Mercurial > repos > yufei-luo > s_mart
view commons/core/parsing/test/Test_VarscanHit_v2_2_8.py @ 18:94ab73e8a190
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author | m-zytnicki |
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date | Mon, 29 Apr 2013 03:20:15 -0400 |
parents | 769e306b7933 |
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import unittest from commons.core.checker.CheckerException import CheckerException from commons.core.parsing.VarscanHit_v2_2_8 import VarscanHit_v2_2_8 from commons.core.parsing.VarscanHit import VarscanHit class Test_VarscanHit_v2_2_8(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\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" varscanHit = VarscanHit_v2_2_8() 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() 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) 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\n" varscanHit = VarscanHit_v2_2_8() 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_19_fields(self): line = "chr1\t1804\tT\tC\t0\t1\t100%\t0\t1\t53\t0.98\t0\t1\t0\t0\t1\t0\tC\n" varscanHit = VarscanHit_v2_2_8() 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'] 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" varscanHit = VarscanHit_v2_2_8() 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() 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) 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'] lineNumber = 1 varscanHit = VarscanHit_v2_2_8() 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'] lineNumber = 1 varscanHit = VarscanHit_v2_2_8() 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'] lineNumber = 1 varscanHit = VarscanHit_v2_2_8() 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'] lineNumber = 1 varscanHit = VarscanHit_v2_2_8() 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', ''] lineNumber = 1 varscanHit = VarscanHit_v2_2_8() 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() varscanHit1.setChrom('C02HBa0291P19_LR48') varscanHit1.setPosition('32') varscanHit1.setRef('C') varscanHit1.setCns('T') varscanHit1.setVar('T') varscanHit2 = VarscanHit_v2_2_8() varscanHit2.setChrom('C02HBa0291P19_LR48') varscanHit2.setPosition('34') varscanHit2.setRef('A') varscanHit2.setCns('T') varscanHit2.setVar('T') self.assertFalse(varscanHit1 == varscanHit2) def test__eq__Equals(self): varscanHit1 = VarscanHit_v2_2_8() varscanHit1.setChrom('C02HBa0291P19_LR48') varscanHit1.setPosition('34') varscanHit1.setRef('A') varscanHit1.setCns('T') varscanHit1.setVar('T') varscanHit2 = VarscanHit_v2_2_8() varscanHit2.setChrom('C02HBa0291P19_LR48') varscanHit2.setPosition('34') varscanHit2.setRef('A') varscanHit2.setCns('T') varscanHit2.setVar('T') self.assertTrue(varscanHit1 == varscanHit2) def test_convertVarscanHit_v2_2_8_To_VarscanHit(self): line = "chr1\t1804\tT\tC\t0\t1\t100%\t0\t1\t0\t53\t0.98\t0\t1\t0\t0\t1\t0\tC\n" iVarscanHit_v2_2_8_WithTag = VarscanHit_v2_2_8() iVarscanHit_v2_2_8_WithTag.setAttributesFromString(line) obsVarcanHit_WithTag = iVarscanHit_v2_2_8_WithTag.convertVarscanHit_v2_2_8_To_VarscanHit() line = "chr1\t1804\tT\tC\t0\t1\t100%\t0\t1\t0\t53\t0.98\n" expVarcanHit_WithTag = VarscanHit() expVarcanHit_WithTag.setAttributesFromString(line) self.assertEquals(expVarcanHit_WithTag, obsVarcanHit_WithTag) if __name__ == "__main__": unittest.main()