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1 import unittest
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2 import os
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3 from commons.core.utils.FileUtils import FileUtils
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4
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5
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6 class Test_F_BlatToGffForBesPaired(unittest.TestCase):
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7
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8
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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._writeBlatInputFileName(blatInputFileName)
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12 fastaInputFileName = '%s/commons/core/parsing/test/sequences.fasta' % os.environ['REPET_PATH']
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13 self._writeFastaInputFile(fastaInputFileName)
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14
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15 obsOutputFileName = '%s/commons/core/parsing/test/obsOutputFileName.gff' % os.environ['REPET_PATH']
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16 cmd = 'python %s/commons/core/parsing/BlatToGffForBesPaired.py -i %s -f %s -o %s' % (os.environ['REPET_PATH'], blatInputFileName, fastaInputFileName, obsOutputFileName)
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17 os.system(cmd)
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18
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19 expOutputFileName = '%s/commons/core/parsing/test/expOutputFileName.gff' % os.environ['REPET_PATH']
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20 self._writeExpOutputFileName(expOutputFileName)
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21 self.assertTrue(FileUtils.are2FilesIdentical(expOutputFileName, obsOutputFileName))
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22 os.remove(blatInputFileName)
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23 os.remove(fastaInputFileName)
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24 os.remove(expOutputFileName)
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25 os.remove(obsOutputFileName)
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26
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27 def test_run_with_methodName(self):
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28 blatInputFileName = '%s/commons/core/parsing/test/inputFile.tab' % os.environ['REPET_PATH']
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29 self._writeBlatInputFileName(blatInputFileName)
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30 fastaInputFileName = '%s/commons/core/parsing/test/sequences.fasta' % os.environ['REPET_PATH']
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31 self._writeFastaInputFile(fastaInputFileName)
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32
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33 obsOutputFileName = '%s/commons/core/parsing/test/obsOutputFileName.gff' % os.environ['REPET_PATH']
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34 cmd = 'python %s/commons/core/parsing/BlatToGffForBesPaired.py -i %s -f %s -o %s -n TestF' % (os.environ['REPET_PATH'], blatInputFileName, fastaInputFileName, obsOutputFileName)
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35 os.system(cmd)
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36
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37 expOutputFileName = '%s/commons/core/parsing/test/expOutputFileName.gff' % os.environ['REPET_PATH']
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38 self._writeExpOutputFileName_with_methodName(expOutputFileName)
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39 self.assertTrue(FileUtils.are2FilesIdentical(expOutputFileName, obsOutputFileName))
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40 os.remove(blatInputFileName)
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41 os.remove(fastaInputFileName)
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42 os.remove(expOutputFileName)
