Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/commons/core/parsing/test/Test_F_BlatToGff.py @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
1 import unittest
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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2 import os
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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3 from commons.core.utils.FileUtils import FileUtils
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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6 class Test_F_BlatToGff(unittest.TestCase):
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9 def test_run(self):
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10 blatInputFileName = '%s/commons/core/parsing/test/inputFile.tab' % os.environ['REPET_PATH']
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11 self._writeBlatInputFile(blatInputFileName)
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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13 obsOutputFileName = '%s/commons/core/parsing/test/obsOutputFile.tab' % os.environ['REPET_PATH']
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14 cmd = 'python %s/commons/core/parsing/BlatToGff.py -i %s -o %s' % (os.environ['REPET_PATH'], blatInputFileName, obsOutputFileName)
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15 os.system(cmd)
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17 expOutputFileName = '%s/commons/core/parsing/test/expOutputFile.tab' % os.environ['REPET_PATH']
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18 self._writeExpOutputFile(expOutputFileName)
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20 self.assertTrue(FileUtils.are2FilesIdentical(expOutputFileName, obsOutputFileName))
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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21 os.remove(blatInputFileName)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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22 os.remove(obsOutputFileName)
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23 os.remove(expOutputFileName)
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25 def test_run_with_methodName(self):
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26 blatInputFileName = '%s/commons/core/parsing/test/inputFile.tab' % os.environ['REPET_PATH']
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27 self._writeBlatInputFile(blatInputFileName)
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29 obsOutputFileName = '%s/commons/core/parsing/test/obsOutputFile.tab' % os.environ['REPET_PATH']
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30 cmd = 'python %s/commons/core/parsing/BlatToGff.py -i %s -o %s -n Test_F' % (os.environ['REPET_PATH'], blatInputFileName, obsOutputFileName)
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31 os.system(cmd)
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32
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33 expOutputFileName = '%s/commons/core/parsing/test/expOutputFile.tab' % os.environ['REPET_PATH']
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34 self._writeExpOutputFile_with_methodName(expOutputFileName)
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35
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36 self.assertTrue(FileUtils.are2FilesIdentical(expOutputFileName, obsOutputFileName))
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37 os.remove(blatInputFileName)
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38 os.remove(obsOutputFileName)
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39 os.remove(expOutputFileName)
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40
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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41 def _writeBlatInputFile(self, blatInputFileName):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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42 file = open(blatInputFileName, 'w')
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43 file.write('psLayout version 3\n')
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44 file.write('\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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45 file.write('match mis- rep. N\'s Q gap Q gap T gap T gap strand Q Q Q Q T T T T block blockSizes qStarts tStarts\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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46 file.write(' match match count bases count bases name size start end name size start end count\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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47 file.write('---------------------------------------------------------------------------------------------------------------------------------------------------------------\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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48 file.write('315\t20\t0\t0\t3\t10\t2\t9\t+\tMRRE1H001H13FM1\t378\t0\t345\tchr16\t22053297\t21686950\t21687294\t4\t76,185,7,67,\t0,77,263,278,\t21686950,21687026,21687213,21687227,\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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49 file.write('690\t11\t0\t0\t1\t3\t2\t4\t-\tmachin1\t704\t0\t704\tchr16\t22053297\t21736364\t21737069\t3\t40,647,14,\t0,43,690,\t21736364,21736406,21737055,\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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50 file.write('554\t26\t0\t0\t1\t16\t1\t17\t-\tMRRE1H032F08FM1\t606\t10\t606\tchr11\t19818926\t3725876\t3726473\t2\t553,27,\t10,579,\t3725876,3726446,\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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51 file.write('620\t23\t0\t0\t0\t0\t0\t0\t-\tmachin2\t643\t0\t643\tchr11\t19818926\t3794984\t3795627\t1\t643,\t0,\t3794984,\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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52 file.write('347\t25\t0\t0\t0\t0\t0\t0\t-\tmachin3\t393\t21\t393\tchr18\t29360087\t12067347\t12067719\t1\t372,\t0,\t12067347,\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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53 file.close()
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54
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55 def _writeExpOutputFile(self, expOutputFileName):
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56 file = open(expOutputFileName, 'w')
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57 file.write('##gff-version 3\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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58 file.write('chr16\tBlatToGff\tBES\t21686950\t21687294\t.\t+\t.\tID=MRRE1H001H13FM1;Name=MRRE1H001H13FM1;bes_start=21686950;bes_end=21687294;bes_size=22053297\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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59 file.write('chr16\tBlatToGff\tBES\t21736364\t21737069\t.\t+\t.\tID=machin1;Name=machin1;bes_start=21736364;bes_end=21737069;bes_size=22053297\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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60 file.write('chr11\tBlatToGff\tBES\t3725876\t3726473\t.\t+\t.\tID=MRRE1H032F08FM1;Name=MRRE1H032F08FM1;bes_start=3725876;bes_end=3726473;bes_size=19818926\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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61 file.write('chr11\tBlatToGff\tBES\t3794984\t3795627\t.\t+\t.\tID=machin2;Name=machin2;bes_start=3794984;bes_end=3795627;bes_size=19818926\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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62 file.write('chr18\tBlatToGff\tBES\t12067347\t12067719\t.\t+\t.\tID=machin3;Name=machin3;bes_start=12067347;bes_end=12067719;bes_size=29360087\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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63 file.close()
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64
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65 def _writeExpOutputFile_with_methodName(self, expOutputFileName):
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66 file = open(expOutputFileName, 'w')
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67 file.write('##gff-version 3\n')
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68 file.write('chr16\tBlatToGff\tTest_F:BES\t21686950\t21687294\t.\t+\t.\tID=MRRE1H001H13FM1;Name=MRRE1H001H13FM1;bes_start=21686950;bes_end=21687294;bes_size=22053297\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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69 file.write('chr16\tBlatToGff\tTest_F:BES\t21736364\t21737069\t.\t+\t.\tID=machin1;Name=machin1;bes_start=21736364;bes_end=21737069;bes_size=22053297\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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70 file.write('chr11\tBlatToGff\tTest_F:BES\t3725876\t3726473\t.\t+\t.\tID=MRRE1H032F08FM1;Name=MRRE1H032F08FM1;bes_start=3725876;bes_end=3726473;bes_size=19818926\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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71 file.write('chr11\tBlatToGff\tTest_F:BES\t3794984\t3795627\t.\t+\t.\tID=machin2;Name=machin2;bes_start=3794984;bes_end=3795627;bes_size=19818926\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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72 file.write('chr18\tBlatToGff\tTest_F:BES\t12067347\t12067719\t.\t+\t.\tID=machin3;Name=machin3;bes_start=12067347;bes_end=12067719;bes_size=29360087\n')
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73 file.close()
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74
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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75
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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76 if __name__ == "__main__":
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77 unittest.main()