>
<a name="L496"></a><tt class="py-lineno">496</tt> <tt class="py-line"> <tt class="py-name">rec</tt> <tt class="py-op">=</tt> <tt class="py-name">reader</tt><tt class="py-op">.</tt><tt id="link-342" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-342', 'next', 'link-4');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L497"></a><tt class="py-lineno">497</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">rec</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-string">"Expecting None after final read, got %r"</tt> <tt class="py-op">%</tt> \ </tt>
<a name="L498"></a><tt class="py-lineno">498</tt> <tt class="py-line"> <tt class="py-name">rec</tt> </tt>
<a name="L499"></a><tt class="py-lineno">499</tt> <tt class="py-line"> <tt class="py-name">rec</tt> <tt class="py-op">=</tt> <tt class="py-name">reader</tt><tt class="py-op">.</tt><tt id="link-343" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-343', 'next', 'link-4');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L500"></a><tt class="py-lineno">500</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">rec</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-string">"Expecting None (again), got %r"</tt> <tt class="py-op">%</tt> <tt class="py-name">rec</tt> </tt>
</div><a name="L501"></a><tt class="py-lineno">501</tt> <tt class="py-line"> </tt>
<a name="L502"></a><tt class="py-lineno">502</tt> <tt class="py-line"> </tt>
<a name="L503"></a><tt class="py-lineno">503</tt> <tt class="py-line"> </tt>
<a name="L504"></a><tt class="py-lineno">504</tt> <tt class="py-line"><tt class="py-comment">### test driver</tt> </tt>
<a name="L505"></a><tt class="py-lineno">505</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="test"></a><div id="test-def"><a name="L506"></a><tt class="py-lineno">506</tt> <a class="py-toggle" href="#" id="test-toggle" onclick="return toggle('test');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.test.test_RecordReader2-module.html#test">test</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="test-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="test-expanded"><a name="L507"></a><tt class="py-lineno">507</tt> <tt class="py-line"> <tt id="link-344" class="py-name" targets="Function Martel.test.test_RecordReader2.test_startswith()=Martel.test.test_RecordReader2-module.html#test_startswith"><a title="Martel.test.test_RecordReader2.test_startswith" class="py-name" href="#" onclick="return doclink('link-344', 'test_startswith', 'link-344');">test_startswith</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L508"></a><tt class="py-lineno">508</tt> <tt class="py-line"> <tt id="link-345" class="py-name" targets="Function Martel.test.test_RecordReader2.test_endswith()=Martel.test.test_RecordReader2-module.html#test_endswith"><a title="Martel.test.test_RecordReader2.test_endswith" class="py-name" href="#" onclick="return doclink('link-345', 'test_endswith', 'link-345');">test_endswith</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L509"></a><tt class="py-lineno">509</tt> <tt class="py-line"> <tt id="link-346" class="py-name" targets="Function Martel.test.test_RecordReader.test_until()=Martel.test.test_RecordReader-module.html#test_until,Function Martel.test.test_RecordReader2.test_until()=Martel.test.test_RecordReader2-module.html#test_until"><a title="Martel.test.test_RecordReader.test_until
Martel.test.test_RecordReader2.test_until" class="py-name" href="#" onclick="return doclink('link-346', 'test_until', 'link-346');">test_until</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L510"></a><tt class="py-lineno">510</tt> <tt class="py-line"> <tt id="link-347" class="py-name" targets="Function Martel.test.test_RecordReader.test_count_lines()=Martel.test.test_RecordReader-module.html#test_count_lines,Function Martel.test.test_RecordReader2.test_count_lines()=Martel.test.test_RecordReader2-module.html#test_count_lines"><a title="Martel.test.test_RecordReader.test_count_lines
