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1 import unittest
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2 import os
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3 from SMART.Java.Python.misc import Utils
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4 from commons.core.utils.FileUtils import FileUtils
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5
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6
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7 class Test_F_convertTranscriptFile(unittest.TestCase):
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8
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9 def setUp(self):
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10 self._inputFileName = None
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11 self._expOutputFileName = None
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12 self._outputFileName = None
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13
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14 def tearDown(self):
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15 for fileName in (self._expOutputFileName, self._outputFileName):
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16 if fileName != None and os.path.exists(fileName):
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17 os.remove(fileName)
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18
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19 def test_run_SAMtoGFF3(self):
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20 self._inputFileName = "%s/SMART/Java/Python/test/input.sam" % (os.environ["REPET_PATH"])
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21 self._writeInputSam(self._inputFileName)
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22 self._outputFileName = '%s/SMART/Java/Python/test/obsOutput.gff3' % (os.environ["REPET_PATH"])
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23 cmd = 'python %s/SMART/Java/Python/convertTranscriptFile.py -i %s -f sam -o %s -g gff3 -v 0' % (os.environ["REPET_PATH"], self._inputFileName, self._outputFileName)
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24 os.system(cmd)
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25 self._expOutputFileName = '%s/SMART/Java/Python/test/expOutput.gff3' % (os.environ["REPET_PATH"])
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26 self._writeExpGff3File_test1(self._expOutputFileName)
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27
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28 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
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29 os.remove(self._inputFileName)
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30
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31 def test_run_BEDtoGFF3(self):
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32 self._inputFileName = "%s/SMART/Java/Python/TestFiles/test_distance.bed" % (os.environ["REPET_PATH"])
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33 self._outputFileName = '%s/SMART/Java/Python/test/obsOutput.gff3' % (os.environ["REPET_PATH"])
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34 cmd = 'python %s/SMART/Java/Python/convertTranscriptFile.py -i %s -f bed -o %s -g gff3 -v 0' % (os.environ["REPET_PATH"], self._inputFileName, self._outputFileName)
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35 os.system(cmd)
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36 self._expOutputFileName = '%s/SMART/Java/Python/test/expOutput.gff3' % (os.environ["REPET_PATH"])
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37 self._writeExpGff3File_test2(self._expOutputFileName)
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38 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
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39
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40 def test_run_GFF3toCSV(self):
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41 self._inputFileName = "%s/SMART/Java/Python/TestFiles/mapperAnalyzerExpected.gff3" % (os.environ["REPET_PATH"])
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42 self._outputFileName = '%s/SMART/Java/Python/test/obsOutput.csv' % (os.environ["REPET_PATH"])
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43 cmd = 'python %s/SMART/Java/Python/convertTranscriptFile.py -i %s -f gff3 -o %s -g csv -v 0' % (os.environ["REPET_PATH"], self._inputFileName, self._outputFileName)
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44 os.system(cmd)
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45 self._expOutputFileName = '%s/SMART/Java/Python/test/expOutput.csv' % (os.environ["REPET_PATH"])
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46 self._writeExpCsvFile(self._expOutputFileName)
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47
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48 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
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49
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50 def test_run_GFF3toSam(self):
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51 self._inputFileName = "%s/SMART/Java/Python/TestFiles/mapperAnalyzerExpected.gff3" % (os.environ["REPET_PATH"])
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52 self._outputFileName = '%s/SMART/Java/Python/test/obsOutput.sam' % (os.environ["REPET_PATH"])
