def testMismatchNames(self): trans = {"start": 1, "stop": 648, "name": "not a name"} try: cds = build_coordinates(self.gene, trans) self.fail("expected exception for name mismatch.") except: pass
def testMismatchNames(self): trans = {"start":1, "stop": 648, "name":"not a name"} try: cds = build_coordinates(self.gene,trans) self.fail("expected exception for name mismatch.") except: pass
def testMiddle(self): trans = {"start": 147, "stop": 550, "name":"off1end"} cds = build_coordinates(self.gene, trans) expect = [{ "start": 301, "stop": 700}, { "start": 801, "stop": 804} ] self.assertEqual(expect, cds, "included last region")
def testNegativeNumbers(self): trans = {"start": -200, "stop": 400, "name": "off1end"} try: cds = build_coordinates(self.gene,trans) self.fail("expected exception for negative number.") except: pass trans = {"start": 200, "stop": -400, "name": "off1end"} try: cds = build_coordinates(self.gene, trans) self.fail("expected exception for negative number") except: pass trans = {"start": -200, "stop": -100, "name": "off1end"} try: cds = build_coordinates(self.gene, trans) self.fail("expected exception for negative number") except: pass
def testTooShort(self): trans = {"start": 1, "stop": 646, "name":"off1end"} cds = build_coordinates(self.gene, trans) expect = [{ "start": 101, "stop": 105}, { "start": 111, "stop": 200}, { "start": 225, "stop": 275}, { "start": 301, "stop": 700}, { "start": 801, "stop": 900} ] self.assertEqual(expect, cds, "included last region") #should map off by one
def testNegativeNumbers(self): trans = {"start": -200, "stop": 400, "name": "off1end"} try: cds = build_coordinates(self.gene, trans) self.fail("expected exception for negative number.") except: pass trans = {"start": 200, "stop": -400, "name": "off1end"} try: cds = build_coordinates(self.gene, trans) self.fail("expected exception for negative number") except: pass trans = {"start": -200, "stop": -100, "name": "off1end"} try: cds = build_coordinates(self.gene, trans) self.fail("expected exception for negative number") except: pass
def testCorrectPlusPlus(self): """ Plus Plus works exactly as expected. No reverse transcription required. ATG appears immediately at final[522:3012], and the sequence in the transdecoder.cds match the subsequence. """ gene = {'start': 74641, 'stop': 78761, 'name':'plusplus', 'exons': ({ 'start': 74641, 'stop': 76014 } , { 'start': 76111, 'stop': 76277 } , { 'start': 76368, 'stop': 76465 } , { 'start': 76558, 'stop': 76914 } , { 'start': 77029, 'stop': 77445 } , { 'start': 77628, 'stop': 78761 } )} transcript = {'name':'plusplus', 'start': 523, 'stop':3012} cds = build_coordinates(gene, transcript) #??? what should this do... # should equal start-1:stop self.assertEqual(self.plusplusgen[522:3012], self.plusplusorf)
def testTooShort(self): trans = {"start": 1, "stop": 646, "name": "off1end"} cds = build_coordinates(self.gene, trans) expect = [{ "start": 101, "stop": 105 }, { "start": 111, "stop": 200 }, { "start": 225, "stop": 275 }, { "start": 301, "stop": 700 }, { "start": 801, "stop": 900 }] self.assertEqual(expect, cds, "included last region") #should map off by one
def testCorrectPlusPlus(self): """ Plus Plus works exactly as expected. No reverse transcription required. ATG appears immediately at final[522:3012], and the sequence in the transdecoder.cds match the subsequence. """ gene = { 'start': 74641, 'stop': 78761, 'name': 'plusplus', 'exons': ({ 'start': 74641, 'stop': 76014 }, { 'start': 76111, 'stop': 76277 }, { 'start': 76368, 'stop': 76465 }, { 'start': 76558, 'stop': 76914 }, { 'start': 77029, 'stop': 77445 }, { 'start': 77628, 'stop': 78761 }) } transcript = {'name': 'plusplus', 'start': 523, 'stop': 3012} cds = build_coordinates(gene, transcript) #??? what should this do... # should equal start-1:stop self.assertEqual(self.plusplusgen[522:3012], self.plusplusorf)
def testSingleExon(self): trans = {"start":6, "stop": 48, "name":"off1end"} cds = build_coordinates(self.gene, trans) expect = [{"start": 111, "stop":153}] self.assertEqual(expect, cds)
def testTooLong(self): trans = {"start": 1, "stop": 648, "name":"off1end"} cds = build_coordinates(self.gene, trans) self.assertEqual(self.gene['exons'], cds, "Did not correct for an input that goes past maximum length")
def testPerfectMatch(self): trans = {"start": 1, "stop": 647, "name":"off1end"} cds = build_coordinates(self.gene, trans) self.assertEqual(self.gene['exons'], cds, "Full gene does not match.") #should map perfectly
def testSingleExon(self): trans = {"start": 6, "stop": 48, "name": "off1end"} cds = build_coordinates(self.gene, trans) expect = [{"start": 111, "stop": 153}] self.assertEqual(expect, cds)
def testMiddle(self): trans = {"start": 147, "stop": 550, "name": "off1end"} cds = build_coordinates(self.gene, trans) expect = [{"start": 301, "stop": 700}, {"start": 801, "stop": 804}] self.assertEqual(expect, cds, "included last region")
def testTooLong(self): trans = {"start": 1, "stop": 648, "name": "off1end"} cds = build_coordinates(self.gene, trans) self.assertEqual( self.gene['exons'], cds, "Did not correct for an input that goes past maximum length")
def testPerfectMatch(self): trans = {"start": 1, "stop": 647, "name": "off1end"} cds = build_coordinates(self.gene, trans) self.assertEqual(self.gene['exons'], cds, "Full gene does not match.") #should map perfectly