Mercurial > repos > yufei-luo > s_mart
comparison commons/core/parsing/test/Test_VarscanToVCF.py @ 18:94ab73e8a190
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| author | m-zytnicki |
|---|---|
| date | Mon, 29 Apr 2013 03:20:15 -0400 |
| parents | |
| children |
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| 17:b0e8584489e6 | 18:94ab73e8a190 |
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| 1 import unittest | |
| 2 from commons.core.parsing.VarscanToVCF import VarscanToVCF | |
| 3 | |
| 4 class Test_VarscanToVCF(unittest.TestCase): | |
| 5 | |
| 6 def setUp(self): | |
| 7 self._iVarscanToVCF = VarscanToVCF(doClean = True, verbosity = 2) | |
| 8 | |
| 9 # def test_convertVarscanLineToVCFRecord(self): | |
| 10 ## Chrom Position Ref Cons Reads1 Reads2 VarFreq Strands1 Strands2 Qual1 Qual2 Pvalue | |
| 11 ## chr1 10 C Y 1 1 50% 1 1 68 69 0.49999999999999994 | |
| 12 ## MapQual1 MapQual2 Reads1Plus Reads1Minus Reads2Plus Reads2Minus VarAllele | |
| 13 ## 1 1 1 0 1 0 T | |
| 14 # varscanLine = "chr1\t10\tC\tY\t1\t1\t50%\t1\t1\t68\t69\t0.49999999999999994\t1\t1\t1\t0\t1\t0\tT" | |
| 15 # obsRecord = self._iVarscanToVCF._convertVarscanLineToVCFRecord(varscanLine, 1) | |
| 16 # | |
| 17 # expInfo = {"AF": "50%", | |
| 18 # "DP": 2, | |
| 19 # "MQ": "1"} | |
| 20 # | |
| 21 # expRecord = vcf.model._Record("chr1", 10, "1", "C", "T", 3.010299957, ".", expInfo, ".", None) | |
| 22 ## CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, FORMAT, sample_indexes, samples=None | |
| 23 # | |
| 24 # self.assertEqual(expRecord.ID, obsRecord.ID) | |
| 25 # self.assertEqual(expRecord.QUAL, obsRecord.QUAL) | |
| 26 # self.assertEqual(expRecord.FILTER, obsRecord.FILTER) | |
| 27 # self.assertEqual(expRecord.INFO, obsRecord.INFO) | |
| 28 # self.assertEqual(expRecord.FORMAT, obsRecord.FORMAT) | |
| 29 # self.assertEqual(expRecord, obsRecord) | |
| 30 | |
| 31 def test_convertVarscanLineToVCFLine(self): | |
| 32 # Chrom Position Ref Cons Reads1 Reads2 VarFreq Strands1 Strands2 Qual1 Qual2 Pvalue | |
| 33 # chr1 10 C Y 1 1 50% 1 1 68 69 0.49999999999999994 | |
| 34 # MapQual1 MapQual2 Reads1Plus Reads1Minus Reads2Plus Reads2Minus VarAllele | |
| 35 # 1 1 1 0 1 0 T | |
| 36 varscanLine = "chr1\t10\tC\tY\t1\t1\t50%\t1\t1\t68\t69\t0.49999999999999994\t1\t1\t1\t0\t1\t0\tT" | |
| 37 obsVCFLine = self._iVarscanToVCF._convertVarscanLineToVCFRecord(varscanLine, 1) | |
| 38 | |
| 39 expVCFLine = "chr1\t10\t.\tC\tT\t3.010299957\t.\tAF=0.5000;DP=2;RBQ=68;ABQ=69\n" | |
| 40 # CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO | |
| 41 self.assertEqual(expVCFLine, obsVCFLine) | |
| 42 | |
| 43 def test_convertVarscanLineToVCFLine_false_VarAllele(self): | |
| 44 varscanLine = "chr1\t10\tC\tY\t1\t1\t50%\t1\t1\t68\t69\t0.49999999999999994\t1\t1\t1\t0\t1\t0\tA" | |
| 45 obsVCFLine = self._iVarscanToVCF._convertVarscanLineToVCFRecord(varscanLine, 1) | |
| 46 | |
| 47 expVCFLine = "chr1\t10\t.\tC\tT\t3.010299957\t.\tAF=0.5000;DP=2;RBQ=68;ABQ=69\n" | |
| 48 # CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO | |
| 49 self.assertEqual(expVCFLine, obsVCFLine) | |
| 50 | |
| 51 def test_convertVarscanLineToVCFRecord_empty_line(self): | |
| 52 obsMsg = "" | |
| 53 try: | |
| 54 self._iVarscanToVCF._convertVarscanLineToVCFRecord("", 10) | |
| 55 except Exception as e: | |
| 56 obsMsg = e.msg | |
| 57 | |
| 58 self.assertEqual("This varscan line (l.10) is not complete", obsMsg) | |
| 59 | |
| 60 if __name__ == "__main__": | |
| 61 unittest.main() |