Mercurial > repos > yufei-luo > s_mart

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

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author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
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17:b0e8584489e6 18:94ab73e8a190
1 import unittest
2 import os
3 from SMART.Java.Python.GetRandomSubset import GetRandomSubset
4 from commons.core.parsing.BedParser import BedParser
5 from commons.core.parsing.GffParser import GffParser
6
7 class Test_F_GetRandomSubset(unittest.TestCase):
8
9 def setUp(self):
10 self._inputFileName = "inputFileTest.bed"
11 self._writeInputFile()
12 self._outputFileName = "output.gff3"
13
14 def tearDown(self):
15 os.remove(self._inputFileName)
16 os.remove(self._outputFileName)
17
18 def test_run_simple(self):
19 nbElements = 2
20 inputTranscripts = []
21 parser = BedParser(self._inputFileName, 0)
22 for transcript in parser.getIterator():
23 inputTranscripts.append(transcript)
24 grs = GetRandomSubset(0)
25 grs.setInputFile(self._inputFileName, "bed")
26 grs.setNumber(nbElements, None)
27 grs.setOutputFile(self._outputFileName)
28 grs.run()
29 outputTranscripts = []
30 parser = GffParser(self._outputFileName, 0)
31 for transcript in parser.getIterator():
32 outputTranscripts.append(transcript)
33 self.assertEqual(len(outputTranscripts), nbElements)
34 for outputTranscript in outputTranscripts:
35 for inputTranscript in inputTranscripts:
36 if outputTranscript.getChromosome() == inputTranscript.getChromosome() and outputTranscript.getDirection() == inputTranscript.getDirection() and outputTranscript.getStart() == inputTranscript.getStart() and outputTranscript.getEnd() == inputTranscript.getEnd() and outputTranscript.getName() == inputTranscript.getName():
37 break
38 else:
39 self.fail()
40
41 def _writeInputFile(self):
42 f = open(self._inputFileName, "w")
43 f.write("arm_X\t10000100\t10000200\ttest1.1\t100\t+\t10000100\t10000200\t0\t1\t100,\t0,\n")
44 f.write("arm_X\t10000100\t10000200\ttest1.2\t100\t-\t10000100\t10000200\t0\t1\t100,\t0,\n")
45 f.write("arm_2R\t10000100\t10000200\ttest1.3\t100\t+\t10000100\t10000200\t0\t1\t100,\t0,\n")
46 f.write("arm_X\t10000000\t10000100\ttest1.4\t100\t+\t10000000\t10000100\t0\t1\t100,\t0,\n")
47 f.write("arm_X\t10000200\t10000300\ttest1.5\t100\t+\t10000200\t10000300\t0\t1\t100,\t0,\n")
48 f.write("arm_X\t9999900\t9999950\ttest1.6\t100\t+\t9999900\t9999950\t0\t1\t50,\t0,\n")
49 f.write("arm_X\t10000000\t10000050\ttest1.7\t100\t-\t10000000\t10000050\t0\t1\t50,\t0,\n")
50 f.close()
51
52
53
54 if __name__ == "__main__":
55 unittest.main()