Mercurial > repos > yufei-luo > s_mart

comparison SMART/Java/Python/test/Test_F_getLetterDistribution.py @ 18:94ab73e8a190

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author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
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17:b0e8584489e6 18:94ab73e8a190
1 import os
2 import sys
3 import unittest
4 from SMART.Java.Python.test.MockGetLetterDistribution import MockGetLetterDistributionFasta
5 from SMART.Java.Python.test.MockGetLetterDistribution import MockGetLetterDistributionFastq
6 from SMART.Java.Python.test.MockGetLetterDistribution import MockGetLetterDistributionExpectedCSV
7
8 class Test_F_getLetterDistribution(unittest.TestCase):
9
10 def tearDown(self):
11 os.system("rm tmp*.*")
12
13 def test_getLetterDistributionWithFasta(self):
14 iFastaMock = MockGetLetterDistributionFasta()
15 fastaFileName = "MockFasta_GetLetterDistribution.fa"
16 iFastaMock.write(fastaFileName)
17
18 outputName = "dummy_result_fasta"
19 os.system("python %s/SMART/Java/Python/getLetterDistribution.py -i %s -f fasta -o %s" % (os.environ["REPET_PATH"], fastaFileName, outputName))
20
21 self.assertTrue (os.path.exists(outputName + ".png"))
22 self.assertTrue (os.path.exists(outputName + "PerNt.png"))
23
24 os.remove(outputName + ".png")
25 os.remove(outputName + "PerNt.png")
26 os.remove(fastaFileName)
27
28 def test_getLetterDistributionWithFastq(self):
29 iFastqMock = MockGetLetterDistributionFastq()
30 fastqFileName = "MockFastq_GetLetterDistribution.fastq"
31 iFastqMock.write(fastqFileName)
32
33 outputName = "dummy_result_fastq"
34 os.system("python %s/SMART/Java/Python/getLetterDistribution.py -i %s -f fastq -o %s" % (os.environ["REPET_PATH"], fastqFileName, outputName))
35
36 self.assertTrue (os.path.exists(outputName + ".png"))
37 self.assertTrue (os.path.exists(outputName + "PerNt.png"))
38
39 os.remove(fastqFileName)
40 os.remove(outputName + ".png")
41 os.remove(outputName + "PerNt.png")
42
43 def test_getLetterDistributionWithFastaCSVOutput(self):
44 iFastaMock = MockGetLetterDistributionFasta()
45 fastaFileName = "MockFasta_GetLetterDistribution.fa"
46 iFastaMock.write(fastaFileName)
47
48 iCSVMock = MockGetLetterDistributionExpectedCSV()
49 expCSVFileName = "expCSV.csv"
50 iCSVMock.write(expCSVFileName)
51
52 outputName = "dummy_result_fasta"
53 os.system("python %s/SMART/Java/Python/getLetterDistribution.py -i %s -f fasta -o %s -c" % (os.environ["REPET_PATH"], fastaFileName, outputName))
54
55 obsCSVFileName = outputName + ".csv"
56
57 self.assertTrue (os.path.exists(outputName + ".png"))
58 self.assertTrue (os.path.exists(outputName + "PerNt.png"))
59 self.assertTrue (self._are2FilesIdentical(expCSVFileName, obsCSVFileName))
60
61 os.remove(outputName + ".png")
62 os.remove(outputName + "PerNt.png")
63 os.remove(fastaFileName)
64 os.remove(expCSVFileName)
65 os.remove(obsCSVFileName)
66
67 def test_getLetterDistributionWithFastqCVSOutput(self):
68 iFastqMock = MockGetLetterDistributionFastq()
69 fastqFileName = "MockFastq_GetLetterDistribution.fastq"
70 iFastqMock.write(fastqFileName)
71
72 iCSVMock = MockGetLetterDistributionExpectedCSV()
73 expCSVFileName = "expCSV.csv"
74 iCSVMock.write(expCSVFileName)
75
76 outputName = "dummy_result_fastq"
77 os.system("python %s/SMART/Java/Python/getLetterDistribution.py -i %s -f fastq -o %s -c" % (os.environ["REPET_PATH"], fastqFileName, outputName))
78
79 obsCSVFileName = outputName + ".csv"
80
81 self.assertTrue (os.path.exists(outputName + ".png"))
82 self.assertTrue (os.path.exists(outputName + "PerNt.png"))
83 self.assertTrue (self._are2FilesIdentical(expCSVFileName, obsCSVFileName))
84
85 os.remove(fastqFileName)
86 os.remove(outputName + ".png")
87 os.remove(outputName + "PerNt.png")
88 os.remove(expCSVFileName)
89 os.remove(obsCSVFileName)
90
91 def _are2FilesIdentical(self, file1, file2 ):
92 tmpFile = "diff_%s_%s" % ( os.path.basename(file1), os.path.basename(file2) )
93 cmd = "diff %s %s >> %s" % ( file1, file2, tmpFile )
94 returnStatus = os.system( cmd )
95 if returnStatus != 0:
96 msg = "ERROR: 'diff' returned '%i'" % ( returnStatus )
97 sys.stderr.write( "%s\n" % msg )
98 sys.stderr.flush()
99 os.remove( tmpFile )
100 return False
101 if self.isEmpty( tmpFile ):
102 os.remove( tmpFile )
103 return True
104 else:
105 os.remove( tmpFile )
106 return False
107
108 def getNbLinesInSingleFile(self, fileName):
109 fileHandler = open(fileName, "r" )
110 lines = fileHandler.readlines()
111 fileHandler.close()
112 return len(lines)
113
114 def isEmpty(self, fileName):
115 return 0 == self.getNbLinesInSingleFile( fileName )
116
117 if __name__ == "__main__":
118 unittest.main()