Mercurial > repos > yufei-luo > s_mart
diff commons/core/parsing/test/Test_VarscanToVCF.py @ 18:94ab73e8a190
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author | m-zytnicki |
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date | Mon, 29 Apr 2013 03:20:15 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/commons/core/parsing/test/Test_VarscanToVCF.py Mon Apr 29 03:20:15 2013 -0400 @@ -0,0 +1,61 @@ +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() \ No newline at end of file