Mercurial > repos > yufei-luo > s_mart
comparison commons/core/parsing/test/Test_BowtieParser.py @ 31:0ab839023fe4
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author | m-zytnicki |
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date | Tue, 30 Apr 2013 14:33:21 -0400 |
parents | 769e306b7933 |
children |
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30:5677346472b5 | 31:0ab839023fe4 |
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1 from commons.core.parsing.BowtieParser import BowtieParser | |
2 import unittest, os | |
3 | |
4 | |
5 class Test_BlatParser(unittest.TestCase): | |
6 | |
7 | |
8 def test_simple(self): | |
9 fileName = "tmpFile.bowtie" | |
10 handle = open(fileName, "w") | |
11 handle.write("HWI-EAS179_0053:2:1:1365:7879#0/2\t+\tchrXHet\t191698\tACCGCTGAACCACTTTCATNCNTGGGATTGTGAACTGAAACTGTTCACATGAACTTGGAATTCCCAGTAAGTGTGA\tLcaYcacLaTdd`dacacYBaBTa^^TL^M`]`^aa`Tca`LaLTUa]a_bcLcTMMMMa^a^`bT`ccT_UbM_B\t0\t19:G>N,21:T>N\n") | |
12 handle.write("HWI-EAS179_0053:2:1:1365:7879#0/1\t-\tchrXHet\t191803\tCCCCTTGTACACACCGCCCGTCGCTACTACCGATTGAATTATGTAGTGAGGTCTCCGGACGTGATCACTGTGACGC\tBBBBBBBBB`O`DS]]aYabaaa[ULYLY]^b`^a^aZZZ_LLLca_a_b^^aYdbd``d^ccaY`_caccc^acc\t0\t33:T>G,72:T>C\n") | |
13 handle.write("HWI-EAS179_0053:2:1:1371:11420#0/2\t+\tchr3L\t16569206\tTATGAGCGCCAATTTTGCANTTTTATTTTTGTACAAGCCAAGGGTTTTGCAACATTCACAGCGCTTGCCACTTGTC\tcY^bcYLcaL]`]]`aaTaBaab^_ZZ__R[`[cYccc^Ybb^_L`L`Y`aM_a_TcTcc`LL]]MYaYabbTY`^\t0\t19:G>N\n") | |
14 handle.write("HWI-EAS179_0053:2:1:1371:11420#0/1\t-\tchr3L\t16569298\tAATGAACCATTGTAATTACCCACAACACATACAGTCACACACGAGATGCACACAAGTCGGAAACGGAAGCGAGACG\tBBBBBBBBBBBBBBBBBBBBBB^T`]Y^`KZY__LY_a]^T^ccYaYY__YT]VZbL]`b^cLT^a^caccYbT^b\t0\n") | |
15 handle.close() | |
16 | |
17 parser = BowtieParser("tmpFile.bowtie", 0) | |
18 for cpt, mapping in enumerate(parser.getIterator()): | |
19 transcript = mapping.getTranscript() | |
20 if cpt == 0: | |
21 self.assertEquals(transcript.getName(), "HWI-EAS179_0053:2:1:1365:7879#0/2") | |
22 self.assertEquals(transcript.getChromosome(), "chrXHet") | |
23 self.assertEquals(transcript.getDirection(), 1) | |
24 self.assertEquals(transcript.getStart(), 191699) | |
25 self.assertEquals(transcript.getEnd(), 191774) | |
26 self.assertEquals(transcript.getTagValue("nbMismatches"), 2) | |
27 elif cpt == 1: | |
28 self.assertEquals(transcript.getName(), "HWI-EAS179_0053:2:1:1365:7879#0/1") | |
29 self.assertEquals(transcript.getChromosome(), "chrXHet") | |
30 self.assertEquals(transcript.getDirection(), -1) | |
31 self.assertEquals(transcript.getStart(), 191804) | |
32 self.assertEquals(transcript.getEnd(), 191879) | |
33 self.assertEquals(transcript.getTagValue("nbMismatches"), 2) | |
34 elif cpt == 2: | |
35 self.assertEquals(transcript.getName(), "HWI-EAS179_0053:2:1:1371:11420#0/2") | |
36 self.assertEquals(transcript.getChromosome(), "chr3L") | |
37 self.assertEquals(transcript.getDirection(), 1) | |
38 self.assertEquals(transcript.getStart(), 16569207) | |
39 self.assertEquals(transcript.getEnd(), 16569282) | |
40 self.assertEquals(transcript.getTagValue("nbMismatches"), 1) | |
41 elif cpt == 3: | |
42 self.assertEquals(transcript.getName(), "HWI-EAS179_0053:2:1:1371:11420#0/1") | |
43 self.assertEquals(transcript.getChromosome(), "chr3L") | |
44 self.assertEquals(transcript.getDirection(), -1) | |
45 self.assertEquals(transcript.getStart(), 16569299) | |
46 self.assertEquals(transcript.getEnd(), 16569374) | |
47 self.assertEquals(transcript.getTagValue("nbMismatches"), 0) | |
48 else: | |
49 self.fail() | |
50 | |
51 os.remove(fileName) | |
52 | |
53 | |
54 | |
55 if __name__ == "__main__": | |
56 unittest.main() | |
57 |