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43 os.remove(obsOutputFileName)
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44
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45 def _writeBlatInputFileName(self, blatInputFileName):
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46 file = open(blatInputFileName, 'w')
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47 file.write('psLayout version 3\n')
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48 file.write('\n')
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49 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')
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50 file.write(' match match count bases count bases name size start end name size start end count\n')
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51 file.write('---------------------------------------------------------------------------------------------------------------------------------------------------------------\n')
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52 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')
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53 file.write('690\t11\t0\t0\t1\t3\t2\t4\t-\tMRRE1H001H13RM1\t704\t0\t704\tchr16\t22053297\t21736364\t21737069\t3\t40,647,14,\t0,43,690,\t21736364,21736406,21737055,\n')
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54 file.write('554\t26\t0\t0\t1\t16\t1\t17\t+\tMACHINFM1\t606\t10\t606\tchr11\t19818926\t3725876\t3726473\t2\t553,27,\t10,579,\t3725876,3726446,\n')
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55 file.write('620\t23\t0\t0\t0\t0\t0\t0\t-\tBIDULERM1\t643\t0\t643\tchr11\t19818926\t3794984\t3795627\t1\t643,\t0,\t3794984,\n')
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56 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')
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57 file.write('620\t23\t0\t0\t0\t0\t0\t0\t-\tMRRE1H032F08RM1\t643\t0\t643\tchr11\t19818926\t3794984\t3795627\t1\t643,\t0,\t3794984,\n')
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58 file.write('347\t25\t0\t0\t0\t0\t0\t0\t-\tMRRE1B072N12FM1\t393\t21\t393\tchr18\t29360087\t12067347\t12067719\t1\t372,\t0,\t12067347,\n')
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59 file.write('294\t16\t0\t0\t0\t0\t2\t393\t+\tMRRE1B072N12RM1\t339\t21\t331\tchr18\t29360087\t11978635\t11979338\t3\t146,154,10,\t21,167,321,\t11978635,11978783,11979328,\n')
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60 file.close()
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61
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62 def _writeExpOutputFileName(self, expOutputFileName):
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63 file = open(expOutputFileName, 'w')
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64 file.write('##gff-version 3\n')
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65 file.write('chr16\tBlatToGffForBesPaired\tBES\t21686950\t21687294\t.\t+\t.\tID=MRRE1H001H13FM1;Name=MRRE1H001H13FM1;bes_start=21686950;bes_end=21687294;bes_size=22053297;muscadine_seq=ATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCCTACGTAGCTAGCTAGCTAGCTGATCGATCGATCGTAGCTAGCTAGCTAGCACTGCTAGCTACG\n')
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66 file.write('chr16\tBlatToGffForBesPaired\tBES\t21736364\t21737069\t.\t+\t.\tID=MRRE1H001H13RM1;Name=MRRE1H001H13RM1;bes_start=21736364;bes_end=21737069;bes_size=22053297;muscadine_seq=ACTGATCGATCGTACGTACGATCGCTGATCGTACGTACGATCGATCGATCGACTCGATCGTAGCTAGCTACGTCAGTCAGACTGACTGCTGCGCTGCATCGTACTGATCGACTGATCGACTGC\n')
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67 file.write('chr16\tBlatToGffForBesPaired\tBAC\t21686950\t21737069\t.\t.\t.\tID=MRRE1H001H13;Name=MRRE1H001H13;bac_start=21686950;bac_end=21737069;bac_size=50120;besFM_name=MRRE1H001H13FM1;muscadine_besFM_seq=ATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCCTACGTAGCTAGCTAGCTAGCTGATCGATCGATCGTAGCTAGCTAGCTAGCACTGCTAGCTACG;besRM_name=MRRE1H001H13RM1;muscadine_besRM_seq=ACTGATCGATCGTACGTACGATCGCTGATCGTACGTACGATCGATCGATCGACTCGATCGTAGCTAGCTACGTCAGTCAGACTGACTGCTGCGCTGCATCGTACTGATCGACTGATCGACTGC\n')
