Mercurial > repos > yufei-luo > s_mart

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
parents
children
comparison
equal deleted inserted replaced
17:b0e8584489e6 18:94ab73e8a190
1 import unittest
2 import os
3 from commons.core.utils.FileUtils import FileUtils
4 from SMART.Java.Python.getWigDistance import *
5
6 class Test_F_getWigDistance(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._outFileName = 'outGffWig.png'
14
15 def tearDown(self):
16 os.remove(self._inputGffFileName)
17 os.remove(self._outFileName)
18
19 def test_getWigDistance_defaultOption(self):
20 cmd = 'python ../getWigDistance.py -i %s -f gff3 -w %s -d 10 -o %s' % (self._inputGffFileName, self._inputWigFileName, self._outFileName)
21 os.system(cmd)
22
23 def test_getWigDistance_strandsOption(self):
24 cmd = 'python ../getWigDistance.py -i %s -f gff3 -w %s -d 10 -o %s -s' % (self._inputGffFileName, self._inputWigFileName, self._outFileName)
25 os.system(cmd)
26
27 def test_getWigDistance_logOption(self):
28 cmd = 'python ../getWigDistance.py -i %s -f gff3 -w %s -d 10 -o %s -l' % (self._inputGffFileName, self._inputWigFileName, self._outFileName)
29 os.system(cmd)
30
31 def _writeInputGff(self, fileName):
32 f = open(fileName, 'w')
33 f.write("chr1\tquery\ttest1.1\t25\t150\t126\t+\t.\tID=query_1;Name=test1.1\n")
34 f.write("chr1\tquery\ttest1.2\t70\t850\t781\t-\t.\tID=query_2;Name=test1.2\n")
35 f.write("chr1\tquery\ttest1.3\t550\t850\t201\t-\t.\tID=query_3;Name=test1.3\n")
36 f.write("chr1\tquery\ttest1.4\t925\t1025\t101\t+\t.\tID=query_4;Name=test1.4\n")
37 f.write("chr1\tquery\ttest1.5\t1201\t1210\t10\t+\t.\tID=query_5;Name=test1.5\n")
38 f.write("chr1\tquery\ttest1.6\t1500\t1600\t101\t+\t.\tID=query_6;Name=test1.6\n")
39 f.close()
40
41
42
43 if __name__ == "__main__":
44 #import sys;sys.argv = ['', 'Test.testName']
45 unittest.main()