diff commons/core/parsing/test/Test_VarscanHit_v2_2_8_WithTag.py @ 6:769e306b7933

Change the repository level.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/parsing/test/Test_VarscanHit_v2_2_8_WithTag.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,300 @@
+import unittest
+from commons.core.checker.CheckerException import CheckerException
+from commons.core.parsing.VarscanHit_v2_2_8_WithTag import VarscanHit_v2_2_8_WithTag
+from commons.core.parsing.VarscanHit_WithTag import VarscanHit_WithTag
+
+class Test_VarscanHit_v2_2_8_WithTag(unittest.TestCase):
+
+    def test_setAttributesFromString(self):
+        line = "chr1\t1804\tT\tC\t0\t1\t100%\t0\t1\t0\t53\t0.98\t0\t1\t0\t0\t1\t0\tC\tEspeceA\n"
+        
+        expChrom = "chr1"
+        expPosition = "1804"
+        expRef = "T"
+        expCns = "C"
+        expReadsRef = "0"
+        expReadsVar = "1"
+        expVarFreq = "100%"
+        expStrandsRef = "0"
+        expStrandsVar = "1"
+        expQualRef = "0"
+        expQualVar = "53"
+        expPValue = "0.98"
+        expMapQualRef = "0"
+        expMapQualVar = "1"
+        expReadsRefPlus = "0"
+        expReadsRefMinus = "0"
+        expReadsVarPlus = "1"
+        expReadsVarMinus = "0"
+        expVar = "C"
+        expTag = "EspeceA"
+        
+        varscanHit = VarscanHit_v2_2_8_WithTag()
+        varscanHit.setAttributesFromString(line)
+        
+        obsChrom = varscanHit.getChrom()
+        obsPosition = varscanHit.getPosition()
+        obsRef = varscanHit.getRef()
+        obsCns = varscanHit.getCns()
+        obsReadsRef = varscanHit.getReadsRef()
+        obsReadsVar = varscanHit.getReadsVar()
+        obsVarFreq = varscanHit.getVarFreq()
+        obsStrandsRef = varscanHit.getStrandsRef()
+        obsStrandsVar = varscanHit.getStrandsVar()
+        obsQualRef = varscanHit.getQualRef()
+        obsQualVar = varscanHit.getQualVar()
+        obsPValue = varscanHit.getPValue()
+        obsMapQualRef = varscanHit.getMapQualRef()
+        obsMapQualVar = varscanHit.getMapQualVar()
+        obsReadsRefPlus = varscanHit.getReadsRefPlus()
+        obsReadsRefMinus = varscanHit.getReadsRefMinus()
+        obsReadsVarPlus = varscanHit.getReadsVarPlus()
+        obsReadsVarMinus = varscanHit.getReadsVarMinus()
+        obsVar = varscanHit.getVar()
+        obsTag = varscanHit.getTag()
+        
+        self.assertEquals(expChrom, obsChrom)
+        self.assertEquals(expPosition, obsPosition)
+        self.assertEquals(expRef, obsRef)
+        self.assertEquals(expCns, obsCns)
+        self.assertEquals(expReadsRef, obsReadsRef)
+        self.assertEquals(expReadsVar, obsReadsVar)
+        self.assertEquals(expVarFreq, obsVarFreq)
+        self.assertEquals(expStrandsRef, obsStrandsRef)
+        self.assertEquals(expStrandsVar, obsStrandsVar)
+        self.assertEquals(expQualRef, obsQualRef)
+        self.assertEquals(expQualVar, obsQualVar)
+        self.assertEquals(expPValue, obsPValue)
+        self.assertEquals(expMapQualRef, obsMapQualRef)
+        self.assertEquals(expMapQualVar, obsMapQualVar)
+        self.assertEquals(expReadsRefPlus, obsReadsRefPlus)
+        self.assertEquals(expReadsRefMinus, obsReadsRefMinus)
