|
18
|
1 import unittest
|
|
|
2 import os, os.path
|
|
|
3 from SMART.Java.Python.misc import Utils
|
|
|
4 from SMART.Java.Python.getWigData import *
|
|
|
5
|
|
|
6 class Test_F_getWigData(unittest.TestCase):
|
|
|
7
|
|
|
8
|
|
|
9 def setUp(self):
|
|
|
10 self._inputGffFileName = 'inputGff.gff3'
|
|
|
11 self._writeInputGff(self._inputGffFileName)
|
|
|
12 self._inputWigFileName = '../TestFiles/sorted_query_wig.wig'
|
|
|
13 self._expOutFileName = 'expOut.gff3'
|
|
|
14 self._outFileName = 'outGffWig.gff3'
|
|
|
15
|
|
|
16
|
|
|
17 def tearDown(self):
|
|
|
18 os.remove(self._inputGffFileName)
|
|
|
19 os.remove(self._expOutFileName)
|
|
|
20 os.remove(self._outFileName)
|
|
|
21
|
|
|
22
|
|
|
23 def test_getWigData_DefaultOption_asScript(self):
|
|
|
24 cmd = 'python ../getWigData.py -i %s -f gff3 -w %s -t wigValue -o %s -v 0' % (self._inputGffFileName, self._inputWigFileName, self._outFileName)
|
|
|
25 os.system(cmd)
|
|
|
26 self._writeExpDefaultOption(self._expOutFileName)
|
|
|
27 self.assertTrue(Utils.diff(self._expOutFileName, self._outFileName))
|
|
|
28
|
|
|
29 def test_getWigData_strandsOption(self):
|
|
|
30 cmd = 'python ../getWigData.py -i %s -f gff3 -w %s -t wigValue -o %s -s -v 0' % (self._inputGffFileName, self._inputWigFileName, self._outFileName)
|
|
|
31 os.system(cmd)
|
|
|
32 self._writeExpStransOption(self._expOutFileName)
|
|
|
33 self.assertTrue(Utils.diff(self._expOutFileName, self._outFileName))
|
|
|
34
|
|
|
35
|
|
|
36 def _writeInputGff(self, fileName):
|
|
|
37 f = open(fileName, 'w')
|
|
|
38 f.write("chr1\tquery\ttest1.1\t25\t150\t126\t+\t.\tID=query_1;Name=test1.1\n")
|
|
|
39 f.write("chr1\tquery\ttest1.2\t70\t850\t781\t-\t.\tID=query_2;Name=test1.2\n")
|
|
|
40 f.write("chr1\tquery\ttest1.3\t550\t850\t201\t-\t.\tID=query_3;Name=test1.3\n")
|
|
|
41 f.write("chr1\tquery\ttest1.4\t925\t1025\t101\t+\t.\tID=query_4;Name=test1.4\n")
|
|
|
42 f.write("chr1\tquery\ttest1.5\t1201\t1210\t10\t+\t.\tID=query_5;Name=test1.5\n")
|
|
|
43 f.write("chr1\tquery\ttest1.6\t1500\t1600\t101\t+\t.\tID=query_6;Name=test1.6\n")
|
|
|
44 f.close()
|
|
|
45
|
|
|
46 def _writeExpDefaultOption(self, fileName):
|
|
|
47 f = open(fileName, 'w')
|
|
|
48 f.write("chr1\tS-MART\ttest1.1\t25\t150\t126\t+\t.\twigValue=1.64285714286;ID=query_1;Name=test1.1\n")
|
|
|
49 f.write("chr1\tS-MART\ttest1.2\t70\t850\t781\t-\t.\twigValue=1.48911651729;ID=query_2;Name=test1.2\n")
|
|
|
50 f.write("chr1\tS-MART\ttest1.3\t550\t850\t201\t-\t.\twigValue=2.0;ID=query_3;Name=test1.3\n")
|
|
|
51 f.write("chr1\tS-MART\ttest1.4\t925\t1025\t101\t+\t.\twigValue=1.0;ID=query_4;Name=test1.4\n")
|
|
|
52 f.write("chr1\tS-MART\ttest1.5\t1201\t1210\t10\t+\t.\twigValue=1.0;ID=query_5;Name=test1.5\n")
|
|
|
53 f.write("chr1\tS-MART\ttest1.6\t1500\t1600\t101\t+\t.\twigValue=1.0;ID=query_6;Name=test1.6\n")
|
|
|
54 f.close()
|
|
|
55
|
|
|
56 def _writeExpStransOption(self, fileName):
|
|
|
57 f = open(fileName, 'w')
|
|
|
58 f.write("chr1\tS-MART\ttest1.1\t25\t150\t126\t+\t.\twigValue=0.0;ID=query_1;Name=test1.1\n")
|
|
|
59 f.write("chr1\tS-MART\ttest1.2\t70\t850\t781\t-\t.\twigValue=0.0;ID=query_2;Name=test1.2\n")
|
|
|
60 f.write("chr1\tS-MART\ttest1.3\t550\t850\t201\t-\t.\twigValue=0.0;ID=query_3;Name=test1.3\n")
|
|
|
61 f.write("chr1\tS-MART\ttest1.4\t925\t1025\t101\t+\t.\twigValue=0.0;ID=query_4;Name=test1.4\n")
|
|
|
62 f.write("chr1\tS-MART\ttest1.5\t1201\t1210\t10\t+\t.\twigValue=0.0;ID=query_5;Name=test1.5\n")
|
|
|
63 f.write("chr1\tS-MART\ttest1.6\t1500\t1600\t101\t+\t.\twigValue=0.0;ID=query_6;Name=test1.6\n")
|
|
|
64 f.close()
|
|
|
65
|
|
|
66
|
|
|
67
|
|
|
68
|
|
|
69
|
|
|
70 if __name__ == "__main__":
|
|
|
71 unittest.main()
|
