Mercurial > repos > yufei-luo > s_mart

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

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Uploaded
author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
children
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30:5677346472b5 31:0ab839023fe4
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()