+        self.assertEquals(expReadsVarPlus, obsReadsVarPlus)
+        self.assertEquals(expReadsVarMinus, obsReadsVarMinus)
+        self.assertEquals(expVar, obsVar)
+        self.assertEquals(expTag, obsTag)
+        
+    def test_setAttributesFromString_empty_chrom(self):
+        line = "\t1804\tT\tC\t0\t1\t100%\t0\t1\t0\t53\t0.98\t0\t1\t0\t0\t1\t0\tC\tEspeceA\n"
+        varscanHit = VarscanHit_v2_2_8_WithTag()
+        try :
+            varscanHit.setAttributesFromString(line)
+        except CheckerException, e:
+            checkerExceptionInstance = e
+        expMessage = "The field Chrom is empty in varscan file in line "
+        obsMessage = checkerExceptionInstance.msg
+        self.assertEquals(expMessage, obsMessage)
+
+    def test_setAttributesFromString_less_than_20_fields(self):
+        line = "chr1\t1804\tT\tC\t0\t1\t100%\t0\t1\t53\t0.98\t0\t1\t0\t0\t1\t0\tC\tEspeceA\n"
+        varscanHit = VarscanHit_v2_2_8_WithTag()
+        try :
+            varscanHit.setAttributesFromString(line)
+        except CheckerException, e:
+            checkerExceptionInstance = e
+        expMessage = "This varscan line (l.) is not complete"
+        obsMessage = checkerExceptionInstance.msg
+        self.assertEquals(expMessage, obsMessage)
+        
+    def test_setAttributes(self):
+        lResults = ['chr1', '1804', 'T', 'C', '0', '1', '100%', '0', '1', '0', '53', '0.98', '0', '1', '0', '0', '1', '0', 'C', 'EspeceA']
+        lineNumber = 1
+        
+        expChrom = "chr1"
+        expPosition = "1804"
+        expRef = "T"
+        expCns = "C"
+        expReadsRef = "0"
+        expReadsVar = "1"
+        expVarFreq = "100%"
+        expStrandsRef = "0"
+        expStrandsVar = "1"
+        expQualRef = "0"
+        expQualVar = "53"
+        expPValue = "0.98"
+        expMapQualRef = "0"
+        expMapQualVar = "1"
+        expReadsRefPlus = "0"
+        expReadsRefMinus = "0"
+        expReadsVarPlus = "1"
+        expReadsVarMinus = "0"
+        expVar = "C"
+        expTag = "EspeceA"
+        
+        varscanHit = VarscanHit_v2_2_8_WithTag()
+        varscanHit.setAttributes(lResults, lineNumber)
+        
+        obsChrom = varscanHit.getChrom()
+        obsPosition = varscanHit.getPosition()
+        obsRef = varscanHit.getRef()
+        obsCns = varscanHit.getCns()
+        obsReadsRef = varscanHit.getReadsRef()
+        obsReadsVar = varscanHit.getReadsVar()
+        obsVarFreq = varscanHit.getVarFreq()
+        obsStrandsRef = varscanHit.getStrandsRef()
+        obsStrandsVar = varscanHit.getStrandsVar()
+        obsQualRef = varscanHit.getQualRef()
+        obsQualVar = varscanHit.getQualVar()
+        obsPValue = varscanHit.getPValue()
+        obsMapQualRef = varscanHit.getMapQualRef()
+        obsMapQualVar = varscanHit.getMapQualVar()
+        obsReadsRefPlus = varscanHit.getReadsRefPlus()
+        obsReadsRefMinus = varscanHit.getReadsRefMinus()
+        obsReadsVarPlus = varscanHit.getReadsVarPlus()
+        obsReadsVarMinus = varscanHit.getReadsVarMinus()
+        obsVar = varscanHit.getVar()
+        obsTag = varscanHit.getTag()
+        
+        self.assertEquals(expChrom, obsChrom)
+        self.assertEquals(expPosition, obsPosition)
