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

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Change the repository level.
author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/parsing/test/Test_BlatParser.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,445 @@
+from commons.core.parsing.BlatParser import BlatParser
+import unittest
+
+
+class Test_BlatParser(unittest.TestCase):
+
+
+    def test_setAttributesFromString(self):
+        blatLine = "315\t20\t0\t0\t3\t10\t2\t9\t+\tMRRE1H001H13FM1\t378\t0\t345\tchr16\t22053297\t21686950\t21687294\t4\t76,185,7,67,\t0,77,263,278,\t21686950,21687026,21687213,21687227,"
+        
+        iBlatParser = BlatParser()
+        iBlatParser.setAttributesFromString(blatLine)
+        
+        obsmatch = iBlatParser.getMatch()
+        obsmismatch = iBlatParser.getMismatch()
+        obsrepMatch = iBlatParser.getRepMatch()
+        obsN = iBlatParser.getN()
+        obsQGapCount = iBlatParser.getQGapCount()
+        obsQGapBases = iBlatParser.getQGapBases()
+        obsTGapCount = iBlatParser.getTGapCount()
+        obsTGapBases = iBlatParser.getTGapBases()
+        obsstrand = iBlatParser.getStrand()
+        obsQName = iBlatParser.getQName()
+        obsQSize = iBlatParser.getQSize()
+        obsQStart = iBlatParser.getQStart()
+        obsQEnd = iBlatParser.getQEnd()
+        obsTName = iBlatParser.getTName()
+        obsTSize = iBlatParser.getTSize()
+        obsTStart = iBlatParser.getTStart()
+        obsTEnd = iBlatParser.getTEnd()
+        obsblockCount = iBlatParser.getBlockCount()
+        obsblockSizes = iBlatParser.getBlockSizes()
+        obsqStarts = iBlatParser.getQStarts()
+        obstStarts = iBlatParser.getTStarts()
+        
+        expmatch = "315"
+        expmismatch = "20"
+        exprepMatch = "0"
+        expN = "0"
+        expQGapCount = "3"
+        expQGapBases = "10"
+        expTGapCount = "2"
+        expTGapBases = "9"
+        expstrand = "+"
+        expQName = "MRRE1H001H13FM1"
+        expQSize = "378"
+        expQStart = "0"
+        expQEnd = "345"
+        expTName = "chr16"
+        expTSize = "22053297"
+        expTStart = "21686950"
+        expTEnd = "21687294"
+        expblockCount = "4"
+        expblockSizes = "76,185,7,67,"
+        expqStarts = "0,77,263,278,"
+        exptStarts = "21686950,21687026,21687213,21687227,"
+        
+        self.assertEquals(expmatch, obsmatch)
+        self.assertEquals(expmismatch, obsmismatch)
+        self.assertEquals(exprepMatch, obsrepMatch)
+        self.assertEquals(expN, obsN)
+        self.assertEquals(expQGapCount, obsQGapCount)
+        self.assertEquals(expQGapBases, obsQGapBases)
+        self.assertEquals(expTGapCount, obsTGapCount)
+        self.assertEquals(expTGapBases, obsTGapBases)
+        self.assertEquals(expstrand, obsstrand)
+        self.assertEquals(expQName, obsQName)
+        self.assertEquals(expQSize, obsQSize)
+        self.assertEquals(expQStart, obsQStart)
+        self.assertEquals(expQEnd, obsQEnd)
+        self.assertEquals(expTName, obsTName)
+        self.assertEquals(expTSize, obsTSize)
+        self.assertEquals(expTStart, obsTStart)
+        self.assertEquals(expTEnd, obsTEnd)
+        self.assertEquals(expblockCount, obsblockCount)
+        self.assertEquals(expblockSizes, obsblockSizes)
+        self.assertEquals(expqStarts, obsqStarts)
+        self.assertEquals(exptStarts, obstStarts)
+        
+    def test_setAttributesFromString_empty_QName(self):
+        blatLine = "315\t20\t0\t0\t3\t10\t2\t9\t+\t\t378\t0\t345\tchr16\t22053297\t21686950\t21687294\t4\t76,185,7,67,\t0,77,263,278,\t21686950,21687026,21687213,21687227,"
