Mercurial > repos > yufei-luo > s_mart
view commons/core/parsing/test/Test_BowtieParser.py @ 6:769e306b7933
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author | yufei-luo |
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date | Fri, 18 Jan 2013 04:54:14 -0500 |
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from commons.core.parsing.BowtieParser import BowtieParser import unittest, os class Test_BlatParser(unittest.TestCase): def test_simple(self): fileName = "tmpFile.bowtie" handle = open(fileName, "w") 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") 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") 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") 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") handle.close() parser = BowtieParser("tmpFile.bowtie", 0) for cpt, mapping in enumerate(parser.getIterator()): transcript = mapping.getTranscript() if cpt == 0: self.assertEquals(transcript.getName(), "HWI-EAS179_0053:2:1:1365:7879#0/2") self.assertEquals(transcript.getChromosome(), "chrXHet") self.assertEquals(transcript.getDirection(), 1) self.assertEquals(transcript.getStart(), 191699) self.assertEquals(transcript.getEnd(), 191774) self.assertEquals(transcript.getTagValue("nbMismatches"), 2) elif cpt == 1: self.assertEquals(transcript.getName(), "HWI-EAS179_0053:2:1:1365:7879#0/1") self.assertEquals(transcript.getChromosome(), "chrXHet") self.assertEquals(transcript.getDirection(), -1) self.assertEquals(transcript.getStart(), 191804) self.assertEquals(transcript.getEnd(), 191879) self.assertEquals(transcript.getTagValue("nbMismatches"), 2) elif cpt == 2: self.assertEquals(transcript.getName(), "HWI-EAS179_0053:2:1:1371:11420#0/2") self.assertEquals(transcript.getChromosome(), "chr3L") self.assertEquals(transcript.getDirection(), 1) self.assertEquals(transcript.getStart(), 16569207) self.assertEquals(transcript.getEnd(), 16569282) self.assertEquals(transcript.getTagValue("nbMismatches"), 1) elif cpt == 3: self.assertEquals(transcript.getName(), "HWI-EAS179_0053:2:1:1371:11420#0/1") self.assertEquals(transcript.getChromosome(), "chr3L") self.assertEquals(transcript.getDirection(), -1) self.assertEquals(transcript.getStart(), 16569299) self.assertEquals(transcript.getEnd(), 16569374) self.assertEquals(transcript.getTagValue("nbMismatches"), 0) else: self.fail() os.remove(fileName) if __name__ == "__main__": unittest.main()