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

Change the repository level.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/parsing/test/Test_VarscanFile.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,287 @@
+from commons.core.parsing.VarscanFile import VarscanFile
+from commons.core.parsing.VarscanHit import VarscanHit
+import unittest
+import os
+from commons.core.parsing.VarscanHit_WithTag import VarscanHit_WithTag
+from commons.core.parsing.VarscanHit_v2_2_8 import VarscanHit_v2_2_8
+from commons.core.parsing.VarscanHit_v2_2_8_WithTag import VarscanHit_v2_2_8_WithTag
+from commons.core.checker.CheckerException import CheckerException
+
+class Test_VarscanFile(unittest.TestCase):
+
+    def test_parse_fileWithHeader(self):
+        varscanFileName = "file.varscan"
+        self._writeVarscanFile(varscanFileName)
+        
+        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')
+        expVarscanHitsList = [varscanHit1, varscanHit2]
+        
+        iVarscanFile = VarscanFile(varscanFileName)
+        iVarscanFile.parse()
+        obsVarscanHitsList = iVarscanFile.getVarscanHitsList()
+        os.remove(varscanFileName)
+        
+        self.assertEquals(expVarscanHitsList, obsVarscanHitsList)   
+
+    def test_parse_FileWithoutHeader(self):
+        varscanFileName = "file.varscan"
+        self._writeVarscanFileWithoutHeader(varscanFileName)
+        
+        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')
+        expVarscanHitsList = [varscanHit1, varscanHit2]
+        
+        iVarscanFile = VarscanFile(varscanFileName)
+        iVarscanFile.parse()
+        obsVarscanHitsList = iVarscanFile.getVarscanHitsList()
+        obsTypeOfVarscanFile = iVarscanFile.getTypeOfVarscanFile()
+        expTypeOfVarscanFile = "Varscan_2_2"
+        
+        self.assertEquals(expVarscanHitsList, obsVarscanHitsList) 
+        self.assertEquals(expTypeOfVarscanFile, obsTypeOfVarscanFile) 
+        os.remove(varscanFileName)
+        
+    def test_parse_VarscanFileWithTag(self):
+        inputFileName = "%s/commons/core/parsing/test/varscan.tab" % os.environ["REPET_PATH"]
+        self._writeVarscanFileWithTag(inputFileName)
+        launcher = VarscanFile(inputFileName)
+        launcher.parse()
+        obsListOfVarscanHits = launcher.getListOfVarscanHits() 
+        
+        varscanHit1 = VarscanHit_WithTag()
+        varscanHit1.setChrom('C02HBa0291P19_LR48')
+        varscanHit1.setPosition('32')
+        varscanHit1.setRef('C')
+        varscanHit1.setVar('T')
+        varscanHit1.setTag('EspeceA')
+        
+        varscanHit2 = VarscanHit_WithTag()
+        varscanHit2.setChrom('C02HBa0291P19_LR48')
+        varscanHit2.setPosition('34')
+        varscanHit2.setRef('A')
+        varscanHit2.setVar('T')
+        varscanHit2.setTag('EspeceA')
+        expVarscanHitsList = [varscanHit1, varscanHit2] 
+        
+        obsTypeOfVarscanFile = launcher.getTypeOfVarscanFile()
+        expTypeOfVarscanFile = "Varscan_2_2_WithTag"
+        
+        self.assertEquals(expVarscanHitsList, obsListOfVarscanHits) 
+        self.assertEquals(expTypeOfVarscanFile, obsTypeOfVarscanFile) 
+        os.remove(inputFileName)
+        
+    def test_parse_VarscanFile_v2_2_8(self):
+        inputFileName = "%s/commons/core/parsing/test/varscan.tab" % os.environ["REPET_PATH"]
+        self._writeVarscanFile_v2_2_8(inputFileName)
+        launcher = VarscanFile(inputFileName)
+        launcher.parse()
+        obsListOfVarscanHits = launcher.getListOfVarscanHits() 
+        
+        varscanHit1 = VarscanHit_v2_2_8()
+        varscanHit1.setChrom('C11HBa0064J13_LR285')
+        varscanHit1.setPosition('3227')
+        varscanHit1.setRef('G')
+        varscanHit1.setVar('A')
+        varscanHit1.setCns('A')
+        
+        varscanHit2 = VarscanHit_v2_2_8()
+        varscanHit2.setChrom('C11HBa0064J13_LR285')
+        varscanHit2.setPosition('3230')
+        varscanHit2.setRef('G')
+        varscanHit2.setVar('T')
+        varscanHit2.setCns('T')
+        expVarscanHitsList = [varscanHit1, varscanHit2] 
+        
+        obsTypeOfVarscanFile = launcher.getTypeOfVarscanFile()
+        expTypeOfVarscanFile = "Varscan_2_2_8"
+        
+        self.assertEquals(expVarscanHitsList, obsListOfVarscanHits) 
+        self.assertEquals(expTypeOfVarscanFile, obsTypeOfVarscanFile) 
+        os.remove(inputFileName)
+    
+    def test_parse_other(self):
+        inputFileName = "%s/commons/core/parsing/test/varscan.tab" % os.environ["REPET_PATH"]
+        self._writeOther(inputFileName)
+        launcher = VarscanFile(inputFileName)
+        try:
+            launcher.parse()
+        except CheckerException, e:
+            checkerExceptionInstance = e
+        expMessage = "Warning: this line (l.1) is not a valid varscan line !"