Martel.test.test_RecordReader2.test_count_lines" class="py-name" href="#" onclick="return doclink('link-347', 'test_count_lines', 'link-347');">test_count_lines</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L511"></a><tt class="py-lineno">511</tt> <tt class="py-line"> <tt id="link-348" class="py-name" targets="Function Martel.test.test_RecordReader.test_nothing()=Martel.test.test_RecordReader-module.html#test_nothing,Function Martel.test.test_RecordReader2.test_nothing()=Martel.test.test_RecordReader2-module.html#test_nothing"><a title="Martel.test.test_RecordReader.test_nothing
Martel.test.test_RecordReader2.test_nothing" class="py-name" href="#" onclick="return doclink('link-348', 'test_nothing', 'link-348');">test_nothing</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L512"></a><tt class="py-lineno">512</tt> <tt class="py-line"> <tt id="link-349" class="py-name" targets="Function Martel.test.test_RecordReader.test_everything()=Martel.test.test_RecordReader-module.html#test_everything,Function Martel.test.test_RecordReader2.test_everything()=Martel.test.test_RecordReader2-module.html#test_everything"><a title="Martel.test.test_RecordReader.test_everything
Martel.test.test_RecordReader2.test_everything" class="py-name" href="#" onclick="return doclink('link-349', 'test_everything', 'link-349');">test_everything</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L513"></a><tt class="py-lineno">513</tt> <tt class="py-line"> </tt>
<a name="L514"></a><tt class="py-lineno">514</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="L515"></a><tt class="py-lineno">515</tt> <tt class="py-line"> <tt id="link-350" class="py-name" targets="Function Bio.Decode.test()=Bio.Decode-module.html#test,Function Bio.EUtils.ReseekFile.test()=Bio.EUtils.ReseekFile-module.html#test,Package Martel.test=Martel.test-module.html,Method Martel.test.support.Storage.test()=Martel.test.support.Storage-class.html#test,Function Martel.test.test()=Martel.test-module.html#test,Function Martel.test.test_Expression.test()=Martel.test.test_Expression-module.html#test,Function Martel.test.test_Generate.test()=Martel.test.test_Generate-module.html#test,Function Martel.test.test_IterParser.test()=Martel.test.test_IterParser-module.html#test,Function Martel.test.test_Iterator.test()=Martel.test.test_Iterator-module.html#test,Function Martel.test.test_LAX.test()=Martel.test.test_LAX-module.html#test,Function Martel.test.test_ParseRecords.test()=Martel.test.test_ParseRecords-module.html#test,Function Martel.test.test_Parser.test()=Martel.test.test_Parser-module.html#test,Function Martel.test.test_RecordReader.test()=Martel.test.test_RecordReader-module.html#test,Function Martel.test.test_RecordReader2.test()=Martel.test.test_RecordReader2-module.html#test,Function Martel.test.test_Time.test()=Martel.test.test_Time-module.html#test,Function Martel.test.test_attrs.test()=Martel.test.test_attrs-module.html#test,Function Martel.test.test_convert_re.test()=Martel.test.test_convert_re-module.html#test,Function Martel.test.test_delimiter.test()=Martel.test.test_delimiter-module.html#test,Function Martel.test.test_macros.test()=Martel.test.test_macros-module.html#test,Function Martel.test.test_optimize.test()=Martel.test.test_optimize-module.html#test,Function Martel.test.test_swissprot38.test()=Martel.test.test_swissprot38-module.html#test"><a title="Bio.Decode.test
Bio.EUtils.ReseekFile.test
Martel.test
Martel.test.support.Storage.test
Martel.test.test
Martel.test.test_Expression.test
Martel.test.test_Generate.test
Martel.test.test_IterParser.test
Martel.test.test_Iterator.test
Martel.test.test_LAX.test
Martel.test.test_ParseRecords.test
Martel.test.test_Parser.test
Martel.test.test_RecordReader.test
Martel.test.test_RecordReader2.test
Martel.test.test_Time.test
Martel.test.test_attrs.test
Martel.test.test_convert_re.test
Martel.test.test_delimiter.test
Martel.test.test_macros.test
Martel.test.test_optimize.test
Martel.test.test_swissprot38.test" class="py-name" href="#" onclick="return doclink('link-350', 'test', 'link-350');">test</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L516"></a><tt class="py-lineno">516</tt> <tt class="py-line"> </tt><script type="text/javascript">
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