+        self.assertEquals(expRef, obsRef)
+        self.assertEquals(expCns, obsCns)
+        self.assertEquals(expReadsRef, obsReadsRef)
+        self.assertEquals(expReadsVar, obsReadsVar)
+        self.assertEquals(expVarFreq, obsVarFreq)
+        self.assertEquals(expStrandsRef, obsStrandsRef)
+        self.assertEquals(expStrandsVar, obsStrandsVar)
+        self.assertEquals(expQualRef, obsQualRef)
+        self.assertEquals(expQualVar, obsQualVar)
+        self.assertEquals(expPValue, obsPValue)
+        self.assertEquals(expMapQualRef, obsMapQualRef)
+        self.assertEquals(expMapQualVar, obsMapQualVar)
+        self.assertEquals(expReadsRefPlus, obsReadsRefPlus)
+        self.assertEquals(expReadsRefMinus, obsReadsRefMinus)
+        self.assertEquals(expReadsVarPlus, obsReadsVarPlus)
+        self.assertEquals(expReadsVarMinus, obsReadsVarMinus)
+        self.assertEquals(expVar, obsVar)
+        self.assertEquals(expTag, obsTag)
+
+    def test_setAttributes_empty_chrom(self):
+        lResults = ['', '1804', 'T', 'C', '0', '1', '100%', '0', '1', '0', '53', '0.98', '0', '1', '0', '0', '1', '0', 'C', 'EspeceA']
+        lineNumber = 1
+        
+        varscanHit = VarscanHit_v2_2_8_WithTag()
+        checkerExceptionInstance = None
+        try:
+            varscanHit.setAttributes(lResults, lineNumber)
+        except CheckerException, e:
+            checkerExceptionInstance = e
+        
+        expMessage = "The field Chrom is empty in varscan file in line 1"
+        obsMessage = checkerExceptionInstance.msg
+           
+        self.assertEquals(expMessage, obsMessage)
+
+    def test_setAttributes_empty_position(self):
+        lResults = ['chr1', '', 'T', 'C', '0', '1', '100%', '0', '1', '0', '53', '0.98', '0', '1', '0', '0', '1', '0', 'C', 'EspeceA']
+        lineNumber = 1
+        
+        varscanHit = VarscanHit_v2_2_8_WithTag()
+        checkerExceptionInstance = None
+        try:
+            varscanHit.setAttributes(lResults, lineNumber)
+        except CheckerException, e:
+            checkerExceptionInstance = e
+        
+        expMessage = "The field Position is empty in varscan file in line 1"
+        obsMessage = checkerExceptionInstance.msg
+           
+        self.assertEquals(expMessage, obsMessage)
+
+    def test_setAttributes_empty_ref(self):
+        lResults = ['chr1', '1000', '', 'C', '0', '1', '100%', '0', '1', '0', '53', '0.98', '0', '1', '0', '0', '1', '0', 'C', 'EspeceA']
+        lineNumber = 1
+        
+        varscanHit = VarscanHit_v2_2_8_WithTag()
+        checkerExceptionInstance = None
+        try:
+            varscanHit.setAttributes(lResults, lineNumber)
+        except CheckerException, e:
+            checkerExceptionInstance = e
+        
+        expMessage = "The field Ref is empty in varscan file in line 1"
+        obsMessage = checkerExceptionInstance.msg
+           
+        self.assertEquals(expMessage, obsMessage)
+
+    def test_setAttributes_empty_cns(self):
+        lResults = ['chr1', '1000', 'T', '', '0', '1', '100%', '0', '1', '0', '53', '0.98', '0', '1', '0', '0', '1', '0', 'C', 'EspeceA']
+        lineNumber = 1
+        
+        varscanHit = VarscanHit_v2_2_8_WithTag()