+        
+        iBlatParser = BlatParser()
+        iBlatParser.setAttributesFromString(blatLine)
+        
+        obsmatch = iBlatParser.getMatch()
+        obsmismatch = iBlatParser.getMismatch()
+        obsrepMatch = iBlatParser.getRepMatch()
+        obsN = iBlatParser.getN()
+        obsQGapCount = iBlatParser.getQGapCount()
+        obsQGapBases = iBlatParser.getQGapBases()
+        obsTGapCount = iBlatParser.getTGapCount()
+        obsTGapBases = iBlatParser.getTGapBases()
+        obsstrand = iBlatParser.getStrand()
+        obsQName = iBlatParser.getQName()
+        obsQSize = iBlatParser.getQSize()
+        obsQStart = iBlatParser.getQStart()
+        obsQEnd = iBlatParser.getQEnd()
+        obsTName = iBlatParser.getTName()
+        obsTSize = iBlatParser.getTSize()
+        obsTStart = iBlatParser.getTStart()
+        obsTEnd = iBlatParser.getTEnd()
+        obsblockCount = iBlatParser.getBlockCount()
+        obsblockSizes = iBlatParser.getBlockSizes()
+        obsqStarts = iBlatParser.getQStarts()
+        obstStarts = iBlatParser.getTStarts()
+        
+        expmatch = ""
+        expmismatch = ""
+        exprepMatch = ""
+        expN = ""
+        expQGapCount = ""
+        expQGapBases = ""
+        expTGapCount = ""
+        expTGapBases = ""
+        expstrand = ""
+        expQName = ""
+        expQSize = ""
+        expQStart = ""
+        expQEnd = ""
+        expTName = ""
+        expTSize = ""
+        expTStart = ""
+        expTEnd = ""
+        expblockCount = ""
+        expblockSizes = ""
+        expqStarts = ""
+        exptStarts = ""
+        
+        self.assertEquals(expmatch, obsmatch)
+        self.assertEquals(expmismatch, obsmismatch)
+        self.assertEquals(exprepMatch, obsrepMatch)
+        self.assertEquals(expN, obsN)
+        self.assertEquals(expQGapCount, obsQGapCount)
+        self.assertEquals(expQGapBases, obsQGapBases)
+        self.assertEquals(expTGapCount, obsTGapCount)
+        self.assertEquals(expTGapBases, obsTGapBases)
+        self.assertEquals(expstrand, obsstrand)
+        self.assertEquals(expQName, obsQName)
+        self.assertEquals(expQSize, obsQSize)
+        self.assertEquals(expQStart, obsQStart)
+        self.assertEquals(expQEnd, obsQEnd)
+        self.assertEquals(expTName, obsTName)
+        self.assertEquals(expTSize, obsTSize)
+        self.assertEquals(expTStart, obsTStart)
+        self.assertEquals(expTEnd, obsTEnd)
+        self.assertEquals(expblockCount, obsblockCount)
+        self.assertEquals(expblockSizes, obsblockSizes)
+        self.assertEquals(expqStarts, obsqStarts)
+        self.assertEquals(exptStarts, obstStarts)
+
+    def test_setAttributesFromString_less_than_21_fields(self):
+        blatLine = "315\t20\t0\t0\t3\t10\t2\t9\t378\t0\t345\tchr16\t22053297\t21686950\t21687294\t4\t76,185,7,67,\t0,77,263,278,\t21686950,21687026,21687213,21687227,"
+        
+        iBlatParser = BlatParser()
+        iBlatParser.setAttributesFromString(blatLine)
+        
+        obsmatch = iBlatParser.getMatch()
+        obsmismatch = iBlatParser.getMismatch()
+        obsrepMatch = iBlatParser.getRepMatch()
+        obsN = iBlatParser.getN()
+        obsQGapCount = iBlatParser.getQGapCount()
+        obsQGapBases = iBlatParser.getQGapBases()
+        obsTGapCount = iBlatParser.getTGapCount()
+        obsTGapBases = iBlatParser.getTGapBases()
+        obsstrand = iBlatParser.getStrand()
+        obsQName = iBlatParser.getQName()
+        obsQSize = iBlatParser.getQSize()
+        obsQStart = iBlatParser.getQStart()
+        obsQEnd = iBlatParser.getQEnd()
