''' Created on Aug 30, 2010 @author: sau ''' import unittest import os import string from array import array from erange import commoncode from erange import Region from cistematic.genomes import Genome class TestCommoncode(unittest.TestCase): logFile = "testLogFile" celegansChroms = ["I", "II", "III", "IV", "V", "X", "MtDNA"] genome = Genome("celegans") def setUp(self): pass def tearDown(self): try: os.remove(self.logFile) except OSError: pass def testGetReverseComplement(self): self.assertEquals("T", commoncode.getReverseComplement("A")) self.assertEquals("A", commoncode.getReverseComplement("T")) self.assertEquals("C", commoncode.getReverseComplement("G")) self.assertEquals("G", commoncode.getReverseComplement("C")) self.assertEquals("N", commoncode.getReverseComplement("N")) self.assertRaises(KeyError, commoncode.getReverseComplement, "") self.assertRaises(KeyError, commoncode.getReverseComplement, "B") def testCountDuplicatesInList(self): testList = [] self.assertEquals([], commoncode.countDuplicatesInList(testList)) testList = [0, 1] result = [(0, 1), (1, 1)] self.assertEquals(result, commoncode.countDuplicatesInList(testList)) testList = [0, 1, 1] result = [(0, 1), (1, 2)] self.assertEquals(result, commoncode.countDuplicatesInList(testList)) testList = [0, 1, 2, 1] result = [(0, 1), (1, 2), (2, 1)] self.assertEquals(result, commoncode.countDuplicatesInList(testList)) def testWriteLog(self): messenger = "testMessenger" message = "testMessage" commoncode.writeLog(self.logFile, messenger, message) file = open(self.logFile) line = file.readline() fields = line.split() self.assertEquals(fields[2], "[%s]" % messenger) self.assertEquals(fields[3], message) line = file.readline() self.assertEquals("", line) messenger2 = "testMessenger2" message2 = "testMessage2" commoncode.writeLog(self.logFile, messenger2, message2) file = open(self.logFile) line = file.readline() fields = line.split() self.assertEquals(fields[2], "[%s]" % messenger) self.assertEquals(fields[3], message) line = file.readline() fields = line.split() self.assertEquals(fields[2], "[%s]" % messenger2) self.assertEquals(fields[3], message2) line = file.readline() self.assertEquals("", line) os.remove(self.logFile) commoncode.writeLog(self.logFile, messenger, message) file = open(self.logFile) line = file.readline() fields = line.split() self.assertEquals(fields[2], "[%s]" % messenger) self.assertEquals(fields[3], message) line = file.readline() self.assertEquals("", line) os.remove(self.logFile) commoncode.writeLog(self.logFile, "", message) file = open(self.logFile) line = file.readline() fields = line.split() self.assertEquals(fields[2], "[]") self.assertEquals(fields[3], message) line = file.readline() self.assertEquals("", line) os.remove(self.logFile) commoncode.writeLog(self.logFile, "", "") file = open(self.logFile) line = file.readline() fields = line.split() self.assertEquals(fields[2], "[]") self.assertEquals(3, len(fields)) line = file.readline() self.assertEquals("", line) def testGetMergedRegions(self): testfile = open("regionTestFile", "w") regionEntry = string.join(["1", "chr1", "10", "20", "5"], "\t") testfile.write(regionEntry) testfile.close() result = commoncode.getMergedRegions("regionTestFile") self.assertEquals(10, result["1"][0].start) self.assertEquals(20, result["1"][0].stop) self.assertEquals(10, result["1"][0].length) os.remove("regionTestFile") def testGetMergedRegionsFromList(self): self.assertEquals({}, commoncode.getMergedRegionsFromList([])) regionEntry = string.join(["1", "chr1", "10", "20", "5"], "\t") regionList = [regionEntry] result = commoncode.getMergedRegionsFromList(regionList) self.assertEquals(10, result["1"][0].start) self.assertEquals(20, result["1"][0].stop) self.assertEquals(10, result["1"][0].length) result = commoncode.getMergedRegionsFromList(regionList, pad=5) self.assertEquals(5, result["1"][0].start) self.assertEquals(25, result["1"][0].stop) self.assertEquals(20, result["1"][0].length) result = commoncode.getMergedRegionsFromList(regionList, pad=-2) self.assertEquals(12, result["1"][0].start) self.assertEquals(18, result["1"][0].stop) self.assertEquals(6, result["1"][0].length) result = commoncode.getMergedRegionsFromList(regionList, fullChrom=True) self.assertEquals(10, result["chr1"][0].start) self.assertEquals(20, result["chr1"][0].stop) self.assertEquals(10, result["chr1"][0].length) regionEntry = string.join(["1", "chr1:10-20", "5"], "\t") regionList = [regionEntry] result = commoncode.getMergedRegionsFromList(regionList, compact=True, scoreField=2) self.assertEquals(10, result["1"][0].start) self.assertEquals(20, result["1"][0].stop) self.assertEquals(10, result["1"][0].length) regionEntry = string.join(["1", "chr1", "10", "20", "5"], "\t") regionList = [regionEntry] regionEntry = string.join(["2", "chr1", "15", "40", "10"], "\t") regionList.append(regionEntry) result = commoncode.getMergedRegionsFromList(regionList) self.assertEquals(10, result["1"][0].start) self.assertEquals(40, result["1"][0].stop) self.assertEquals(30, result["1"][0].length) result = commoncode.getMergedRegionsFromList(regionList, doMerge=False) self.assertEquals(10, result["1"][0].start) self.assertEquals(20, result["1"][0].stop) self.assertEquals(10, result["1"][0].length) self.assertEquals(15, result["1"][1].start) self.assertEquals(40, result["1"][1].stop) self.assertEquals(25, result["1"][1].length) result = commoncode.getMergedRegionsFromList(regionList, doMerge=False, keepLabel=True) self.assertEquals(10, result["1"][0].start) self.assertEquals(20, result["1"][0].stop) self.assertEquals(10, result["1"][0].length) self.assertEquals("1", result["1"][0].label) self.assertEquals(15, result["1"][1].start) self.assertEquals(40, result["1"][1].stop) self.assertEquals(25, result["1"][1].length) self.assertEquals("2", result["1"][1].label) regionEntry = string.join(["1", "spacer", "chr1", "10", "20", "5"], "\t") regionList = [regionEntry] regionEntry = string.join(["2", "spacer2", "chr1", "15", "40", "10"], "\t") regionList.append(regionEntry) result = commoncode.getMergedRegionsFromList(regionList, doMerge=False, keepLabel=True, chromField=2) self.assertEquals(10, result["1"][0].start) self.assertEquals(20, result["1"][0].stop) self.assertEquals(10, result["1"][0].length) self.assertEquals("1\tspacer", result["1"][0].label) self.assertEquals(15, result["1"][1].start) self.assertEquals(40, result["1"][1].stop) self.assertEquals(25, result["1"][1].length) self.assertEquals("2\tspacer2", result["1"][1].label) regionEntry = string.join(["1", "chr1", "10", "20", "5"], "\t") regionList = [regionEntry] regionEntry = string.join(["2", "chr1", "2030", "2040", "15"], "\t") regionList.append(regionEntry) result = commoncode.getMergedRegionsFromList(regionList) self.assertEquals(10, result["1"][0].start) self.assertEquals(20, result["1"][0].stop) self.assertEquals(10, result["1"][0].length) self.assertEquals(2030, result["1"][1].start) self.assertEquals(2040, result["1"][1].stop) self.assertEquals(10, result["1"][1].length) result = commoncode.getMergedRegionsFromList(regionList, maxDist=3000) self.assertEquals(10, result["1"][0].start) self.assertEquals(2040, result["1"][0].stop) self.assertEquals(2030, result["1"][0].length) result = commoncode.getMergedRegionsFromList(regionList, minHits=5) self.assertEquals(10, result["1"][0].start) self.assertEquals(20, result["1"][0].stop) self.assertEquals(10, result["1"][0].length) self.assertEquals(2030, result["1"][1].start) self.assertEquals(2040, result["1"][1].stop) self.assertEquals(10, result["1"][1].length) result = commoncode.getMergedRegionsFromList(regionList, minHits=12) self.assertEquals(2030, result["1"][0].start) self.assertEquals(2040, result["1"][0].stop) self.assertEquals(10, result["1"][0].length) result = commoncode.getMergedRegionsFromList(regionList, minHits=12) self.assertEquals(2030, result["1"][0].start) self.assertEquals(2040, result["1"][0].stop) self.assertEquals(10, result["1"][0].length) regionEntry = string.join(["1", "chr1", "10", "20", "+", "5"], "\t") regionList = [regionEntry] regionEntry = string.join(["2", "chr2", "15", "40", "+", "15"], "\t") regionList.append(regionEntry) result = commoncode.getMergedRegionsFromList(regionList, scoreField=5, minHits=12) self.assertEquals(15, result["2"][0].start) self.assertEquals(40, result["2"][0].stop) self.assertEquals(25, result["2"][0].length) self.assertRaises(IndexError, commoncode.getMergedRegionsFromList, regionList, scoreField=6, returnTop=1) self.assertEquals({}, commoncode.getMergedRegionsFromList(regionList, scoreField=6)) self.assertEquals({}, commoncode.getMergedRegionsFromList(regionList, scoreField=1)) regionEntry = string.join(["1", "chr1", "10", "20", "5", "3", "40"], "\t") regionList = [regionEntry] result = commoncode.getMergedRegionsFromList(regionList) self.assertEquals(10, result["1"][0].start) self.assertEquals(20, result["1"][0].stop) self.assertEquals(10, result["1"][0].length) result = commoncode.getMergedRegionsFromList(regionList, keepPeak=True) self.assertEquals(10, result["1"][0].start) self.assertEquals(20, result["1"][0].stop) self.assertEquals(10, result["1"][0].length) self.assertEquals(3, result["1"][0].peakPos) self.assertEquals(40, result["1"][0].peakHeight) result = commoncode.getMergedRegionsFromList(regionList, keepPeak=True, keepLabel=True) self.assertEquals(10, result["1"][0].start) self.assertEquals(20, result["1"][0].stop) self.assertEquals(10, result["1"][0].length) self.assertEquals(3, result["1"][0].peakPos) self.assertEquals(40, result["1"][0].peakHeight) self.assertEquals("1", result["1"][0].label) regionEntry = string.join(["2", "chr2", "15", "40", "32", "17"], "\t") regionList.append(regionEntry) result = commoncode.getMergedRegionsFromList(regionList, keepPeak=True, keepLabel=True) self.assertEquals(10, result["1"][0].start) self.assertEquals(20, result["1"][0].stop) self.assertEquals(10, result["1"][0].length) self.assertEquals(3, result["1"][0].peakPos) self.assertEquals(40, result["1"][0].peakHeight) self.assertEquals("1", result["1"][0].label) self.assertEquals(15, result["2"][0].start) self.assertEquals(40, result["2"][0].stop) self.assertEquals(25, result["2"][0].length) self.assertEquals(32, result["2"][0].peakPos) self.assertEquals(17, result["2"][0].peakHeight) self.assertEquals("2", result["2"][0].label) regionEntry = string.join(["3", "chr1", "15", "40", "32", "17"], "\t") regionList.append(regionEntry) result = commoncode.getMergedRegionsFromList(regionList, keepPeak=True, keepLabel=True) self.assertEquals(10, result["1"][0].start) self.assertEquals(40, result["1"][0].stop) self.assertEquals(30, result["1"][0].length) self.assertEquals(3, result["1"][0].peakPos) self.assertEquals(40, result["1"][0].peakHeight) self.assertEquals("3", result["1"][0].label) self.assertEquals(15, result["2"][0].start) self.assertEquals(40, result["2"][0].stop) self.assertEquals(25, result["2"][0].length) self.assertEquals(32, result["2"][0].peakPos) self.assertEquals(17, result["2"][0].peakHeight) self.assertEquals("2", result["2"][0].label) regionEntry = string.join(["4", "chr2", "65", "88", "72", "7"], "\t") regionList.append(regionEntry) result = commoncode.getMergedRegionsFromList(regionList, keepPeak=True, keepLabel=True) self.assertEquals(10, result["1"][0].start) self.assertEquals(40, result["1"][0].stop) self.assertEquals(30, result["1"][0].length) self.assertEquals(3, result["1"][0].peakPos) self.assertEquals(40, result["1"][0].peakHeight) self.assertEquals("3", result["1"][0].label) self.assertEquals(15, result["2"][0].start) self.assertEquals(88, result["2"][0].stop) self.assertEquals(73, result["2"][0].length) self.assertEquals(32, result["2"][0].peakPos) self.assertEquals(17, result["2"][0].peakHeight) self.assertEquals("4", result["2"][0].label) result = commoncode.getMergedRegionsFromList(regionList, keepPeak=True, keepLabel=True, doMerge=False) self.assertEquals(10, result["1"][0].start) self.assertEquals(20, result["1"][0].stop) self.assertEquals(10, result["1"][0].length) self.assertEquals(3, result["1"][0].peakPos) self.assertEquals(40, result["1"][0].peakHeight) self.assertEquals("1", result["1"][0].label) self.assertEquals(15, result["1"][1].start) self.assertEquals(40, result["1"][1].stop) self.assertEquals(25, result["1"][1].length) self.assertEquals(32, result["1"][1].peakPos) self.assertEquals(17, result["1"][1].peakHeight) self.assertEquals("3", result["1"][1].label) self.assertEquals(15, result["2"][0].start) self.assertEquals(40, result["2"][0].stop) self.assertEquals(25, result["2"][0].length) self.assertEquals(32, result["2"][0].peakPos) self.assertEquals(17, result["2"][0].peakHeight) self.assertEquals("2", result["2"][0].label) self.assertEquals(65, result["2"][1].start) self.assertEquals(88, result["2"][1].stop) self.assertEquals(23, result["2"][1].length) self.assertEquals(72, result["2"][1].peakPos) self.assertEquals(7, result["2"][1].peakHeight) self.assertEquals("4", result["2"][1].label) regionList = ["# comment"] regionEntry = string.join(["1", "chr1", "10", "20", "5", "3", "40"], "\t") regionList.append(regionEntry) result = commoncode.getMergedRegionsFromList(regionList, keepPeak=True) self.assertEquals(10, result["1"][0].start) self.assertEquals(20, result["1"][0].stop) self.assertEquals(10, result["1"][0].length) self.assertEquals(3, result["1"][0].peakPos) self.assertEquals(40, result["1"][0].peakHeight) regionList = ["# pvalue"] regionEntry = string.join(["1", "chr1", "10", "20", "5", "3", "40", "any value"], "\t") regionList.append(regionEntry) result = commoncode.getMergedRegionsFromList(regionList, keepPeak=True) self.assertEquals(10, result["1"][0].start) self.assertEquals(20, result["1"][0].stop) self.assertEquals(10, result["1"][0].length) self.assertEquals(3, result["1"][0].peakPos) self.assertEquals(40, result["1"][0].peakHeight) result = commoncode.getMergedRegionsFromList(regionList, keepPeak=True, returnTop=1) self.assertEquals(10, result["1"][0].start) self.assertEquals(20, result["1"][0].stop) self.assertEquals(10, result["1"][0].length) self.assertEquals(3, result["1"][0].peakPos) self.assertEquals(40, result["1"][0].peakHeight) regionList = ["# readShift"] regionEntry = string.join(["1", "chr1", "10", "20", "5", "3", "40", "any value"], "\t") regionList.append(regionEntry) result = commoncode.getMergedRegionsFromList(regionList, keepPeak=True) self.assertEquals(10, result["1"][0].start) self.assertEquals(20, result["1"][0].stop) self.assertEquals(10, result["1"][0].length) self.assertEquals(3, result["1"][0].peakPos) self.assertEquals(40, result["1"][0].peakHeight) result = commoncode.getMergedRegionsFromList(regionList, keepPeak=True, returnTop=1) self.assertEquals(10, result["1"][0].start) self.assertEquals(20, result["1"][0].stop) self.assertEquals(10, result["1"][0].length) self.assertEquals(3, result["1"][0].peakPos) self.assertEquals(40, result["1"][0].peakHeight) regionList = ["# pvalue readShift"] regionEntry = string.join(["1", "chr1", "10", "20", "5", "3", "40", "any value", "any shift"], "\t") regionList.append(regionEntry) result = commoncode.getMergedRegionsFromList(regionList, keepPeak=True) self.assertEquals(10, result["1"][0].start) self.assertEquals(20, result["1"][0].stop) self.assertEquals(10, result["1"][0].length) self.assertEquals(3, result["1"][0].peakPos) self.assertEquals(40, result["1"][0].peakHeight) result = commoncode.getMergedRegionsFromList(regionList, keepPeak=True, returnTop=1) self.assertEquals(10, result["1"][0].start) self.assertEquals(20, result["1"][0].stop) self.assertEquals(10, result["1"][0].length) self.assertEquals(3, result["1"][0].peakPos) self.assertEquals(40, result["1"][0].peakHeight) #Test fails - the header line is required if there are fields after the peak which isn't so good #self.assertEquals(result, commoncode.getMergedRegionsFromList(regionList[1:], keepPeak=True)) def testRegionsOverlap(self): self.assertTrue(commoncode.regionsOverlap(100, 200, 1, 300)) self.assertTrue(commoncode.regionsOverlap(100, 200, 150, 300)) self.assertTrue(commoncode.regionsOverlap(100, 500, 1, 300)) self.assertTrue(commoncode.regionsOverlap(100, 200, 110, 160)) self.assertFalse(commoncode.regionsOverlap(100, 200, 250, 300)) self.assertFalse(commoncode.regionsOverlap(100, 200, 1, 60)) self.assertFalse(commoncode.regionsOverlap(-200, -100, 1, 300)) self.assertFalse(commoncode.regionsOverlap(100, 