diff smart_toolShed/commons/core/parsing/test/Test_VarscanHit.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/commons/core/parsing/test/Test_VarscanHit.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,165 @@
+import unittest
+from commons.core.parsing.VarscanHit import VarscanHit
+from commons.core.checker.CheckerException import CheckerException
+
+class Test_VarscanHit(unittest.TestCase):
+
+    def test_setAttributesFromString(self):
+        line = "C02HBa0291P19_LR48\t32\tC\tT\t1\t2\t66,67%\t1\t1\t37\t35\t0.3999999999999999\n"
+        
+        expChrom = "C02HBa0291P19_LR48"
+        expPosition = "32"
+        expRef = "C"
+        expVar = "T"
+        
+        varscanHit = VarscanHit()
+        varscanHit.setAttributesFromString(line)
+        
+        obsChrom = varscanHit.getChrom()
+        obsPosition = varscanHit.getPosition()
+        obsRef = varscanHit.getRef()
+        obsVar = varscanHit.getVar()
+        
+        self.assertEquals(expChrom, obsChrom)
+        self.assertEquals(expPosition, obsPosition)
+        self.assertEquals(expRef, obsRef)
+        self.assertEquals(expVar, obsVar)
+        
+    def test_setAttributesFromString_empty_chrom(self):
+        line = "\t32\tC\tT\t1\t2\t66,67%\t1\t1\t37\t35\t0.3999999999999999\n"
+        iVarscanHit = VarscanHit()
+        try :
+            iVarscanHit.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_12_fields(self):
+        line = "C02HBa0291P19_LR48\t32\tC\tT\t1\t2\t66,67%\t1\t1\t37\n"
+        iVarscanHit = VarscanHit()
+        iVarscanHit.setAttributesFromString(line)
+        self.assertEquals("", iVarscanHit.getQualVar())
+        self.assertEquals("", iVarscanHit.getPValue())
+        
+    def test_setAttributes(self):
+        lResults = ["C02HBa0291P19_LR48", "32", "C", "T", "1", "2", "66,67%", "1", "1", "37", "35", "0.3999999999999999"]
+        lineNumber = 1
+        
+        expChrom = "C02HBa0291P19_LR48"
+        expPosition = "32"
+        expRef = "C"
+        expVar = "T"
+        
+        varscanHit = VarscanHit()
+        varscanHit.setAttributes(lResults, lineNumber)
+        
+        obsChrom = varscanHit.getChrom()
+        obsPosition = varscanHit.getPosition()
+        obsRef = varscanHit.getRef()
+        obsVar = varscanHit.getVar()
+        
+        self.assertEquals(expChrom, obsChrom)
+        self.assertEquals(expPosition, obsPosition)
+        self.assertEquals(expRef, obsRef)
+        self.assertEquals(expVar, obsVar)
+
+    def test_setAttributes_empty_chrom(self):
+        lResults = ["", "", "", "", "", "", "10", "", "", "", "", ""]
+        lineNumber = 1
+        
+        varscanHit = VarscanHit()
+        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 = ["chrom", "", "", "", "", "", "10", "", "", "", "", ""]
+        lineNumber = 5
+        
+        varscanHit = VarscanHit()
+        checkerExceptionInstance = None
+        try:
+            varscanHit.setAttributes(lResults, lineNumber)
+        except CheckerException, e:
+            checkerExceptionInstance = e
+        
+        expMessage = "The field Position is empty in varscan file in line 5"
+        obsMessage = checkerExceptionInstance.msg
+           
+        self.assertEquals(expMessage, obsMessage)
+
+    def test_setAttributes_empty_ref(self):
+        lResults = ["chrom", "position", "", "", "", "", "10", "", "", "", "", ""]
+        lineNumber = 5
+        
+        varscanHit = VarscanHit()
+        checkerExceptionInstance = None
+        try:
+            varscanHit.setAttributes(lResults, lineNumber)
+        except CheckerException, e:
+            checkerExceptionInstance = e
+        
+        expMessage = "The field Ref is empty in varscan file in line 5"
+        obsMessage = checkerExceptionInstance.msg
+           
+        self.assertEquals(expMessage, obsMessage)
+
+    def test_setAttributes_empty_var(self):
+        lResults = ["chrom", "position", "ref", "", "", "", "10", "", "", "", "", ""]
+        lineNumber = 5
+        
+        varscanHit = VarscanHit()
+        checkerExceptionInstance = None
+        try:
+            varscanHit.setAttributes(lResults, lineNumber)
+        except CheckerException, e:
+            checkerExceptionInstance = e
+        
+        expMessage = "The field Var is empty in varscan file in line 5"
+        obsMessage = checkerExceptionInstance.msg
+           
+        self.assertEquals(expMessage, obsMessage)
+
+    def test__eq__notEquals(self):
+        varscanHit1 = VarscanHit()
+        varscanHit1.setChrom('C02HBa0291P19_LR48')
+        varscanHit1.setPosition('32')
+        varscanHit1.setRef('C')
+        varscanHit1.setVar('T')
+        
+        varscanHit2 = VarscanHit()
+        varscanHit2.setChrom('C02HBa0291P19_LR48')
+        varscanHit2.setPosition('34')
+        varscanHit2.setRef('A')
+        varscanHit2.setVar('T')
+        
+        self.assertFalse(varscanHit1 == varscanHit2)
+
+    def test__eq__Equals(self):
+        varscanHit1 = VarscanHit()
+        varscanHit1.setChrom('C02HBa0291P19_LR48')
+        varscanHit1.setPosition('32')
+        varscanHit1.setRef('C')
+        varscanHit1.setVar('T')
+        
+        varscanHit2 = VarscanHit()
+        varscanHit2.setChrom('C02HBa0291P19_LR48')
+        varscanHit2.setPosition('32')
+        varscanHit2.setRef('C')
+        varscanHit2.setVar('T')
+        
+        self.assertTrue(varscanHit1 == varscanHit2)        
+
+if __name__ == "__main__":
+    unittest.main()
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