+        obsMessage = checkerExceptionInstance.msg
+        os.remove(inputFileName)
+        self.assertEquals(expMessage, obsMessage) 
+        
+    def test__eq__notEqual(self):
+        lVarscanHits1 = [VarscanHit("chrom", "12", "T", "G"), VarscanHit("chrom", "14", "T", "G")]
+        iVarscanFile1 = VarscanFile()
+        iVarscanFile1.setVarscanHitsList(lVarscanHits1)
+        lVarscanHits2 = [VarscanHit("chrom", "12", "T", "G"), VarscanHit("chrom", "14", "T", "C")]
+        iVarscanFile2 = VarscanFile()
+        iVarscanFile2.setVarscanHitsList(lVarscanHits2)
+
+        self.assertNotEquals(iVarscanFile1, iVarscanFile2)
+        
+    def test__eq__equal(self):
+        lVarscanHits1 = [VarscanHit("chrom", "12", "T", "G"), VarscanHit("chrom", "14", "T", "G")]
+        iVarscanFile1 = VarscanFile()
+        iVarscanFile1.setVarscanHitsList(lVarscanHits1)
+        lVarscanHits2 = [VarscanHit("chrom", "12", "T", "G"), VarscanHit("chrom", "14", "T", "G")]
+        iVarscanFile2 = VarscanFile()
+        iVarscanFile2.setVarscanHitsList(lVarscanHits2)
+
+        self.assertEquals(iVarscanFile1, iVarscanFile2)
+        
+    def test_selectTypeOfVarscanHitObject_noVarscanHit(self):
+        launcher = VarscanFile()
+        launcher.setTypeOfVarscanFile("")
+        try:
+            launcher.selectTypeOfVarscanHitObject()
+        except CheckerException, e:
+            checkerExceptionInstance = e
+        expMessage = "Error: no varscan object found !"