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53 cmd = 'python %s/SMART/Java/Python/convertTranscriptFile.py -i %s -f gff3 -o %s -g sam -v 0' % (os.environ["REPET_PATH"], self._inputFileName, self._outputFileName)
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54 os.system(cmd)
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55 self._expOutputFileName = '%s/SMART/Java/Python/test/expOutput.sam' % (os.environ["REPET_PATH"])
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56 self._writeExpSamFile(self._expOutputFileName)
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57 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
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58
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59 def test_run_Gff3toWig(self):
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60 self._inputFileName = '%s/SMART/Java/Python/TestFiles/sorted_query.gff3' % (os.environ["REPET_PATH"])
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61 self._outputFileName = '%s/SMART/Java/Python/test/obsOutput.wig' % (os.environ["REPET_PATH"])
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62 cmd = 'python %s/SMART/Java/Python/convertTranscriptFile.py -i %s -f gff3 -o %s -g wig -v 0' % (os.environ["REPET_PATH"], self._inputFileName, self._outputFileName)
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63 os.system(cmd)
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64 outputFile = '%s/SMART/Java/Python/TestFiles/sorted_query_wig.wig' % (os.environ["REPET_PATH"])
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65 self.assertTrue(Utils.diff(outputFile, self._outputFileName))
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66
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67 def _writeInputSam(self, fileName):
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68 file = open(fileName, 'w')
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69 file.write( 'HWI-EAS337_3:7:1:415:1217\t83\tC02HBa0185P07_LR40\t3889\t60\t36M\t=\t3830\t-95\tACAGTGATGTAGTCCTGCGTGAAAAGTCTGCACATC\tQTUQUUWVWVVWWPVKVVVVWWWWVWWWPWVVVWWW\tXT:A:U\tNM:i:0\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n' )
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70 file.write( 'HWI-EAS337_3:7:1:415:1217\t163\tC02HBa0185P07_LR40\t3830\t60\t36M\t=\t3889\t95\tTAAGAACTTGGCTGATCGCCTACTTACTGCTTTTAC\tVWWWVWVVVVVVVVUVWVWVVWWVWVVVUVTTTTTN\tXT:A:U\tNM:i:0\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n' )
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71 file.write( 'HWI-EAS337_3:7:1:208:1489\t77\t*\t0\t0\t*\t*\t0\t0\tGGAAACATATGCACATAAACGTTGAAATCATGCTTA\tWWWWWWWWWWWWWWWWWVWWVWWVWWWWWWUUUUUU\n' )
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72 file.write( 'HWI-EAS337_3:7:1:208:1489\t141\t*\t0\t0\t*\t*\t0\t0\tCGTGTTTTTGGTTGTGCATAAGGCTTTTTAAAGTAA\tWWWWWWWWWVVWWQWVWVWWVUVWWWWWWVRTRTTR\n' )
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73 file.write( 'HWI-EAS337_3:7:1:278:1153\t77\t*\t0\t0\t*\t*\t0\t0\tGAGAAAACCTGTAATAAATACTGAGAGAAAGTAGGG\tWWWWWWWWWWWWWWWWWWWWWWVWVVVWWVUUUUUR\n' )
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74 file.write( 'HWI-EAS337_3:7:1:278:1153\t141\t*\t0\t0\t*\t*\t0\t0\tGTCAGGCCGCATTGATGGGGGATGGGTTTCCCCCCA\tWWWVWWWWWWWWWVVVVVVVVVVWWWVVVVTTTTTR\n' )
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75 file.write( 'HWI-EAS337_3:7:1:1178:755\t83\tC11SLe0053P22_LR298\t2130\t60\t36M\t=\t1980\t-186\tATTCAATGGTTTTACCATCAACCAACCACTCTCACC\tUUUUUUVVVWVWVVVVWVVWWVVWWWVWWWWWWWWW\tXT:A:U\tNM:i:0\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n' )
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76 file.write( 'HWI-EAS337_3:7:1:1178:755\t163\tC11SLe0053P22_LR298\t1980\t60\t36M\t=\t2130\t186\tGACATTTCAATTACATTCATCTTACCATCACCTATA\tWVWVWWWWWVWWVWWVWWVVWWWVVWVWVVTTTTTR\tXT:A:U\tNM:i:0\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n' )
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77 file.write( 'HWI-EAS337_3:7:1:277:1259\t99\tC06HBa0144J05_LR355\t1\t60\t36M\t=\t101\t136\tGGGTGACAAAGAAAACAAAAGGGACATGGTACTTGG\tWWWWWWWWWWWWWWWWWWWWWWVWWWWWWVUUUUUU\tXT:A:U\tNM:i:0\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n' )
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78 file.write( 'HWI-EAS337_3:7:1:277:1259\t147\tC06HBa0144J05_LR355\t101\t60\t36M\t=\t1\t-136\tTCTTCAAGTGATTCAGAAGATCCTGATGAGCCAAAA\tSTTTRTWWVWWVVVVWWWWWVVWWWWWWWWWWWWWW\tXT:A:U\tNM:i:0\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n' )
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79 file.write( 'HWI-EAS337_3:7:1:447:1231\t83\tC08HBa0165B06_LR218\t3619\t60\t36M\t=\t3575\t-80\tAGGCTCCAGCTTTCCATTCCAACTCTTCCACAAGTC\tUUSURUVVVVVVVVVWWWVWWWVWVWWWWWWWWWWW\tXT:A:U\tNM:i:0\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n' )
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80 file.write( 'HWI-EAS337_3:7:1:447:1231\t163\tC08HBa0165B06_LR218\t3575\t60\t36M\t=\t3619\t80\tTCAACAAGAGAAAGGAGACGAAAAAGTAAATCCAAC\tWWWWWWWWVWWWWVVWWWWWVVWWWWVVWWTTTTTR\tXT:A:U\tNM:i:0\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n' )
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81 file.close()
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82
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83 def _writeExpGff3File_test1(self, fileName):
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84 file = open(fileName, 'w')