200, -300, -1)) self.assertTrue(commoncode.regionsOverlap(-200, -100, -300, -1)) self.assertTrue(commoncode.regionsOverlap(-100, -200, -300, -1)) self.assertTrue(commoncode.regionsOverlap(-200, -100, -1, -300)) self.assertTrue(commoncode.regionsOverlap(-100, -200, -1, -300)) def testRegionsAreWithinDistance(self): self.assertTrue(commoncode.regionsAreWithinDistance(10, 20, 40, 50, 30)) self.assertTrue(commoncode.regionsAreWithinDistance(10, 20, 1, 5, 5)) self.assertTrue(commoncode.regionsAreWithinDistance(10, 20, 25, 50, 10)) self.assertTrue(commoncode.regionsAreWithinDistance(10, 20, 1, 5, 5)) self.assertFalse(commoncode.regionsAreWithinDistance(10, 20, 100, 150, 5)) self.assertFalse(commoncode.regionsAreWithinDistance(100, 200, 10, 15, 5)) self.assertTrue(commoncode.regionsAreWithinDistance(20, 10, 30, 150, 10)) self.assertFalse(commoncode.regionsAreWithinDistance(20, 10, 100, 150, 5)) self.assertFalse(commoncode.regionsAreWithinDistance(10, 20, 150, 100, 5)) #TODO: write test def testFindPeak(self): hitList = [] result = commoncode.findPeak(hitList, 0, 0) self.assertEquals([], result.topPos) self.assertEquals(0.0, result.numHits) self.assertEquals(array("f"), result.smoothArray) self.assertEquals(0.0, result.numPlus) hitList= [{"start": 4, "sense": "+", "weight": 0.5}] result = commoncode.findPeak(hitList, 0, 10) self.assertEquals([6, 7], result.topPos) self.assertEquals(1.0, result.numHits) self.assertEquals(array("f", [0.0, 0.0, 0.1111111119389534, 0.3333333432674408, 0.66666668653488159, 0.8888888955116272, 1.0, 1.0, 0.0, 0.0]), result.smoothArray) self.assertEquals(1.0, result.numPlus) result = commoncode.findPeak(hitList, 0, 10, doWeight=True) self.assertEquals([6, 7], result.topPos) self.assertEquals(0.5, result.numHits) self.assertEquals(array('f', [0.0, 0.0, 0.0555555559694767, 0.1666666716337204, 0.3333333432674408, 0.4444444477558136, 0.5, 0.5, 0.0, 0.0]), result.smoothArray) self.assertEquals(0.5, result.numPlus) result = commoncode.findPeak(hitList, 0, 10, shift="auto") self.assertEquals([0, 1, 2, 3, 4, 5, 6, 7, 8, 9], result.topPos) self.assertEquals(0.0, result.numHits) self.assertEquals(array("f", [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]), result.smoothArray) self.assertEquals(0.0, result.numPlus) result = commoncode.findPeak(hitList, 0, 10, shift="auto") self.assertEquals([0, 1, 2, 3, 4, 5, 6, 7, 8, 9], result.topPos) self.assertEquals(0.0, result.numHits) self.assertEquals(array("f", [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]), result.smoothArray) self.assertEquals(0.0, result.numPlus) self.assertEquals(6, result.shift) hitList= [{"start": 4, "sense": "+", "weight": 0.5}] result = commoncode.findPeak(hitList, 0, 10, shift=3) self.assertEquals([7], result.topPos) self.assertEquals(1.0, result.numHits) self.assertEquals(array('f', [0.0, 0.0, 0.0, 0.0, 0.0, 0.1111111119389534, 0.3333333432674408, 0.66666668653488159, 0.0, 0.0]), result.smoothArray) self.assertEquals(1.0, result.numPlus) self.assertEquals(3, result.shift) hitList= [{"start": 4, "sense": "+", "weight": 0.5}] result = commoncode.findPeak(hitList, 0, 10, leftPlus=True) self.assertEquals([6, 7], result.topPos) self.assertEquals(1.0, result.numHits) self.assertEquals(array('f', [0.0, 0.0, 0.1111111119389534, 0.3333333432674408, 0.66666668653488159, 0.8888888955116272, 1.0, 1.0, 0.0, 0.0]), result.smoothArray) self.assertEquals(1.0, result.numPlus) self.assertEquals(1.0, result.numLeftPlus) result = commoncode.findPeak(hitList, 0, 10, leftPlus=True, shift=3) self.assertEquals([7], result.topPos) self.assertEquals(1.0, result.numHits) self.assertEquals(array('f', [0.0, 0.0, 0.0, 0.0, 0.0, 0.1111111119389534, 0.3333333432674408, 0.66666668653488159, 0.0, 0.0]), result.smoothArray) self.assertEquals(1.0, result.numPlus) self.assertEquals(1.0, result.numLeftPlus) self.assertEquals(3, result.shift) #TODO: write test def testGetBestShiftForRegion(self): hitList = [{"start": 14, "sense": "-", "weight": 1.0}, {"start": 16, "sense": "-", "weight": 1.0}, {"start": 24, "sense": "+", "weight": 1.0}, {"start": 26, "sense": "+", "weight": 10.0} ] self.assertEquals(74, commoncode.getBestShiftForRegion(hitList, 