+        obsMessage = checkerExceptionInstance.msg
+        self.assertEquals(expMessage, obsMessage) 
+        
+    def test_selectTypeOfVarscanHitObject_VarscanHit(self):
+        launcher = VarscanFile()
+        launcher.setTypeOfVarscanFile("Varscan_2_2")
+        obsVarscanHit = launcher.selectTypeOfVarscanHitObject()
+        expVarscanHit = VarscanHit()
+        self.assertEquals(expVarscanHit, obsVarscanHit)
+        
+    def test_selectTypeOfVarscanHitObject_VarscanHitWithTag(self):
+        launcher = VarscanFile()
+        launcher.setTypeOfVarscanFile("Varscan_2_2_WithTag")
+        obsVarscanHit = launcher.selectTypeOfVarscanHitObject()
+        expVarscanHit = VarscanHit_WithTag()
+        self.assertEquals(expVarscanHit, obsVarscanHit)
+        
+    def test_selectTypeOfVarscanHitObject_noVarscanHit_2_2_8(self):
+        launcher = VarscanFile()
+        launcher.setTypeOfVarscanFile("Varscan_2_2_8")
+        obsVarscanHit = launcher.selectTypeOfVarscanHitObject()
+        expVarscanHit = VarscanHit_v2_2_8()
+        self.assertEquals(expVarscanHit, obsVarscanHit)
+        
+    def test_selectTypeOfVarscanHitObject_noVarscanHit_2_2_8_WithTag(self):
+        launcher = VarscanFile()
+        launcher.setTypeOfVarscanFile("Varscan_2_2_8_WithTag")
+        obsVarscanHit = launcher.selectTypeOfVarscanHitObject()
+        expVarscanHit = VarscanHit_v2_2_8_WithTag()
+        self.assertEquals(expVarscanHit, obsVarscanHit)
+        
+    def test_createVarscanObjectFromLine_VarscanHit(self):
+        line = "C02HBa0291P19_LR48\t32\tC\tT\t1\t2\t66,67%\t1\t1\t37\t35\t0.3999999999999999\n"
+        nbLine = 1
+        launcher = VarscanFile()
+        launcher.setTypeOfVarscanFile("Varscan_2_2")
+        obsVarscanHit = launcher.createVarscanObjectFromLine(line, nbLine)
+        expVarscanHit = VarscanHit()
+        expVarscanHit.setChrom('C02HBa0291P19_LR48')
+        expVarscanHit.setPosition('32')
+        expVarscanHit.setRef('C')
+        expVarscanHit.setVar('T')
+        self.assertEquals(expVarscanHit, obsVarscanHit)
+        
+    def test_createVarscanObjectFromLine_VarscanHitWithTag(self):
+        line = "C02HBa0291P19_LR48\t32\tC\tT\t1\t2\t66,67%\t1\t1\t37\t35\t0.3999999999999999\tEspeceA\n"
+        nbLine = 1
+        launcher = VarscanFile()
+        launcher.setTypeOfVarscanFile("Varscan_2_2_WithTag")
+        obsVarscanHit = launcher.createVarscanObjectFromLine(line, nbLine)
+        expVarscanHit = VarscanHit_WithTag()
+        expVarscanHit.setChrom('C02HBa0291P19_LR48')
+        expVarscanHit.setPosition('32')
+        expVarscanHit.setRef('C')
+        expVarscanHit.setVar('T')
+        expVarscanHit.setTag('EspeceA')
+        self.assertEquals(expVarscanHit, obsVarscanHit)
+        
+    def test_createVarscanObjectFromLine_VarscanHit_v2_2_8(self):
+        line = "C11HBa0064J13_LR285\t3227\tG\tA\t0\t1\t100%\t0\t1\t0\t54\t0.98\t0\t1\t0\t0\t1\t0\tA\n"
+        nbLine = 1
+        launcher = VarscanFile()
+        launcher.setTypeOfVarscanFile("Varscan_2_2_8")
+        obsVarscanHit = launcher.createVarscanObjectFromLine(line, nbLine)
+        expVarscanHit = VarscanHit_v2_2_8()
+        expVarscanHit.setChrom('C11HBa0064J13_LR285')
+        expVarscanHit.setPosition('3227')
+        expVarscanHit.setRef('G')
+        expVarscanHit.setVar('A')
+        expVarscanHit.setCns('A')
+        self.assertEquals(expVarscanHit, obsVarscanHit)
+        
+    def test_createVarscanObjectFromLine_VarscanHit_v2_2_8_WithTag(self):
