Mercurial > repos > yufei-luo > s_mart

comparison SMART/Java/Python/test/Test_F_clusterizeBySlidingWindows.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.misc import Utils
5
6
7 class Test_F_clusterizeBySlidingWindows(unittest.TestCase):
8
9 def setUp(self):
10 self._outputFileName = 'output.gff3'
11 self._outputCsvFileName = 'output.csv'
12 self._outputPngFileName = 'output.png'
13 self._expectedOutputFileName = 'expOut.png'
14
15 def tearDown(self):
16 for fileName in (self._outputFileName, self._outputCsvFileName, self._outputPngFileName, self._expectedOutputFileName):
17 if os.path.exists(fileName):
18 os.remove(fileName)
19
20 def test_run_default_option(self):
21 cmd = "python ../clusterizeBySlidingWindows.py -i ../TestFiles/mapperAnalyzerExpected.gff3 -f gff3 -o %s -s 50000 -e 50 -v 0" % (self._outputFileName)
22 os.system(cmd)
23 exp = '../TestFiles/clusterize_default_expected.gff3'
24 self.assertTrue(Utils.diff(exp, self._outputFileName))
25
26 def test_run_default_option_map_output(self):
27 self._outputFileName = 'output.map'
28 cmd = "python ../clusterizeBySlidingWindows.py -i ../TestFiles/mapperAnalyzerExpected.gff3 -f gff3 -o %s -s 50000 -e 50 -u map -v 0" % (self._outputFileName)
29 os.system(cmd)
30 exp = '../TestFiles/clusterize_default_expected.map'
31 self.assertTrue(Utils.diff(exp, self._outputFileName))
32
33 def test_run_newTag_option(self):
34 cmd = "python ../clusterizeBySlidingWindows.py -i ../TestFiles/mapperAnalyzerExpected.gff3 -f gff3 -o %s -s 50000 -e 50 -w newTag -v 0" % (self._outputFileName)
35 os.system(cmd)
36 exp = '../TestFiles/clusterize_output_tag_expected.gff3'
37 self.assertTrue(Utils.diff(exp, self._outputFileName))
38
39 def test_run_normalize_option(self):
40 cmd = "python ../clusterizeBySlidingWindows.py -i ../TestFiles/mapperAnalyzerOutput.gff3 -f gff3 -o %s -s 50000 -e 50 -m -v 0" % (self._outputFileName)
41 os.system(cmd)
42 exp = '../TestFiles/clusterize_normalize_expected.gff3'
43 self.assertTrue(Utils.diff(exp, self._outputFileName))
44
45 def test_run_strand_option(self):
46 cmd = "python ../clusterizeBySlidingWindows.py -i ../TestFiles/mapperAnalyzerOutput.gff3 -f gff3 -o %s -s 50000 -e 50 -2 -v 0" % (self._outputFileName)
47 os.system(cmd)
48 exp = '../TestFiles/clusterize_strands_expected.gff3'
49 self.assertTrue(Utils.diff(exp, self._outputFileName))
50
51 def test_run_excel_option(self):
52 cmd = "python ../clusterizeBySlidingWindows.py -i ../TestFiles/mapperAnalyzerOutput.gff3 -f gff3 -o %s -s 50000 -e 50 -x %s -v 0" % (self._outputFileName, self._outputCsvFileName)
53 os.system(cmd)
54 self.assertTrue(FileUtils.isRessourceExists(self._outputCsvFileName))
55
56
57 def test_run_normalize_strand_excel_option(self):
58 cmd = "python ../clusterizeBySlidingWindows.py -i ../TestFiles/mapperAnalyzerOutput.gff3 -f gff3 -o %s -s 50000 -e 50 -m -2 -x %s -v 0" % (self._outputFileName, self._outputCsvFileName)
59 os.system(cmd)
60 self.assertTrue(FileUtils.isRessourceExists(self._outputCsvFileName))
61
62 def test_run_tag_operation_options(self):
63 cmd = "python ../clusterizeBySlidingWindows.py -i ../TestFiles/testSW.gff3 -f gff -s 100 -e 0 -g value1 -r min -o %s -v 0" % (self._outputFileName)
64 os.system(cmd)
65 exp = open(self._expectedOutputFileName, 'w')
66 exp.write("chr1\tS-MART\ttranscript\t1\t100\t.\t+\t.\tnbElements=0;minValue1=0;ID=region1;Name=region1\n")
67 exp.write("chr1\tS-MART\ttranscript\t101\t200\t.\t+\t.\tnbElements=2.000000;minValue1=1.0;ID=region2;Name=region2\n")
68 exp.write("chr1\tS-MART\ttranscript\t201\t300\t.\t+\t.\tnbElements=2.000000;minValue1=10.0;ID=region3;Name=region3\n")
69 exp.close()
70 self.assertTrue(Utils.diff(self._outputFileName, self._expectedOutputFileName))
71
72 def test_run_plot_options(self):
73 cmd = "python ../clusterizeBySlidingWindows.py -i ../TestFiles/testSW.gff3 -f gff -s 100 -e 0 -g value1 -r min -o %s -p %s -v 0" % (self._outputFileName, self._outputPngFileName)
74 os.system(cmd)
75 self.assertTrue(FileUtils.isRessourceExists(self._outputPngFileName))
76
77
78 if __name__ == "__main__":
79 unittest.main()