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68 file.write('chr11\tBlatToGffForBesPaired\tBES\t3725876\t3726473\t.\t+\t.\tID=MRRE1H032F08FM1;Name=MRRE1H032F08FM1;bes_start=3725876;bes_end=3726473;bes_size=19818926;muscadine_seq=TCAGCTATCGATCGTACGTACGTCGATCGTACGTACGTACGATCGATCGATATCGATCG\n')
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69 file.write('chr11\tBlatToGffForBesPaired\tBES\t3794984\t3795627\t.\t+\t.\tID=MRRE1H032F08RM1;Name=MRRE1H032F08RM1;bes_start=3794984;bes_end=3795627;bes_size=19818926;muscadine_seq=ATCGACTGATCGTCGATCGTACGATCGACTGATCGATCGATCGACTGACTGTACGTACGTAC\n')
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70 file.write('chr11\tBlatToGffForBesPaired\tBAC\t3725876\t3795627\t.\t.\t.\tID=MRRE1H032F08;Name=MRRE1H032F08;bac_start=3725876;bac_end=3795627;bac_size=69752;besFM_name=MRRE1H032F08FM1;muscadine_besFM_seq=TCAGCTATCGATCGTACGTACGTCGATCGTACGTACGTACGATCGATCGATATCGATCG;besRM_name=MRRE1H032F08RM1;muscadine_besRM_seq=ATCGACTGATCGTCGATCGTACGATCGACTGATCGATCGATCGACTGACTGTACGTACGTAC\n')
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71 file.write('chr18\tBlatToGffForBesPaired\tBES\t12067347\t12067719\t.\t+\t.\tID=MRRE1B072N12FM1;Name=MRRE1B072N12FM1;bes_start=12067347;bes_end=12067719;bes_size=29360087;muscadine_seq=ATCGTACGTACGATCGATCGCATGACTACGT\n')
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72 file.write('chr18\tBlatToGffForBesPaired\tBES\t11978635\t11979338\t.\t+\t.\tID=MRRE1B072N12RM1;Name=MRRE1B072N12RM1;bes_start=11978635;bes_end=11979338;bes_size=29360087;muscadine_seq=TACGTACGATCGACTGATGCTAGCTAGCTCC\n')
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73 file.write('chr18\tBlatToGffForBesPaired\tBAC\t11978635\t12067719\t.\t.\t.\tID=MRRE1B072N12;Name=MRRE1B072N12;bac_start=11978635;bac_end=12067719;bac_size=89085;besFM_name=MRRE1B072N12FM1;muscadine_besFM_seq=ATCGTACGTACGATCGATCGCATGACTACGT;besRM_name=MRRE1B072N12RM1;muscadine_besRM_seq=TACGTACGATCGACTGATGCTAGCTAGCTCC\n')
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74 file.close()
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75
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76 def _writeExpOutputFileName_with_methodName(self, expOutputFileName):
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77 file = open(expOutputFileName, 'w')
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78 file.write('##gff-version 3\n')
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79 file.write('chr16\tBlatToGffForBesPaired\tTestF:BES\t21686950\t21687294\t.\t+\t.\tID=MRRE1H001H13FM1;Name=MRRE1H001H13FM1;bes_start=21686950;bes_end=21687294;bes_size=22053297;muscadine_seq=ATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCCTACGTAGCTAGCTAGCTAGCTGATCGATCGATCGTAGCTAGCTAGCTAGCACTGCTAGCTACG\n')
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80 file.write('chr16\tBlatToGffForBesPaired\tTestF:BES\t21736364\t21737069\t.\t+\t.\tID=MRRE1H001H13RM1;Name=MRRE1H001H13RM1;bes_start=21736364;bes_end=21737069;bes_size=22053297;muscadine_seq=ACTGATCGATCGTACGTACGATCGCTGATCGTACGTACGATCGATCGATCGACTCGATCGTAGCTAGCTACGTCAGTCAGACTGACTGCTGCGCTGCATCGTACTGATCGACTGATCGACTGC\n')
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81 file.write('chr16\tBlatToGffForBesPaired\tTestF:BAC\t21686950\t21737069\t.\t.\t.\tID=MRRE1H001H13;Name=MRRE1H001H13;bac_start=21686950;bac_end=21737069;bac_size=50120;besFM_name=MRRE1H001H13FM1;muscadine_besFM_seq=ATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCCTACGTAGCTAGCTAGCTAGCTGATCGATCGATCGTAGCTAGCTAGCTAGCACTGCTAGCTACG;besRM_name=MRRE1H001H13RM1;muscadine_besRM_seq=ACTGATCGATCGTACGTACGATCGCTGATCGTACGTACGATCGATCGATCGACTCGATCGTAGCTAGCTACGTCAGTCAGACTGACTGCTGCGCTGCATCGTACTGATCGACTGATCGACTGC\n')
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82 file.write('chr11\tBlatToGffForBesPaired\tTestF:BES\t3725876\t3726473\t.\t+\t.\tID=MRRE1H032F08FM1;Name=MRRE1H032F08FM1;bes_start=3725876;bes_end=3726473;bes_size=19818926;muscadine_seq=TCAGCTATCGATCGTACGTACGTCGATCGTACGTACGTACGATCGATCGATATCGATCG\n')
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83 file.write('chr11\tBlatToGffForBesPaired\tTestF:BES\t3794984\t3795627\t.\t+\t.\tID=MRRE1H032F08RM1;Name=MRRE1H032F08RM1;bes_start=3794984;bes_end=3795627;bes_size=19818926;muscadine_seq=ATCGACTGATCGTCGATCGTACGATCGACTGATCGATCGATCGACTGACTGTACGTACGTAC\n')