+        checkerExceptionInstance = None
+        try:
+            varscanHit.setAttributes(lResults, lineNumber)
+        except CheckerException, e:
+            checkerExceptionInstance = e
+        
+        expMessage = "The field Cons is empty in varscan file in line 1"
+        obsMessage = checkerExceptionInstance.msg
+           
+        self.assertEquals(expMessage, obsMessage)
+
+    def test_setAttributes_empty_var(self):
+        lResults = ['chr1', '1000', 'T', 'C', '0', '1', '100%', '0', '1', '0', '53', '0.98', '0', '1', '0', '0', '1', '0', '', 'EspeceA']
+        lineNumber = 1
+        
+        varscanHit = VarscanHit_v2_2_8_WithTag()
+        checkerExceptionInstance = None
+        try:
+            varscanHit.setAttributes(lResults, lineNumber)
+        except CheckerException, e:
+            checkerExceptionInstance = e
+        
+        expMessage = "The field varAllele is empty in varscan file in line 1"
+        obsMessage = checkerExceptionInstance.msg
+           
+        self.assertEquals(expMessage, obsMessage)
+
+    def test__eq__notEquals(self):
+        varscanHit1 = VarscanHit_v2_2_8_WithTag()
+        varscanHit1.setChrom('C02HBa0291P19_LR48')
+        varscanHit1.setPosition('34')
+        varscanHit1.setRef('A')
+        varscanHit1.setCns('T')
+        varscanHit1.setVar('T')
+        varscanHit1.setVar('EspeceA')
+        
+        varscanHit2 = VarscanHit_v2_2_8_WithTag()
+        varscanHit2.setChrom('C02HBa0291P19_LR48')
+        varscanHit2.setPosition('34')
+        varscanHit2.setRef('A')
+        varscanHit2.setCns('T')
+        varscanHit2.setVar('T')
+        varscanHit2.setVar('EspeceB')
+        
+        self.assertFalse(varscanHit1 == varscanHit2)
+
+    def test__eq__Equals(self):
+        varscanHit1 = VarscanHit_v2_2_8_WithTag()
+        varscanHit1.setChrom('C02HBa0291P19_LR48')
+        varscanHit1.setPosition('34')
+        varscanHit1.setRef('A')
+        varscanHit1.setCns('T')
+        varscanHit1.setVar('T')
+        varscanHit1.setVar('EspeceA')
+        
+        varscanHit2 = VarscanHit_v2_2_8_WithTag()
+        varscanHit2.setChrom('C02HBa0291P19_LR48')
+        varscanHit2.setPosition('34')
+        varscanHit2.setRef('A')
+        varscanHit2.setCns('T')
+        varscanHit2.setVar('T')
+        varscanHit2.setVar('EspeceA')
+        
+        self.assertTrue(varscanHit1 == varscanHit2)
+        
+    def test_convertVarscanHit_v2_2_8_WithTag_To_VarscanHit_WithTag(self):
+        line = "chr1\t1804\tT\tC\t0\t1\t100%\t0\t1\t0\t53\t0.98\t0\t1\t0\t0\t1\t0\tC\tEspeceA\n"
+        iVarscanHit_v2_2_8_WithTag = VarscanHit_v2_2_8_WithTag()
+        iVarscanHit_v2_2_8_WithTag.setAttributesFromString(line)
+        obsVarcanHit_WithTag = iVarscanHit_v2_2_8_WithTag.convertVarscanHit_v2_2_8_WithTag_To_VarscanHit_WithTag()
+        
+        line = "chr1\t1804\tT\tC\t0\t1\t100%\t0\t1\t0\t53\t0.98\tEspeceA\n"
+        expVarcanHit_WithTag = VarscanHit_WithTag()
+        expVarcanHit_WithTag.setAttributesFromString(line)
+        
+        self.assertEquals(expVarcanHit_WithTag, obsVarcanHit_WithTag)
+
+if __name__ == "__main__":
+    unittest.main()
\ No newline at end of file