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<a href="Martel-module.html">Package Martel</a> ::
<a href="Martel.test-module.html">Package test</a> ::
Module run_tests
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<h1 class="epydoc">Source Code for <a href="Martel.test.run_tests-module.html">Module Martel.test.run_tests</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># test suite for the formats</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">import</tt> <tt class="py-name">os</tt><tt class="py-op">,</tt> <tt class="py-name">glob</tt><tt class="py-op">,</tt> <tt class="py-name">imp</tt><tt class="py-op">,</tt> <tt class="py-name">sys</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"> </tt>
<a name="main"></a><div id="main-def"><a name="L4"></a><tt class="py-lineno"> 4</tt> <a class="py-toggle" href="#" id="main-toggle" onclick="return toggle('main');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.test.run_tests-module.html#main">main</a><tt class="py-op">(</tt><tt class="py-param">args</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="main-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="main-expanded"><a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"> <tt class="py-name">dirname</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">dirname</tt><tt class="py-op">(</tt><tt class="py-name">__file__</tt><tt class="py-op">)</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">NameError</tt><tt class="py-op">:</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"> <tt class="py-name">dirname</tt> <tt class="py-op">=</tt> <tt class="py-string">"."</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"> <tt id="link-0" class="py-name" targets="Variable Bio.expressions.hmmpfam.files=Bio.expressions.hmmpfam-module.html#files"><a title="Bio.expressions.hmmpfam.files" class="py-name" href="#" onclick="return doclink('link-0', 'files', 'link-0');">files</a></tt> <tt class="py-op">=</tt> <tt class="py-name">glob</tt><tt class="py-op">.</tt><tt class="py-name">glob</tt><tt class="py-op">(</tt><tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">dirname</tt><tt class="py-op">,</tt> <tt class="py-string">"test_*.py"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"> <tt id="link-1" class="py-name"><a title="Bio.expressions.hmmpfam.files" class="py-name" href="#" onclick="return doclink('link-1', 'files', 'link-0');">files</a></tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Method Bio.PDB.Residue.DisorderedResidue.sort()=Bio.PDB.Residue.DisorderedResidue-class.html#sort,Method Bio.PDB.Residue.Residue.sort()=Bio.PDB.Residue.Residue-class.html#sort,Method Bio.Sequencing.Ace.ACEFileRecord.sort()=Bio.Sequencing.Ace.ACEFileRecord-class.html#sort"><a title="Bio.PDB.Residue.DisorderedResidue.sort
Bio.PDB.Residue.Residue.sort
Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-2', 'sort', 'link-2');">sort</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"> </tt>
<a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">file</tt> <tt class="py-keyword">in</tt> <tt id="link-3" class="py-name"><a title="Bio.expressions.hmmpfam.files" class="py-name" href="#" onclick="return doclink('link-3', 'files', 'link-0');">files</a></tt><tt class="py-op">:</tt> </tt>
<a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"> <tt id="link-4" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.name=Bio.Encodings.IUPACEncoding-module.html#name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-4', 'name', 'link-4');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">basename</tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">)</tt> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"> <tt id="link-5" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-5', 'name', 'link-4');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">splitext</tt><tt class="py-op">(</tt><tt id="link-6" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-6', 'name', 'link-4');">name</a></tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"###### running tests in"</tt><tt class="py-op">,</tt> <tt id="link-7" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-7', 'name', 'link-4');">name</a></tt><tt class="py-op">,</tt> <tt class="py-string">"###############"</tt> </tt>
<a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"> <tt class="py-name">module</tt> <tt class="py-op">=</tt> <tt class="py-name">__import__</tt><tt class="py-op">(</tt><tt id="link-8" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-8', 'name', 'link-4');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"> <tt class="py-name">module</tt><tt class="py-op">.</tt><tt id="link-9" 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-9', 'test', 'link-9');">test</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"><tt class="py-comment"># Run tests uses the local (uninstalled) files</tt> </tt>
