Mercurial > repos > yufei-luo > s_mart

comparison commons/core/parsing/test/Test_PalsToAlign.py @ 6:769e306b7933

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author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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5:ea3082881bf8 6:769e306b7933
1 import unittest
2 from commons.core.utils.FileUtils import FileUtils
3 import os
4 from commons.core.parsing.PalsToAlign import PalsToAlign
5
6 class Test_PalsToAlign(unittest.TestCase):
7
8 def setUp(self):
9 self._palsFileName = "input.gff"
10 self._expAlignFileName = "file.align"
11 self._obsAlignFileName = "output.align"
12
13 def tearDown(self):
14 os.remove(self._palsFileName)
15 os.remove(self._expAlignFileName)
16 os.remove(self._obsAlignFileName)
17
18 def testRun(self):
19 self._writePalsFile(self._palsFileName)
20 self._writeExpAlignFile(self._expAlignFileName)
21
22 iPalsToAlign = PalsToAlign(self._palsFileName,self._obsAlignFileName)
23 iPalsToAlign.run()
24
25 self.assertTrue(FileUtils.are2FilesIdentical(self._expAlignFileName, self._obsAlignFileName))
26
27
28 def _writePalsFile(self, fileName):
29 f = open(fileName, "w")
30 f.write("chunk01\tpals\thit\t32290\t32583\t252\t+\t.\tTarget chunk02 28975 29268; maxe 0.035\n")
31 f.write("chunk01\tpals\thit\t28975\t29268\t252\t+\t.\tTarget chunk02 32290 32583; maxe 0.035\n")
32 f.write("chunk01\tpals\thit\t65932\t66032\t68\t+\t.\tTarget chunk02 59293 59395; maxe 0.085\n")
33 f.close()
34
35 def _writeExpAlignFile(self, fileName):
36 f = open(fileName, "w")
37 f.write("chunk01\t28975\t29268\tchunk02\t32290\t32583\t0.0\t252\t96.5\n")
38 f.write("chunk01\t32290\t32583\tchunk02\t28975\t29268\t0.0\t252\t96.5\n")
39 f.write("chunk01\t65932\t66032\tchunk02\t59293\t59395\t0.0\t68\t91.5\n")
40 f.close()
41
42 if __name__ == "__main__":
43 unittest.main()