Mercurial > repos > yufei-luo > s_mart
diff commons/core/parsing/test/Test_MrepsToSet.py @ 6:769e306b7933
Change the repository level.
| author | yufei-luo |
|---|---|
| date | Fri, 18 Jan 2013 04:54:14 -0500 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/commons/core/parsing/test/Test_MrepsToSet.py Fri Jan 18 04:54:14 2013 -0500 @@ -0,0 +1,105 @@ +import unittest +import os +from commons.core.utils.FileUtils import FileUtils +from commons.core.parsing.MrepsToSet import MrepsToSet + +class Test_MrepsToSet(unittest.TestCase): + def setUp(self): + self._mrepsInputFileName = "mrepsInput.fa" + self._mrepsOuputFileName = "mrepsOutput.xml" + self._obsSetFileName = "obsOuput.set" + self._expSetFileName = "expOuput.set" + + self._writeExpSet(self._expSetFileName) + self._writeMrepsOutput(self._mrepsOuputFileName) + + def tearDown(self): + os.remove(self._expSetFileName) + os.remove(self._obsSetFileName) + os.remove(self._mrepsOuputFileName) + + def test_convert(self): + iMrepsToSet = MrepsToSet(self._mrepsInputFileName, self._mrepsOuputFileName, self._obsSetFileName) + iMrepsToSet.run() + self.assertTrue(FileUtils.are2FilesIdentical(self._obsSetFileName, self._expSetFileName)) + + def _writeExpSet(self, fileName): + f = open(fileName, "w") + f.write("1\t(tatt)3\tseq1\t4\t16\n") + f.write("2\t(tatt)3\tseq1\t23\t35\n") + f.write("3\t(tatt)3\tseq1\t42\t54\n") + f.close() + + def _writeMrepsOutput(self, fileName): + f = open(fileName, "w") + f.write("<?xml version='1.0' encoding='UTF-8' ?>\n") + f.write("<mreps>\n") + f.write("<time>Thu Dec 1 17:25:54 2011\n") + f.write("</time>\n") + f.write("<parameters>\n") + f.write(" <type-of-input>file in fasta format</type-of-input>\n") + f.write(" <err>3</err>\n") + f.write(" <from>1</from>\n") + f.write(" <to>-1</to>\n") + f.write(" <win>-1</win>\n") + f.write(" <minsize>1</minsize>\n") + f.write(" <maxsize>-1</maxsize>\n") + f.write(" <minperiod>1</minperiod>\n") + f.write(" <maxperiod>-1</maxperiod>\n") + f.write(" <minexponent>3.00</minexponent>\n") + f.write("</parameters>\n") + f.write("<results>\n") + f.write("<sequence-name>seq1</sequence-name>\n") + f.write("<repetitions>\n") + f.write("<window>\n") + f.write("<windowstart>1</windowstart>\n") + f.write("<windowend>60</windowend>\n") + f.write(" <repeat>\n") + f.write(" <start>4</start>\n") + f.write(" <end>16</end>\n") + f.write(" <length>13</length>\n") + f.write(" <period>4</period>\n") + f.write(" <exponent>3.25</exponent>\n") + f.write(" <score>0.000</score>\n") + f.write(" <sequence>\n") + f.write(" <unit>tatt</unit>\n") + f.write(" <unit>tatt</unit>\n") + f.write(" <unit>tatt</unit>\n") + f.write(" <unit>t</unit>\n") + f.write(" </sequence>\n") + f.write(" </repeat>\n") + f.write(" <repeat>\n") + f.write(" <start>23</start>\n") + f.write(" <end>35</end>\n") + f.write(" <length>13</length>\n") + f.write(" <period>4</period>\n") + f.write(" <exponent>3.25</exponent>\n") + f.write(" <score>0.000</score>\n") + f.write(" <sequence>\n") + f.write(" <unit>tatt</unit>\n") + f.write(" <unit>tatt</unit>\n") + f.write(" <unit>tatt</unit>\n") + f.write(" <unit>t</unit>\n") + f.write(" </sequence>\n") + f.write(" </repeat>\n") + f.write(" <repeat>\n") + f.write(" <start>42</start>\n") + f.write(" <end>54</end>\n") + f.write(" <length>13</length>\n") + f.write(" <period>4</period>\n") + f.write(" <exponent>3.25</exponent>\n") + f.write(" <score>0.000</score>\n") + f.write(" <sequence>\n") + f.write(" <unit>tatt</unit>\n") + f.write(" <unit>tatt</unit>\n") + f.write(" <unit>tatt</unit>\n") + f.write(" <unit>t</unit>\n") + f.write(" </sequence>\n") + f.write(" </repeat>\n") + f.write("<nbofreps>3</nbofreps>\n") + f.write("</window>\n") + f.write("</repetitions>\n") + f.write("</results>\n") + f.write("<errorcode>0</errorcode>\n") + f.write("</mreps>\n") + f.close()