Mercurial > repos > yufei-luo > s_mart

comparison SMART/Java/Python/test/Test_F_CollapseReads.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 unittest
2 import os
3 from SMART.Java.Python.CollapseReads import CollapseReads
4 from SMART.Java.Python.misc import Utils
5 from commons.core.utils.FileUtils import FileUtils
6 from SMART.Java.Python.ncList.test.MockFindOverlaps_randomExample import MockFindOverlaps_randomExample_NonOrder
7
8 class Test_F_CollapseReads(unittest.TestCase):
9
10 def setUp(self):
11 self._inputFileName = 'inputCR.gff3'
12 self._writeInput(self._inputFileName)
13 self._outputFileName = 'outputCR.gff3'
14 self._expOutputFileName = 'expOutputCR.gff3'
15
16 def tearDown(self):
17 return
18
19 def test_run_default_option(self):
20 iCR = CollapseReads(0)
21 iCR.setInputFile(self._inputFileName, 'gff3')
22 iCR.setOutputFile(self._outputFileName)
23 iCR.strands = False
24 iCR.collapse()
25 self._writeExp_strand_False(self._expOutputFileName)
26 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
27
28 def test_run_strand_option(self):
29 iCR = CollapseReads(0)
30 iCR.setInputFile(self._inputFileName, 'gff3')
31 iCR.setOutputFile(self._outputFileName)
32 iCR.strands = True
33 iCR.collapse()
34 self._writeExp_strand_True(self._expOutputFileName)
35 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
36
37 def test_run_asScript_default_option(self):
38 cmd = 'python ../CollapseReads.py -i %s -f gff3 -o %s -v 0' % (self._inputFileName, self._outputFileName)
39 os.system(cmd)
40 self._writeExp_strand_True(self._expOutputFileName)
41 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
42
43 def test_run_asScript_strand_option(self):
44 cmd = 'python ../CollapseReads.py -i %s -f gff3 -o %s -s -v 0' % (self._inputFileName, self._outputFileName)
45 os.system(cmd)
46 self._writeExp_strand_False(self._expOutputFileName)
47 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
48
49 def test_run_toOrderGff(self):
50 iMRE = MockFindOverlaps_randomExample_NonOrder(self._inputFileName, 'chrom', 10, 1000)
51 iMRE.write()
52 iCR = CollapseReads(0)
53 iCR.setInputFile(self._inputFileName, 'gff3')
54 iCR.setOutputFile(self._outputFileName)
55 iCR.strands = False
56 iCR.collapse()
57 f = open(self._expOutputFileName, "w")
58 f.close()
59 cmd = 'sort -f -n -k4 -k5.4rn -o %s %s'%(self._expOutputFileName, self._inputFileName)
60 os.system(cmd)
61
62 def _writeInput(self, fileName):
63 f = open(fileName, 'w')
64 f.write("chr1\ttest\tmatch\t6155418\t6155441\t.\t+\t.\toccurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=test1/1;identity=100;Name=test1/1\n")
65 f.write("chr2\ttest\tmatch\t26303950\t26303981\t.\t+\t.\toccurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93;Name=test2/1\n")
66 f.write("chr3\ttest\tmatch\t28320540\t28320574\t.\t+\t.\toccurrence=2;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-2;identity=94;Name=test2/1\n")
67 f.write("chr4\ttest\tmatch\t28565007\t28565041\t.\t+\t.\toccurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88;Name=test2/1\n")
68 f.write("chr1\ttest\tmatch\t6155418\t6155441\t.\t+\t.\toccurrence=2;rank=2;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=1;ID=test3/1;identity=50;Name=test3/1\n")
69 f.write("chr1\ttest\tmatch\t6155418\t6155441\t.\t-\t.\toccurrence=2;rank=2;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=1;ID=test3/1;identity=50;Name=test3/1\n")
70 f.close()
71
72 def _writeExp_strand_False(self, fileName):
73 f = open(fileName, 'w')
74 f.write("""chr1 S-MART match 6155418 6155441 . - . nbElements=3.000000;ID=test3/1;Name=test3/1--test3/1--test1/1
75 chr2 S-MART match 26303950 26303981 . + . occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93;Name=test2/1
76 chr3 S-MART match 28320540 28320574 . + . occurrence=2;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-2;identity=94;Name=test2/1
77 chr4 S-MART match 28565007 28565041 . + . occurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88;Name=test2/1
78 """)
79 f.close()
80
81 def _writeExp_strand_True(self, fileName):
82 f = open(fileName, 'w')
83 f.write("""chr1 S-MART match 6155418 6155441 . + . nbElements=2.000000;ID=test3/1;Name=test3/1--test1/1
84 chr1 S-MART match 6155418 6155441 . - . occurrence=2;rank=2;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=1;ID=test3/1;identity=50;Name=test3/1
85 chr2 S-MART match 26303950 26303981 . + . occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93;Name=test2/1
86 chr3 S-MART match 28320540 28320574 . + . occurrence=2;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-2;identity=94;Name=test2/1
87 chr4 S-MART match 28565007 28565041 . + . occurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88;Name=test2/1
88 """)
89 f.close()
90
91 if __name__ == "__main__":
92 unittest.main()