Mercurial > repos > yufei-luo > s_mart
view smart_toolShed/commons/core/parsing/test/Test_VarscanHit.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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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()