Mercurial > repos > yufei-luo > s_mart

comparison commons/core/parsing/test/Test_BlatToGff.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 from commons.core.parsing.BlatToGff import BlatToGff
2 import unittest
3
4
5 class Test_BlatToGff(unittest.TestCase):
6
7
8 def test_convertBlatObjectToGffLine(self):
9 blatLine = '315\t20\t0\t0\t3\t10\t2\t9\t+\tMRRE1H001H13FM1\t378\t0\t345\tchr16\t22053297\t21686950\t21687294\t4\t76,185,7,67,\t0,77,263,278,\t21686950,21687026,21687213,21687227,\n'
10 nbLine = 15
11 iBlatToGff = BlatToGff()
12 BlatToGff._methodName = ''
13 obsGffLine = iBlatToGff.convertBlatObjectToGffLine(blatLine, nbLine)
14 expGffLine = 'chr16\tBlatToGff\tBES\t21686950\t21687294\t.\t+\t.\tID=MRRE1H001H13FM1;Name=MRRE1H001H13FM1;bes_start=21686950;bes_end=21687294;bes_size=22053297\n'
15 self.assertEquals(expGffLine, obsGffLine)
16
17 def test_convertBlatObjectToGffLine_with_methodName(self):
18 blatLine = '315\t20\t0\t0\t3\t10\t2\t9\t+\tMRRE1H001H13FM1\t378\t0\t345\tchr16\t22053297\t21686950\t21687294\t4\t76,185,7,67,\t0,77,263,278,\t21686950,21687026,21687213,21687227,\n'
19 nbLine = 15
20 iBlatToGff = BlatToGff()
21 BlatToGff._methodName = 'Test'
22 obsGffLine = iBlatToGff.convertBlatObjectToGffLine(blatLine, nbLine)
23 expGffLine = 'chr16\tBlatToGff\tTest:BES\t21686950\t21687294\t.\t+\t.\tID=MRRE1H001H13FM1;Name=MRRE1H001H13FM1;bes_start=21686950;bes_end=21687294;bes_size=22053297\n'
24 self.assertEquals(expGffLine, obsGffLine)
25
26
27 if __name__ == "__main__":
28 unittest.main()