Mercurial > repos > yufei-luo > s_mart

comparison SMART/Java/Python/test/Test_F_convertTranscriptFile.py @ 31:0ab839023fe4

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Uploaded
author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
children
comparison
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30:5677346472b5 31:0ab839023fe4
1 import unittest
2 import os
3 from SMART.Java.Python.misc import Utils
4 from commons.core.utils.FileUtils import FileUtils
5
6
7 class Test_F_convertTranscriptFile(unittest.TestCase):
8
9 def setUp(self):
10 self._inputFileName = None
11 self._expOutputFileName = None
12 self._outputFileName = None
13
14 def tearDown(self):
15 for fileName in (self._expOutputFileName, self._outputFileName):
16 if fileName != None and os.path.exists(fileName):
17 os.remove(fileName)
18
19 def test_run_SAMtoGFF3(self):
20 self._inputFileName = "%s/SMART/Java/Python/test/input.sam" % (os.environ["REPET_PATH"])
21 self._writeInputSam(self._inputFileName)
22 self._outputFileName = '%s/SMART/Java/Python/test/obsOutput.gff3' % (os.environ["REPET_PATH"])
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)
24 os.system(cmd)
25 self._expOutputFileName = '%s/SMART/Java/Python/test/expOutput.gff3' % (os.environ["REPET_PATH"])
26 self._writeExpGff3File_test1(self._expOutputFileName)
27
28 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
29 os.remove(self._inputFileName)
30
31 def test_run_BEDtoGFF3(self):
32 self._inputFileName = "%s/SMART/Java/Python/TestFiles/test_distance.bed" % (os.environ["REPET_PATH"])
33 self._outputFileName = '%s/SMART/Java/Python/test/obsOutput.gff3' % (os.environ["REPET_PATH"])
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)
35 os.system(cmd)
36 self._expOutputFileName = '%s/SMART/Java/Python/test/expOutput.gff3' % (os.environ["REPET_PATH"])
37 self._writeExpGff3File_test2(self._expOutputFileName)
38 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
39
40 def test_run_GFF3toCSV(self):
41 self._inputFileName = "%s/SMART/Java/Python/TestFiles/mapperAnalyzerExpected.gff3" % (os.environ["REPET_PATH"])
42 self._outputFileName = '%s/SMART/Java/Python/test/obsOutput.csv' % (os.environ["REPET_PATH"])
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)
44 os.system(cmd)
45 self._expOutputFileName = '%s/SMART/Java/Python/test/expOutput.csv' % (os.environ["REPET_PATH"])
46 self._writeExpCsvFile(self._expOutputFileName)
47
48 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
49
50 def test_run_GFF3toSam(self):
51 self._inputFileName = "%s/SMART/Java/Python/TestFiles/mapperAnalyzerExpected.gff3" % (os.environ["REPET_PATH"])
52 self._outputFileName = '%s/SMART/Java/Python/test/obsOutput.sam' % (os.environ["REPET_PATH"])
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)
54 os.system(cmd)
55 self._expOutputFileName = '%s/SMART/Java/Python/test/expOutput.sam' % (os.environ["REPET_PATH"])
56 self._writeExpSamFile(self._expOutputFileName)
57 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
58
59 def test_run_Gff3toWig(self):
60 self._inputFileName = '%s/SMART/Java/Python/TestFiles/sorted_query.gff3' % (os.environ["REPET_PATH"])
61 self._outputFileName = '%s/SMART/Java/Python/test/obsOutput.wig' % (os.environ["REPET_PATH"])
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)
63 os.system(cmd)
64 outputFile = '%s/SMART/Java/Python/TestFiles/sorted_query_wig.wig' % (os.environ["REPET_PATH"])