+        obsTName = iBlatParser.getTName()
+        obsTSize = iBlatParser.getTSize()
+        obsTStart = iBlatParser.getTStart()
+        obsTEnd = iBlatParser.getTEnd()
+        obsblockCount = iBlatParser.getBlockCount()
+        obsblockSizes = iBlatParser.getBlockSizes()
+        obsqStarts = iBlatParser.getQStarts()
+        obstStarts = iBlatParser.getTStarts()
+        
+        expmatch = ""
+        expmismatch = ""
+        exprepMatch = ""
+        expN = ""
+        expQGapCount = ""
+        expQGapBases = ""
+        expTGapCount = ""
+        expTGapBases = ""
+        expstrand = ""
+        expQName = ""
+        expQSize = ""
+        expQStart = ""
+        expQEnd = ""
+        expTName = ""
+        expTSize = ""
+        expTStart = ""
+        expTEnd = ""
+        expblockCount = ""
+        expblockSizes = ""
+        expqStarts = ""
+        exptStarts = ""
+        
+        self.assertEquals(expmatch, obsmatch)
+        self.assertEquals(expmismatch, obsmismatch)
+        self.assertEquals(exprepMatch, obsrepMatch)
+        self.assertEquals(expN, obsN)
+        self.assertEquals(expQGapCount, obsQGapCount)
+        self.assertEquals(expQGapBases, obsQGapBases)
+        self.assertEquals(expTGapCount, obsTGapCount)
+        self.assertEquals(expTGapBases, obsTGapBases)
+        self.assertEquals(expstrand, obsstrand)
+        self.assertEquals(expQName, obsQName)
+        self.assertEquals(expQSize, obsQSize)
+        self.assertEquals(expQStart, obsQStart)
+        self.assertEquals(expQEnd, obsQEnd)
+        self.assertEquals(expTName, obsTName)
+        self.assertEquals(expTSize, obsTSize)
+        self.assertEquals(expTStart, obsTStart)
+        self.assertEquals(expTEnd, obsTEnd)
+        self.assertEquals(expblockCount, obsblockCount)
+        self.assertEquals(expblockSizes, obsblockSizes)
+        self.assertEquals(expqStarts, obsqStarts)
+        self.assertEquals(exptStarts, obstStarts)
+        
+    def test_setAttributes(self):
+        lResults = ['315','20','0','0','3','10','2','9','+','MRRE1H001H13FM1','378','0','345','chr16','22053297','21686950','21687294','4','76,185,7,67,','0,77,263,278,','21686950,21687026,21687213,21687227,']
+        lineNumber = 1
+        
+        iBlatParser = BlatParser()
+        iBlatParser.setAttributes(lResults, lineNumber)
+        
+        obsmatch = iBlatParser.getMatch()
+        obsmismatch = iBlatParser.getMismatch()
+        obsrepMatch = iBlatParser.getRepMatch()
+        obsN = iBlatParser.getN()
+        obsQGapCount = iBlatParser.getQGapCount()
+        obsQGapBases = iBlatParser.getQGapBases()
+        obsTGapCount = iBlatParser.getTGapCount()
+        obsTGapBases = iBlatParser.getTGapBases()
+        obsstrand = iBlatParser.getStrand()
+        obsQName = iBlatParser.getQName()
+        obsQSize = iBlatParser.getQSize()
+        obsQStart = iBlatParser.getQStart()
+        obsQEnd = iBlatParser.getQEnd()
+        obsTName = iBlatParser.getTName()
+        obsTSize = iBlatParser.getTSize()
+        obsTStart = iBlatParser.getTStart()
+        obsTEnd = iBlatParser.getTEnd()
+        obsblockCount = iBlatParser.getBlockCount()
+        obsblockSizes = iBlatParser.getBlockSizes()
+        obsqStarts = iBlatParser.getQStarts()
+        obstStarts = iBlatParser.getTStarts()
+        
+        expmatch = "315"
+        expmismatch = "20"
+        exprepMatch = "0"
+        expN = "0"
+        expQGapCount = "3"
+        expQGapBases = "10"
+        expTGapCount = "2"
+        expTGapBases = "9"
+        expstrand = "+"
+        expQName = "MRRE1H001H13FM1"
+        expQSize = "378"
