Mercurial > repos > yufei-luo > s_mart
view commons/core/parsing/test/Test_VarscanToVCF.py @ 20:c265f13066d8
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author | m-zytnicki |
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date | Mon, 29 Apr 2013 03:24:43 -0400 |
parents | 94ab73e8a190 |
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import unittest from commons.core.parsing.VarscanToVCF import VarscanToVCF class Test_VarscanToVCF(unittest.TestCase): def setUp(self): self._iVarscanToVCF = VarscanToVCF(doClean = True, verbosity = 2) # def test_convertVarscanLineToVCFRecord(self): ## Chrom Position Ref Cons Reads1 Reads2 VarFreq Strands1 Strands2 Qual1 Qual2 Pvalue ## chr1 10 C Y 1 1 50% 1 1 68 69 0.49999999999999994 ## MapQual1 MapQual2 Reads1Plus Reads1Minus Reads2Plus Reads2Minus VarAllele ## 1 1 1 0 1 0 T # varscanLine = "chr1\t10\tC\tY\t1\t1\t50%\t1\t1\t68\t69\t0.49999999999999994\t1\t1\t1\t0\t1\t0\tT" # obsRecord = self._iVarscanToVCF._convertVarscanLineToVCFRecord(varscanLine, 1) # # expInfo = {"AF": "50%", # "DP": 2, # "MQ": "1"} # # expRecord = vcf.model._Record("chr1", 10, "1", "C", "T", 3.010299957, ".", expInfo, ".", None) ## CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, FORMAT, sample_indexes, samples=None # # self.assertEqual(expRecord.ID, obsRecord.ID) # self.assertEqual(expRecord.QUAL, obsRecord.QUAL) # self.assertEqual(expRecord.FILTER, obsRecord.FILTER) # self.assertEqual(expRecord.INFO, obsRecord.INFO) # self.assertEqual(expRecord.FORMAT, obsRecord.FORMAT) # self.assertEqual(expRecord, obsRecord) def test_convertVarscanLineToVCFLine(self): # Chrom Position Ref Cons Reads1 Reads2 VarFreq Strands1 Strands2 Qual1 Qual2 Pvalue # chr1 10 C Y 1 1 50% 1 1 68 69 0.49999999999999994 # MapQual1 MapQual2 Reads1Plus Reads1Minus Reads2Plus Reads2Minus VarAllele # 1 1 1 0 1 0 T varscanLine = "chr1\t10\tC\tY\t1\t1\t50%\t1\t1\t68\t69\t0.49999999999999994\t1\t1\t1\t0\t1\t0\tT" obsVCFLine = self._iVarscanToVCF._convertVarscanLineToVCFRecord(varscanLine, 1) expVCFLine = "chr1\t10\t.\tC\tT\t3.010299957\t.\tAF=0.5000;DP=2;RBQ=68;ABQ=69\n" # CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO self.assertEqual(expVCFLine, obsVCFLine) def test_convertVarscanLineToVCFLine_false_VarAllele(self): varscanLine = "chr1\t10\tC\tY\t1\t1\t50%\t1\t1\t68\t69\t0.49999999999999994\t1\t1\t1\t0\t1\t0\tA" obsVCFLine = self._iVarscanToVCF._convertVarscanLineToVCFRecord(varscanLine, 1) expVCFLine = "chr1\t10\t.\tC\tT\t3.010299957\t.\tAF=0.5000;DP=2;RBQ=68;ABQ=69\n" # CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO self.assertEqual(expVCFLine, obsVCFLine) def test_convertVarscanLineToVCFRecord_empty_line(self): obsMsg = "" try: self._iVarscanToVCF._convertVarscanLineToVCFRecord("", 10) except Exception as e: obsMsg = e.msg self.assertEqual("This varscan line (l.10) is not complete", obsMsg) if __name__ == "__main__": unittest.main()