Mercurial > repos > yufei-luo > s_mart
comparison SMART/Java/Python/test/Test_F_getWigData.py @ 31:0ab839023fe4
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author | m-zytnicki |
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date | Tue, 30 Apr 2013 14:33:21 -0400 |
parents | 94ab73e8a190 |
children |
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30:5677346472b5 | 31:0ab839023fe4 |
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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() |