Mercurial > repos > yufei-luo > s_mart
comparison smart_toolShed/commons/core/parsing/test/Test_BlatToGff.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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-1:000000000000 | 0:e0f8dcca02ed |
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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() |