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84 file.write('chr11\tBlatToGffForBesPaired\tTestF:BAC\t3725876\t3795627\t.\t.\t.\tID=MRRE1H032F08;Name=MRRE1H032F08;bac_start=3725876;bac_end=3795627;bac_size=69752;besFM_name=MRRE1H032F08FM1;muscadine_besFM_seq=TCAGCTATCGATCGTACGTACGTCGATCGTACGTACGTACGATCGATCGATATCGATCG;besRM_name=MRRE1H032F08RM1;muscadine_besRM_seq=ATCGACTGATCGTCGATCGTACGATCGACTGATCGATCGATCGACTGACTGTACGTACGTAC\n')
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85 file.write('chr18\tBlatToGffForBesPaired\tTestF:BES\t12067347\t12067719\t.\t+\t.\tID=MRRE1B072N12FM1;Name=MRRE1B072N12FM1;bes_start=12067347;bes_end=12067719;bes_size=29360087;muscadine_seq=ATCGTACGTACGATCGATCGCATGACTACGT\n')
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86 file.write('chr18\tBlatToGffForBesPaired\tTestF:BES\t11978635\t11979338\t.\t+\t.\tID=MRRE1B072N12RM1;Name=MRRE1B072N12RM1;bes_start=11978635;bes_end=11979338;bes_size=29360087;muscadine_seq=TACGTACGATCGACTGATGCTAGCTAGCTCC\n')
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87 file.write('chr18\tBlatToGffForBesPaired\tTestF:BAC\t11978635\t12067719\t.\t.\t.\tID=MRRE1B072N12;Name=MRRE1B072N12;bac_start=11978635;bac_end=12067719;bac_size=89085;besFM_name=MRRE1B072N12FM1;muscadine_besFM_seq=ATCGTACGTACGATCGATCGCATGACTACGT;besRM_name=MRRE1B072N12RM1;muscadine_besRM_seq=TACGTACGATCGACTGATGCTAGCTAGCTCC\n')
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88 file.close()
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89
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90 def _writeFastaInputFile(self, fileName):
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91 file = open(fileName, 'w')
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92 file.write('>MRRE1H001H13FM1\n')
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93 file.write('ATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\n')
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94 file.write('CTACGTAGCTAGCTAGCTAGCTGATCGATCGATCGTAGCTAGCTAGCTAGC\n')
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95 file.write('ACTGCTAGCTACG\n')
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96 file.write('>MRRE1H001H13RM1\n')
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97 file.write('ACTGATCGATCGTACGTACGATCGCTGATCGTACGTACGATCGATCGATCG\n')
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98 file.write('ACTCGATCGTAGCTAGCTACGTCAGTCAGACTGACTGCTGCGCTGCATCGT\n')
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99 file.write('ACTGATCGACTGATCGACTGC\n')
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100 file.write('>MRRE1H032F08FM1\n')
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101 file.write('TCAGCTATCGATCGTACGTACGTCGATCGTACGTACGTACGATCGATCGAT\n')
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102 file.write('ATCGATCG\n')
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103 file.write('>MRRE1H032F08RM1\n')
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104 file.write('ATCGACTGATCGTCGATCGTACGATCGACTGATCGATCGATCGACTGACTG\n')
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105 file.write('TACGTACGTAC\n')
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106 file.write('>MRRE1B072N12FM1\n')
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107 file.write('ATCGTACGTACGATCGATCGCATGACTACGT\n')
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108 file.write('>MRRE1B072N12RM1\n')
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109 file.write('TACGTACGATCGACTGATGCTAGCTAGCTCC\n')
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110 file.write('>MACHINFM1\n')
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111 file.write('ATCGTACGCTAGCTAGTCGATCGATCGATCGATCG\n')
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112 file.write('>BIDULERM1\n')
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113 file.write('ACTCGATCGACTACGTACGTAGACTG\n')
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114 file.close()
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115
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116 if __name__ == "__main__":
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117 unittest.main() |