<a name="local_test_main"></a><div id="local_test_main-def"><a name="L20"></a><tt class="py-lineno">20</tt> <a class="py-toggle" href="#" id="local_test_main-toggle" onclick="return toggle('local_test_main');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.test.run_tests-module.html#local_test_main">local_test_main</a><tt class="py-op">(</tt><tt class="py-param">args</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="local_test_main-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="local_test_main-expanded"><a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"> <tt class="py-comment"># Find the directory containing the Martel code.</tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># In biopython CVS this is named 'Martel'. In a standalone release</tt> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># it could be named something like 'Martel-0.8'. Discover which.</tt> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt id="link-10" class="py-name" targets="Method Bio.Crystal.Chain.insert()=Bio.Crystal.Chain-class.html#insert,Method Bio.EUtils.POM.Comment.insert()=Bio.EUtils.POM.Comment-class.html#insert,Method Bio.EUtils.POM.ElementNode.insert()=Bio.EUtils.POM.ElementNode-class.html#insert,Method Bio.EUtils.POM.IndentedText.insert()=Bio.EUtils.POM.IndentedText-class.html#insert,Method Bio.Seq.MutableSeq.insert()=Bio.Seq.MutableSeq-class.html#insert,Method Martel.msre_parse.SubPattern.insert()=Martel.msre_parse.SubPattern-class.html#insert"><a title="Bio.Crystal.Chain.insert
Bio.EUtils.POM.Comment.insert
Bio.EUtils.POM.ElementNode.insert
Bio.EUtils.POM.IndentedText.insert
Bio.Seq.MutableSeq.insert
Martel.msre_parse.SubPattern.insert" class="py-name" href="#" onclick="return doclink('link-10', 'insert', 'link-10');">insert</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">".."</tt><tt class="py-op">)</tt> </tt>
<a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"> <tt class="py-name">filename</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">abspath</tt><tt class="py-op">(</tt><tt class="py-name">__file__</tt><tt class="py-op">)</tt> </tt>
<a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"> <tt class="py-name">dirname</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">dirname</tt><tt class="py-op">(</tt><tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">dirname</tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"> </tt>
<a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"> <tt class="py-comment"># Force module loading.</tt> </tt>
<a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">imp</tt><tt class="py-op">.</tt><tt id="link-11" class="py-name" targets="Function Bio.config._support.load_module()=Bio.config._support-module.html#load_module"><a title="Bio.config._support.load_module" class="py-name" href="#" onclick="return doclink('link-11', 'load_module', 'link-11');">load_module</a></tt><tt class="py-op">(</tt><tt class="py-string">"Martel"</tt><tt class="py-op">,</tt> <tt id="link-12" class="py-name" targets="Function Bio.Mindy.FlatDB.open()=Bio.Mindy.FlatDB-module.html#open,Function Bio.Mindy.open()=Bio.Mindy-module.html#open"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-12', 'open', 'link-12');">open</a></tt><tt class="py-op">(</tt><tt class="py-string">"../__init__.py"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">dirname</tt><tt class="py-op">,</tt> </tt>
<a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">".py"</tt><tt class="py-op">,</tt> <tt class="py-string">"r"</tt><tt class="py-op">,</tt> <tt class="py-name">imp</tt><tt class="py-op">.</tt><tt class="py-name">PKG_DIRECTORY</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"> </tt>
<a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"> <tt class="py-comment"># Do the normal tests</tt> </tt>
<a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt id="link-13" class="py-name" targets="Function Bio.EUtils.dtd2py.main()=Bio.EUtils.dtd2py-module.html#main,Function Bio.Mindy.main()=Bio.Mindy-module.html#main,Function Bio.Wise.dnal.main()=Bio.Wise.dnal-module.html#main,Function Bio.Wise.main()=Bio.Wise-module.html#main,Function Bio.Wise.psw.main()=Bio.Wise.psw-module.html#main,Function Bio.biblio.main()=Bio.biblio-module.html#main,Function Bio.expressions.blast.wublast.main()=Bio.expressions.blast.wublast-module.html#main,Function Martel.test.run_tests.main()=Martel.test.run_tests-module.html#main"><a title="Bio.EUtils.dtd2py.main
Bio.Mindy.main
Bio.Wise.dnal.main
Bio.Wise.main
Bio.Wise.psw.main
Bio.biblio.main
Bio.expressions.blast.wublast.main
Martel.test.run_tests.main" class="py-name" href="#" onclick="return doclink('link-13', 'main', 'link-13');">main</a></tt><tt class="py-op">(</tt><tt class="py-name">args</tt><tt class="py-op">)</tt> </tt>
</div><a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"> </tt>
<a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"><tt class="py-comment"># Run tests uses the installed files (not the ones in ..)</tt> </tt>
<a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-name">install_test_main</tt> <tt class="py-op">=</tt> <tt id="link-14" class="py-name"><a title="Bio.EUtils.dtd2py.main
Bio.Mindy.main
Bio.Wise.dnal.main
Bio.Wise.main
Bio.Wise.psw.main
Bio.biblio.main
Bio.expressions.blast.wublast.main
Martel.test.run_tests.main" class="py-name" href="#" onclick="return doclink('link-14', 'main', 'link-13');">main</a></tt> </tt>
<a name="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"> </tt>
<a name="L38"></a><tt class="py-lineno">38</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="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"> <tt class="py-name">install_test_main</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L40"></a><tt class="py-lineno">40</tt> <tt class="py-line"> </tt><script type="text/javascript">
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