0, 100)) self.assertEquals(16, commoncode.getBestShiftForRegion(hitList, 0, 100, maxShift=30)) self.assertEquals(0, commoncode.getBestShiftForRegion(hitList, 0, 100, maxShift=10)) #TODO: write test def testFindPeakSequenceArray(self): pass #TODO: write test def testGetPeakPositionList(self): pass #TODO: write test def testGetFeaturesByChromDict(self): firstFeatures = {"I": (4123, 4219, "Y74C9A.3", "R", "3UTR"), "II": (1866, 1910, "2L52.1", "F", "CDS"), "III": (1270, 1506, "cTel54X.1", "R", "CDS"), "IV": (694, 1064, "Y38C1AB.4", "F", "CDS"), "V": (1479, 1578, "cTel3X.1", "F", "CDS"), "X": (3622, 4099, "CE7X_3.1", "F", "CDS"), "MtDNA": (112, 543, "MTCE.3", "F", "CDS") } featureDict = commoncode.getFeaturesByChromDict(self.genome) for chrom in featureDict.keys(): self.assertTrue(chrom in self.celegansChroms) self.assertEquals(firstFeatures[chrom], featureDict[chrom][0]) restrictList = ["almost certainly not a value feature"] featureDict = commoncode.getFeaturesByChromDict(self.genome, restrictList=restrictList) self.assertEquals({}, featureDict) restrictList = ["Y74C9A.3"] featureDict = commoncode.getFeaturesByChromDict(self.genome, restrictList=restrictList) self.assertEquals(["I"], featureDict.keys()) featureDict, complementDict = commoncode.getFeaturesByChromDict(self.genome, restrictList=restrictList, regionComplement=True) result = {"I": [(0, 4123, "nonExon1", "F", "nonExon"), (4219, 4220, "nonExon2", "F", "nonExon"), (4357, 5194, "nonExon3", "F", "nonExon"), (5295, 6036, "nonExon4", "F", "nonExon"), (6326, 9726, "nonExon5", "F", "nonExon"), (9845, 10094, "nonExon6", "F", "nonExon"), (10147, 10148, "nonExon7", "F", "nonExon"), (10231, 250000000, "nonExon8", "F", "nonExon")] } self.assertEquals(result, complementDict) additionalRegion = Region.Region(100, 150) additionalRegion.label = "new feature" regionDict = {"I": [additionalRegion]} featureDict = commoncode.getFeaturesByChromDict(self.genome, additionalRegionsDict=regionDict) result = (100, 150, "new feature", "+", "custom") self.assertEquals(result, featureDict["I"][0]) def testGetLocusByChromDict(self): firstLoci = {"I": (4123, 10231, "Y74C9A.3", 6108), "II": (1866, 4662, "2L52.1", 2796), "III": (1270, 2916, "cTel54X.1", 1646), "IV": (694, 14925, "Y38C1AB.4", 14231), "V": (1479, 3038, "cTel3X.1", 1559), "X": (3622, 7153, "CE7X_3.1", 3531), "MtDNA": (112, 548, "MTCE.3", 436) } self.assertEquals({}, commoncode.getLocusByChromDict(self.genome, useCDS=False)) self.assertEquals({}, commoncode.getLocusByChromDict(self.genome, upstream=1, downstream=1, useCDS=False)) self.assertEquals({}, commoncode.getLocusByChromDict(self.genome, upstream=-1, downstream=-1, useCDS=False, lengthCDS=1)) self.assertEquals({}, commoncode.getLocusByChromDict(self.genome, upstreamSpanTSS=True, lengthCDS=1)) self.assertEquals({}, commoncode.getLocusByChromDict(self.genome, downstream=1, lengthCDS=1)) self.assertEquals({}, commoncode.getLocusByChromDict(self.genome, upstream=1, lengthCDS=-1)) locusDict = commoncode.getLocusByChromDict(self.genome) for chrom in locusDict.keys(): self.assertTrue(chrom in self.celegansChroms) self.assertEquals(firstLoci[chrom], locusDict[chrom][0]) additionalRegion = Region.Region(100, 150) additionalRegion.label = "new region" regionDict = {"I": [additionalRegion]} locusDict = commoncode.getLocusByChromDict(self.genome, additionalRegionsDict=regionDict) self.assertEquals((100, 150, "new region", 50), locusDict["I"][0]) locusDict = commoncode.getLocusByChromDict(self.genome, additionalRegionsDict=regionDict, keepSense=True) self.assertEquals((100, 150, "new region", 50, "+"), locusDict["I"][0]) # Long Test #locusDict = commoncode.getLocusByChromDict(self.genome, additionalRegionsDict=regionDict, useCDS=False, upstream=100) #self.assertEquals((150, 250, "new region", 100), locusDict["I"][0]) # Long Test #locusDict = commoncode.getLocusByChromDict(self.genome, additionalRegionsDict=regionDict, useCDS=False, downstream=10) #self.assertEquals((90, 100, "new region", 10), locusDict["I"][0]) def testComputeRegionBins(self): regionsByChromDict = {} hitDict = {} bins = 4 readlen = 10 result = ({}, {}) self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen)) regionsByChromDict = {"1": [("regionID", 1, 100, 100, "F")]} result = ({"regionID": [0.0, 0.0, 0.0, 0.0]}, {}) self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen)) regionsByChromDict = {"1": [("regionID", 1, 100, 100, "F")]} hitDict = {"1": [{"start": 1, "sense": "+", "weight": 1.0}]} result = ({"regionID": [1.0, 0.0, 0.0, 0.0]}, {"regionID": 100}) self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen)) regionsByChromDict = {"1": [("regionID", 1, 100, 100, "F")], "2": [("regionID2", 1, 1000, 1000, "F")] } hitDict = {"1": [{"start": 1, "sense": "+", "weight": 1.0}], "2": [{"start": 1, "sense": "+", "weight": 1.0}] } result = ({"regionID2": [1.0, 0.0, 0.0, 0.0], "regionID": [1.0, 0.0, 0.0, 0.0]}, {"regionID2": 1000, "regionID": 100}) self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen)) regionsByChromDict = {"1": [("regionID", 1, 100, 100, "F")]} hitDict = {"1": [{"start": 10, "sense": "+", "weight": 1.0}, {"start": 80, "sense": "+", "weight": 0.5}]} result = ({"regionID": [1.0, 0.0, 0.0, 0.5]}, {"regionID": 100}) self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen)) regionsByChromDict = {"1": [("regionID", 1, 100, 100, "F")]} hitDict = {"1": [{"start": 10, "sense": "+", "weight": 1.0}, {"start": 80, "sense": "+", "weight": 0.5}, {"start": 15, "sense": "+", "weight": 1.0}]} result = ({"regionID": [2.0, 0.0, 0.0, 0.5]}, {"regionID": 100}) self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen)) regionsByChromDict = {"1": [("regionID", 1, 100, 100, "F")]} hitDict = {"1": [{"start": 10, "sense": "+", "weight": 1.0}, {"start": 80, "sense": "+", "weight": 0.5}, {"start": 200, "sense": "+", "weight": 2.0}]} result = ({"regionID": [1.0, 0.0, 0.0, 0.5]}, {"regionID": 100}) self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen)) regionsByChromDict = {"1": [("regionID", 1, 100, 100, "F")]} hitDict = {"1": [{"start": 1, "sense": "+", "weight": 1.0}]} regionList = ["regionID"] result = ({"regionID": [1.0, 0.0, 0.0, 0.0]}, {"regionID": 100}) self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen, regionList)) regionsByChromDict = {"1": [("regionID", 1, 100, 100, "F")]} hitDict = {"1": [{"start": 1, "sense": "+", "weight": 1.0}]} regionList = ["empty region"] result = ({"empty region": [0.0, 0.0, 0.0, 0.0]}, {"regionID": 100}) self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen, regionList)) regionsByChromDict = {"1": [("regionID", 1, 100, 100, "F")], "2": [("regionID2", 1, 1000, 1000, "F")] } hitDict = {"1": [{"start": 1, "sense": "+", "weight": 1.0}], "2": [{"start": 1, "sense": "+", "weight": 1.0}] } regionList = ["regionID", "regionID2"] result = ({"regionID2": [1.0, 0.0, 0.0, 0.0], "regionID": [1.0, 0.0, 0.0, 0.0]}, {"regionID2": 1000, "regionID": 100}) self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen, regionList)) regionsByChromDict = {"1": [("regionID", 1, 100, 100, "F")], "2": [("regionID2", 1, 1000, 1000, "F")] } hitDict = {"1": [{"start": 1, "sense": "+", "weight": 1.0}], "2": [{"start": 1, "sense": "+", "weight": 1.0}] } regionList = ["empty region", "regionID2"] result = ({"regionID2": [1.0, 0.0, 0.0, 0.0], "empty region": [0.0, 0.0, 0.0, 0.0]}, {"regionID2": 1000, "regionID": 100}) self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen, regionList)) regionsByChromDict = {"1": [("regionID", 1, 100, 100, "F")], "2": [("regionID2", 1, 1000, 1000, "F")] } hitDict = {"1": [{"start": 1, "sense": "+", "weight": 1.0}], "2": [{"start": 1, "sense": "+", "weight": 1.0}] } regionList = ["regionID2"] result = ({"regionID2": [1.0, 0.0, 0.0, 0.0]}, {"regionID2": 1000, "regionID": 100}) self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen, regionList)) regionsByChromDict = {"1": [("regionID", 1, 100, 100, "F")]} hitDict = {"1": [{"start": 1, "sense": "+", "weight": 1.0}]} result = ({"regionID": [2.0, 0.0, 0.0, 0.0]}, {"regionID": 100}) self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen, normalizedTag=2.0)) regionsByChromDict = {"1": [(1, 100, "regionID", 100, "F")]} hitDict = {"1": [{"start": 1, "sense": "+", "weight": 1.0}]} result = ({"regionID": [1.0, 0.0, 0.0, 0.0]}, {"regionID": 100}) self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen, defaultRegionFormat=False)) regionsByChromDict = {"1": [("regionID", 1, 100, 100, "F")]} hitDict = {"1": [{"start": 10, "sense": "+", "weight": 1.0}]} fixedFirstBin = 20 result = ({"regionID": [1.0, 0.0, 0.0, 0.0]}, {"regionID": 100}) self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen, fixedFirstBin=fixedFirstBin)) regionsByChromDict = {"1": [("regionID", 1, 100, 100, "F")]} hitDict = {"1": [{"start": 10, "sense": "+", "weight": 1.0}]} fixedFirstBin = 5 result = ({"regionID": [0.0, 1.0, 0.0, 0.0]}, {"regionID": 100}) self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen, fixedFirstBin=fixedFirstBin)) regionsByChromDict = {"1": [("regionID", 1, 100, 100, "F")]} hitDict = {"1": [{"start": 10, "sense": "+", "weight": 1.0}, {"start": 85, "sense": "+", "weight": 0.5}]} fixedFirstBin = 20 result = ({"regionID": [1.0, 0.5, 0.0, 0.0]}, {"regionID": 100}) self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen, fixedFirstBin=fixedFirstBin)) regionsByChromDict = {"1": [("regionID", 1, 100, 100, "F")]} hitDict = {"1": [{"start": 80, "sense": "+", "weight": 1.0}, {"start": 85, "sense": "+", "weight": 0.5}]} fixedFirstBin = 5 result = ({"regionID": [0.0, 1.5, 0.0, 0.0]}, {"regionID": 100}) self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen, fixedFirstBin=fixedFirstBin)) regionsByChromDict = {"1": [("regionID", 1, 100, 100, "F")]} hitDict = {"1": [{"start": 10, "sense": "+", "weight": 1.0}, {"start": 85, "sense": "+", "weight": 0.5}]} binLength = 25 result = ({"regionID": [1.0, 0.0, 0.0, 0.5]}, {"regionID": 100}) self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen, binLength=binLength)) regionsByChromDict = {"1": [("regionID", 1, 100, 100, "F")]} hitDict = {"1": [{"start": 10, "sense": "+", "weight": 1.0}, {"start": 85, "sense": "+", "weight": 0.5}]} binLength = 50 result = ({"regionID": [1.0, 0.5, 0.0, 0.0]}, {"regionID": 100}) self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen, binLength=binLength)) regionsByChromDict = {"1": [("regionID", 1, 100, 100, "F")]} hitDict = {"1": [{"start": 10, "sense": "+", "weight": 1.0}, {"start": 85, "sense": "+", "weight": 0.5}]} binLength = 15 result = ({"regionID": [1.0, 0.0, 0.0, 0.5]}, {"regionID": 100}) self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen, binLength=binLength)) regionsByChromDict = {"1": [("regionID", 1, 100, 100, "F")]} hitDict = {"1": [{"start": 10, "sense": "+", "weight": 1.0}, {"start": 40, "sense": "+", "weight": 0.7}, {"start": 85, "sense": "+", "weight": 0.5}]} binLength = 15 result = ({"regionID": [1.0, 0.0, 0.7, 0.5]}, {"regionID": 100}) self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen, binLength=binLength)) regionsByChromDict = {"1": [("regionID", 1, 100, 100, "R")]} hitDict = {"1": [{"start": 10, "sense": "+", "weight": 1.0}, {"start": 40, "sense": "+", "weight": 0.7}, {"start": 85, "sense": "+", "weight": 0.5}]} result = ({"regionID": [0.5, 0.0, 0.7, 1.0]}, {"regionID": 100}) self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen)) result = ({"regionID": [0.5, 0.0, 0.7, 1.0]}, {"regionID": 100}) fixedFirstBin = 10 result = ({"regionID": [0.0, 2.2, 0.0, 0.0]}, {"regionID": 100}) self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen, fixedFirstBin=fixedFirstBin)) fixedFirstBin = 20 result = ({"regionID": [0.5, 1.7, 0.0, 0.0]}, {"regionID": 100}) self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen, fixedFirstBin=fixedFirstBin)) binLength = 50 result = ({"regionID": [0.5, 1.7, 0.0, 0.0]}, {"regionID": 100}) self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen, binLength=binLength)) binLength = 10 result = ({"regionID": [0.0, 0.5, 0.0, 1.7]}, {"regionID": 100}) self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen, binLength=binLength)) def suite(): suite = unittest.TestSuite() suite.addTest(unittest.makeSuite(TestCommoncode)) return suite if __name__ == "__main__": #import sys;sys.argv = ['', 'Test.testName'] unittest.main()