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85 file.write( 'C02HBa0185P07_LR40\tSMART\ttranscript\t3889\t3924\t.\t-\t.\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:415:1217;identity=100.000000;Name=HWI-EAS337_3:7:1:415:1217\n')
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86 file.write( 'C02HBa0185P07_LR40\tSMART\ttranscript\t3830\t3865\t.\t+\t.\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:415:1217;identity=100.000000;Name=HWI-EAS337_3:7:1:415:1217\n')
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87 file.write( 'C11SLe0053P22_LR298\tSMART\ttranscript\t2130\t2165\t.\t-\t.\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:1178:755;identity=100.000000;Name=HWI-EAS337_3:7:1:1178:755\n')
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88 file.write( 'C11SLe0053P22_LR298\tSMART\ttranscript\t1980\t2015\t.\t+\t.\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:1178:755;identity=100.000000;Name=HWI-EAS337_3:7:1:1178:755\n')
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89 file.write( 'C06HBa0144J05_LR355\tSMART\ttranscript\t1\t36\t.\t+\t.\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:277:1259;identity=100.000000;Name=HWI-EAS337_3:7:1:277:1259\n')
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90 file.write( 'C06HBa0144J05_LR355\tSMART\ttranscript\t101\t136\t.\t-\t.\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:277:1259;identity=100.000000;Name=HWI-EAS337_3:7:1:277:1259\n')
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91 file.write( 'C08HBa0165B06_LR218\tSMART\ttranscript\t3619\t3654\t.\t-\t.\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:447:1231;identity=100.000000;Name=HWI-EAS337_3:7:1:447:1231\n')
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92 file.write( 'C08HBa0165B06_LR218\tSMART\ttranscript\t3575\t3610\t.\t+\t.\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:447:1231;identity=100.000000;Name=HWI-EAS337_3:7:1:447:1231\n')
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93 file.close()
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94
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95 def _writeExpGff3File_test2(self, fileName):
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96 file = open(fileName, 'w')
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97 file.write( 'arm_X\tSMART\ttranscript\t1000\t1999\t.\t+\t.\tID=test2.1;Name=test2.1\n' )
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98 file.write( 'arm_X\tSMART\ttranscript\t250\t349\t.\t+\t.\tID=test2.2;Name=test2.2\n' )
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99 file.write( 'arm_X\tSMART\ttranscript\t150\t249\t.\t+\t.\tID=test2.3;Name=test2.3\n' )
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100 file.close()
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101
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102 def _writeExpCsvFile(self, fileName):
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103 file = open(fileName, 'w')
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104 file.write( 'chromosome,start,end,strand,exons,ID,bestRegion,feature,identity,nbGaps,nbMismatches,nbOccurrences,occurrence,rank,score\n' )
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105 file.write( 'chr1,6155418,6155441,"+",None,test1/1,(self),match,100,0,0,1,1,1,24\n' )
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106 file.write( 'chr2,26303950,26303981,"+",None,test2/1-1,(self),match,93,0,2,3,1,1,32\n' )
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107 file.write( 'chr3,28320540,28320574,"+",None,test2/1-2,chr2:26303950-26303981,match,94,0,2,3,2,None,35\n' )
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108 file.write( 'chr4,28565007,28565041,"+",None,test2/1-3,chr2:26303950-26303981,match,88,0,4,3,3,3,35\n' )
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109 file.close()
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110
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111 def _writeExpSamFile(self, fileName):
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112 file = open(fileName, 'w')
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113 file.write('@SQ\tSN:chr4\tLN:28565041\n')
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114 file.write('@SQ\tSN:chr3\tLN:28320574\n')
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115 file.write('@SQ\tSN:chr2\tLN:26303981\n')
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116 file.write('@SQ\tSN:chr1\tLN:6155441\n')
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117 file.write('test1/1\t0\tchr1\t6155418\t255\t24M\t*\t0\t0\t*\t*\tNM:i:0\n')
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118 file.write('test2/1\t0\tchr2\t26303950\t255\t32M\t*\t0\t0\t*\t*\tNM:i:0\n')
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119 file.write('test2/1\t0\tchr3\t28320540\t255\t35M\t*\t0\t0\t*\t*\tNM:i:0\n')
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120 file.write('test2/1\t0\tchr4\t28565007\t255\t35M\t*\t0\t0\t*\t*\tNM:i:0\n')
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121 file.close()
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122
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123
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124 if __name__ == "__main__":
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125 unittest.main()
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