65 self.assertTrue(Utils.diff(outputFile, self._outputFileName))
66
67 def _writeInputSam(self, fileName):
68 file = open(fileName, 'w')
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' )
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' )
71 file.write( 'HWI-EAS337_3:7:1:208:1489\t77\t*\t0\t0\t*\t*\t0\t0\tGGAAACATATGCACATAAACGTTGAAATCATGCTTA\tWWWWWWWWWWWWWWWWWVWWVWWVWWWWWWUUUUUU\n' )
72 file.write( 'HWI-EAS337_3:7:1:208:1489\t141\t*\t0\t0\t*\t*\t0\t0\tCGTGTTTTTGGTTGTGCATAAGGCTTTTTAAAGTAA\tWWWWWWWWWVVWWQWVWVWWVUVWWWWWWVRTRTTR\n' )
73 file.write( 'HWI-EAS337_3:7:1:278:1153\t77\t*\t0\t0\t*\t*\t0\t0\tGAGAAAACCTGTAATAAATACTGAGAGAAAGTAGGG\tWWWWWWWWWWWWWWWWWWWWWWVWVVVWWVUUUUUR\n' )
74 file.write( 'HWI-EAS337_3:7:1:278:1153\t141\t*\t0\t0\t*\t*\t0\t0\tGTCAGGCCGCATTGATGGGGGATGGGTTTCCCCCCA\tWWWVWWWWWWWWWVVVVVVVVVVWWWVVVVTTTTTR\n' )
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' )
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' )
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' )
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' )
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' )
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' )
81 file.close()
82
83 def _writeExpGff3File_test1(self, fileName):
84 file = open(fileName, 'w')
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')
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')
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')
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')
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')
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')
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')
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')
93 file.close()
94
95 def _writeExpGff3File_test2(self, fileName):
96 file = open(fileName, 'w')
97 file.write( 'arm_X\tSMART\ttranscript\t1000\t1999\t.\t+\t.\tID=test2.1;Name=test2.1\n' )
98 file.write( 'arm_X\tSMART\ttranscript\t250\t349\t.\t+\t.\tID=test2.2;Name=test2.2\n' )
99 file.write( 'arm_X\tSMART\ttranscript\t150\t249\t.\t+\t.\tID=test2.3;Name=test2.3\n' )
100 file.close()
101
102 def _writeExpCsvFile(self, fileName):
103 file = open(fileName, 'w')
104 file.write( 'chromosome,start,end,strand,exons,ID,bestRegion,feature,identity,nbGaps,nbMismatches,nbOccurrences,occurrence,rank,score\n' )
105 file.write( 'chr1,6155418,6155441,"+",None,test1/1,(self),match,100,0,0,1,1,1,24\n' )
106 file.write( 'chr2,26303950,26303981,"+",None,test2/1-1,(self),match,93,0,2,3,1,1,32\n' )
107 file.write( 'chr3,28320540,28320574,"+",None,test2/1-2,chr2:26303950-26303981,match,94,0,2,3,2,None,35\n' )
108 file.write( 'chr4,28565007,28565041,"+",None,test2/1-3,chr2:26303950-26303981,match,88,0,4,3,3,3,35\n' )
109 file.close()
110
111 def _writeExpSamFile(self, fileName):
112 file = open(fileName, 'w')
113 file.write('@SQ\tSN:chr4\tLN:28565041\n')
114 file.write('@SQ\tSN:chr3\tLN:28320574\n')
115 file.write('@SQ\tSN:chr2\tLN:26303981\n')
116 file.write('@SQ\tSN:chr1\tLN:6155441\n')
117 file.write('test1/1\t0\tchr1\t6155418\t255\t24M\t*\t0\t0\t*\t*\tNM:i:0\n')
118 file.write('test2/1\t0\tchr2\t26303950\t255\t32M\t*\t0\t0\t*\t*\tNM:i:0\n')
119 file.write('test2/1\t0\tchr3\t28320540\t255\t35M\t*\t0\t0\t*\t*\tNM:i:0\n')
120 file.write('test2/1\t0\tchr4\t28565007\t255\t35M\t*\t0\t0\t*\t*\tNM:i:0\n')
121 file.close()
122
123
124 if __name__ == "__main__":
125 unittest.main()