+        expQStart = "0"
+        expQEnd = "345"
+        expTName = "chr16"
+        expTSize = "22053297"
+        expTStart = "21686950"
+        expTEnd = "21687294"
+        expblockCount = "4"
+        expblockSizes = "76,185,7,67,"
+        expqStarts = "0,77,263,278,"
+        exptStarts = "21686950,21687026,21687213,21687227,"
+        
+        self.assertEquals(expmatch, obsmatch)
+        self.assertEquals(expmismatch, obsmismatch)
+        self.assertEquals(exprepMatch, obsrepMatch)
+        self.assertEquals(expN, obsN)
+        self.assertEquals(expQGapCount, obsQGapCount)
+        self.assertEquals(expQGapBases, obsQGapBases)
+        self.assertEquals(expTGapCount, obsTGapCount)
+        self.assertEquals(expTGapBases, obsTGapBases)
+        self.assertEquals(expstrand, obsstrand)
+        self.assertEquals(expQName, obsQName)
+        self.assertEquals(expQSize, obsQSize)
+        self.assertEquals(expQStart, obsQStart)
+        self.assertEquals(expQEnd, obsQEnd)
+        self.assertEquals(expTName, obsTName)
+        self.assertEquals(expTSize, obsTSize)
+        self.assertEquals(expTStart, obsTStart)
+        self.assertEquals(expTEnd, obsTEnd)
+        self.assertEquals(expblockCount, obsblockCount)
+        self.assertEquals(expblockSizes, obsblockSizes)
+        self.assertEquals(expqStarts, obsqStarts)
+        self.assertEquals(exptStarts, obstStarts)
+        
+    def test_eq_Equals_case1(self):
+        BlatParser1 = BlatParser()
+        BlatParser1.setMatch("315")
+        BlatParser1.setMismatch("20")
+        BlatParser1.setRepMatch("0")
+        BlatParser1.setN("0")
+        BlatParser1.setQGapCount("3")
+        BlatParser1.setQGapBases("10")
+        BlatParser1.setTGapCount("2")
+        BlatParser1.setTGapBases("9")
+        BlatParser1.setStrand("+")
+        BlatParser1.setQName("MRRE1H001H13FM1")
+        BlatParser1.setQSize("378")
+        BlatParser1.setQStart("0")
+        BlatParser1.setQEnd("345")
+        BlatParser1.setTName("chr16")
+        BlatParser1.setTSize("22053297")
+        BlatParser1.setTStart("21686950")
+        BlatParser1.setTEnd("21687294")
+        BlatParser1.setBlockCount("4")
+        BlatParser1.setBlockSizes("76,185,7,67,")
+        BlatParser1.setQStarts("0,77,263,278,")
+        BlatParser1.setTStarts("21686950,21687026,21687213,21687227,")
+        
+        BlatParser2 = BlatParser()
+        BlatParser2.setMatch("315")
+        BlatParser2.setMismatch("20")
+        BlatParser2.setRepMatch("0")
+        BlatParser2.setN("0")
+        BlatParser2.setQGapCount("3")
+        BlatParser2.setQGapBases("10")
+        BlatParser2.setTGapCount("2")
+        BlatParser2.setTGapBases("9")
+        BlatParser2.setStrand("+")
+        BlatParser2.setQName("MRRE1H001H13FM1")
+        BlatParser2.setQSize("378")
+        BlatParser2.setQStart("0")
+        BlatParser2.setQEnd("345")
+        BlatParser2.setTName("chr16")
+        BlatParser2.setTSize("22053297")
+        BlatParser2.setTStart("21686950")
+        BlatParser2.setTEnd("21687294")
+        BlatParser2.setBlockCount("4")
+        BlatParser2.setBlockSizes("76,185,7,67,")
+        BlatParser2.setQStarts("0,77,263,278,")
+        BlatParser2.setTStarts("21686950,21687026,21687213,21687227,")
+        
+        self.assertTrue(BlatParser1 == BlatParser2) 
+        
+    def test_eq_Equals_case2(self):
+        BlatParser1 = BlatParser()
+        BlatParser1.setMatch("315")
+        BlatParser1.setMismatch("20")
+        BlatParser1.setRepMatch("0")
+        BlatParser1.setN("0")
+        BlatParser1.setQGapCount("3")
