diff commons/core/parsing/test/Test_VarscanToVCF.py @ 18:94ab73e8a190

Uploaded

--- /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()
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