+        line = "C11HBa0064J13_LR285\t3227\tG\tA\t0\t1\t100%\t0\t1\t0\t54\t0.98\t0\t1\t0\t0\t1\t0\tA\tEspeceA\n"
+        nbLine = 1
+        launcher = VarscanFile()
+        launcher.setTypeOfVarscanFile("Varscan_2_2_8_WithTag")
+        obsVarscanHit = launcher.createVarscanObjectFromLine(line, nbLine)
+        expVarscanHit = VarscanHit_v2_2_8_WithTag()
+        expVarscanHit.setChrom('C11HBa0064J13_LR285')
+        expVarscanHit.setPosition('3227')
+        expVarscanHit.setRef('G')
+        expVarscanHit.setVar('A')
+        expVarscanHit.setCns('A')
+        expVarscanHit.setTag('EspeceA')
+        self.assertEquals(expVarscanHit, obsVarscanHit)
+    
+    def _writeVarscanFile(self, varscanFileName):
+        varscanFile = open(varscanFileName, 'w')
+        varscanFile.write("Chrom\tPosition\tRef\tVar\tReads1\tReads2\tVarFreq\tStrands1\tStrands2\tQual1\tQual2\tPvalue\n")
+        varscanFile.write("C02HBa0291P19_LR48\t32\tC\tT\t1\t2\t66,67%\t1\t1\t37\t35\t0.3999999999999999\n")
+        varscanFile.write("C02HBa0291P19_LR48\t34\tA\tT\t1\t2\t66,67%\t1\t1\t40\t34\t0.3999999999999999\n")
+        varscanFile.close()
+
+    def _writeVarscanFileWithoutHeader(self, varscanFileName):
+        varscanFile = open(varscanFileName, 'w')
+        varscanFile.write("C02HBa0291P19_LR48\t32\tC\tT\t1\t2\t66,67%\t1\t1\t37\t35\t0.3999999999999999\n")
+        varscanFile.write("C02HBa0291P19_LR48\t34\tA\tT\t1\t2\t66,67%\t1\t1\t40\t34\t0.3999999999999999\n")
+        varscanFile.close()
+    
+    def _writeVarscanFileWithTag(self, varscanFileName):
+        varscanFile = open(varscanFileName, 'w')
+        varscanFile.write("Chrom\tPosition\tRef\tVar\tReads1\tReads2\tVarFreq\tStrands1\tStrands2\tQual1\tQual2\tPvalue\n")
+        varscanFile.write("C02HBa0291P19_LR48\t32\tC\tT\t1\t2\t66,67%\t1\t1\t37\t35\t0.3999999999999999\tEspeceA\n")
+        varscanFile.write("C02HBa0291P19_LR48\t34\tA\tT\t1\t2\t66,67%\t1\t1\t40\t34\t0.3999999999999999\tEspeceA\n")
+        varscanFile.close()
+    
+    def _writeVarscanFile_v2_2_8(self, varscanFileName):
+        varscanFile = open(varscanFileName, 'w')
+        varscanFile.write("Chrom\tPosition\tRef\tCons\tReads1\tReads2\tVarFreq\tStrands1\tStrands2\tQual1\tQual2\tPvalue\tMapQual1\tMapQual2\tReads1Plus\tReads1Minus\tReads2Plus\tReads2Minus\tVarAllele\n")
+        varscanFile.write("C11HBa0064J13_LR285\t3227\tG\tA\t0\t1\t100%\t0\t1\t0\t54\t0.98\t0\t1\t0\t0\t1\t0\tA\n")
+        varscanFile.write("C11HBa0064J13_LR285\t3230\tG\tT\t0\t1\t100%\t0\t1\t0\t54\t0.98\t0\t1\t0\t0\t1\t0\tT\n")
+        varscanFile.close()
+    
+    def _writeOther(self, fileName):
+        file = open(fileName, 'w')
+        file.write('##gff-version 3\n')
+        file.write('chr16\tBlatToGff\tBES\t21686950\t21687294\t.\t+\t.\tID=MRRE1H001H13FM1;Name=MRRE1H001H13FM1;bes_start=21686950;bes_end=21687294;bes_size=22053297\n')
+        file.write('chr16\tBlatToGff\tBES\t21736364\t21737069\t.\t+\t.\tID=machin1;Name=machin1;bes_start=21736364;bes_end=21737069;bes_size=22053297\n')
+        file.write('chr11\tBlatToGff\tBES\t3725876\t3726473\t.\t+\t.\tID=MRRE1H032F08FM1;Name=MRRE1H032F08FM1;bes_start=3725876;bes_end=3726473;bes_size=19818926\n')
+        file.write('chr11\tBlatToGff\tBES\t3794984\t3795627\t.\t+\t.\tID=machin2;Name=machin2;bes_start=3794984;bes_end=3795627;bes_size=19818926\n')
+        file.write('chr18\tBlatToGff\tBES\t12067347\t12067719\t.\t+\t.\tID=machin3;Name=machin3;bes_start=12067347;bes_end=12067719;bes_size=29360087\n')
+        file.close()
+        
+if __name__ == "__main__":
+    unittest.main()
\ No newline at end of file