+        BlatParser1.setQGapBases("10")
+        BlatParser1.setTGapCount("2")
+        BlatParser1.setTGapBases("9")
+        BlatParser1.setStrand("+")
+        BlatParser1.setQName("MRRE1H001H13FM1")
+        BlatParser1.setQSize("378")
+        BlatParser1.setQStart("0")
+        BlatParser1.setQEnd("345")
+        BlatParser1.setTName("chr16")
+        BlatParser1.setTSize("22053297")
+        BlatParser1.setTStart("21686950")
+        BlatParser1.setTEnd("21687294")
+        BlatParser1.setBlockCount("4")
+        BlatParser1.setBlockSizes("76,185,7,67,")
+        BlatParser1.setQStarts("0,77,263,278,")
+        BlatParser1.setTStarts("21686950,21687026,21687213,21687227,")
+        
+        BlatParser2 = BlatParser()
+        BlatParser2.setMatch("315")
+        BlatParser2.setMismatch("20")
+        BlatParser2.setRepMatch("0")
+        BlatParser2.setN("0")
+        BlatParser2.setQGapCount("3")
+        BlatParser2.setQGapBases("10")
+        BlatParser2.setTGapCount("2")
+        BlatParser2.setTGapBases("9")
+        BlatParser2.setStrand("+")
+        BlatParser2.setQName("TotoFM2")
+        BlatParser2.setQSize("378")
+        BlatParser2.setQStart("0")
+        BlatParser2.setQEnd("345")
+        BlatParser2.setTName("chr16")
+        BlatParser2.setTSize("22053297")
+        BlatParser2.setTStart("21686950")
+        BlatParser2.setTEnd("21687294")
+        BlatParser2.setBlockCount("4")
+        BlatParser2.setBlockSizes("76,185,7,67,")
+        BlatParser2.setQStarts("0,77,263,278,")
+        BlatParser2.setTStarts("21686950,21687026,21687213,21687227,")
+        
+        self.assertTrue(BlatParser1 == BlatParser2) 
+        
+    def test_eq_notEquals(self):
+        BlatParser1 = BlatParser()
+        BlatParser1.setMatch("315")
+        BlatParser1.setMismatch("20")
+        BlatParser1.setRepMatch("0")
+        BlatParser1.setN("0")
+        BlatParser1.setQGapCount("3")
+        BlatParser1.setQGapBases("10")
+        BlatParser1.setTGapCount("2")
+        BlatParser1.setTGapBases("9")
+        BlatParser1.setStrand("+")
+        BlatParser1.setQName("MRRE1H001H13FM1")
+        BlatParser1.setQSize("378")
+        BlatParser1.setQStart("0")
+        BlatParser1.setQEnd("345")
+        BlatParser1.setTName("chr16")
+        BlatParser1.setTSize("22053297")
+        BlatParser1.setTStart("21686950")
+        BlatParser1.setTEnd("21687294")
+        BlatParser1.setBlockCount("4")
+        BlatParser1.setBlockSizes("76,185,7,67,")
+        BlatParser1.setQStarts("0,77,263,278,")
+        BlatParser1.setTStarts("21686950,21687026,21687213,21687227,")
+        
+        BlatParser2 = BlatParser()
+        BlatParser2.setMatch("315")
+        BlatParser2.setMismatch("20")
+        BlatParser2.setRepMatch("0")
+        BlatParser2.setN("0")
+        BlatParser2.setQGapCount("3")
+        BlatParser2.setQGapBases("10")
+        BlatParser2.setTGapCount("2")
+        BlatParser2.setTGapBases("9")
+        BlatParser2.setStrand("+")
+        BlatParser2.setQName("TotoFM2")
+        BlatParser2.setQSize("378")
+        BlatParser2.setQStart("0")
+        BlatParser2.setQEnd("345")
+        BlatParser2.setTName("chr8")
+        BlatParser2.setTSize("2205")
+        BlatParser2.setTStart("2124")
+        BlatParser2.setTEnd("2168")
+        BlatParser2.setBlockCount("4")
+        BlatParser2.setBlockSizes("76,185,7,67,")
+        BlatParser2.setQStarts("0,77,263,278,")
+        BlatParser2.setTStarts("21686950,21687026,21687213,21687227,")
+        
+        self.assertFalse(BlatParser1 == BlatParser2) 
+
+if __name__ == "__main__":
+    unittest.main()
\ No newline at end of file