def setUp(self):
ret = unittest.TestCase.setUp(self)
exon1 = "TCONS_00001425 . gene 1439 1564 . - . ID=g.11422;Name=ORF%20g.11422%20m.11422%20type%3A5prime_partial%20len%3A42%20%28-%29"
exon2 = "TCONS_00001425 . gene 1043 1231 . + . ID=g.11419;Name=ORF%20g.11419%20m.11419%20type%3Acomplete%20len%3A63%20%28%2B%29"
exon3 = "TCONS_00001425 . gene 1 1062 . + . ID=g.11414;Name=ORF%20g.11414%20m.11414%20type%3A5prime_partial%20len%3A354%20%28%2B%29"
self.actual_exon = Exon(
"Spolyrrhiza9509S001 Cufflinks exon 26722 26764 . - . Parent=TCONS_00001425"
)
self.actual_trans = Transcript(exon1)
actual_exon1 = "Spolyrrhiza9509S001 Cufflinks exon 24497 24656 . - . Parent=TCONS_00001425"
actual_exon2 = "Spolyrrhiza9509S001 Cufflinks exon 24809 24938 . - . Parent=TCONS_00001425"
actual_exon3 = "Spolyrrhiza9509S001 Cufflinks exon 26237 26599 . - . Parent=TCONS_00001425"
self.actual_exon1 = Exon(actual_exon1)
self.actual_exon2 = Exon(actual_exon2)
self.actual_exon3 = Exon(actual_exon3)
self.exon1 = Transcript(exon1)
self.exon2 = Transcript(exon2)
self.exon3 = Transcript(exon3)
return ret
def setUp(self):
ret = unittest.TestCase.setUp(self)
exon1 ="TCONS_00001425 . gene 1439 1564 . - . ID=g.11422;Name=ORF%20g.11422%20m.11422%20type%3A5prime_partial%20len%3A42%20%28-%29"
exon2 ="TCONS_00001425 . gene 1043 1231 . + . ID=g.11419;Name=ORF%20g.11419%20m.11419%20type%3Acomplete%20len%3A63%20%28%2B%29"
exon3 ="TCONS_00001425 . gene 1 1062 . + . ID=g.11414;Name=ORF%20g.11414%20m.11414%20type%3A5prime_partial%20len%3A354%20%28%2B%29"
self.actual_exon = Exon("Spolyrrhiza9509S001 Cufflinks exon 26722 26764 . - . Parent=TCONS_00001425")
self.actual_trans = Transcript(exon1)
actual_exon1 = "Spolyrrhiza9509S001 Cufflinks exon 24497 24656 . - . Parent=TCONS_00001425"
actual_exon2 = "Spolyrrhiza9509S001 Cufflinks exon 24809 24938 . - . Parent=TCONS_00001425"
actual_exon3 = "Spolyrrhiza9509S001 Cufflinks exon 26237 26599 . - . Parent=TCONS_00001425"
self.actual_exon1 = Exon(actual_exon1)
self.actual_exon2 = Exon(actual_exon2)
self.actual_exon3 = Exon(actual_exon3)
self.exon1 = Transcript(exon1)
self.exon2 = Transcript(exon2)
self.exon3 = Transcript(exon3)
return ret
class GFFLineTest(unittest.TestCase):
def setUp(self):
ret = unittest.TestCase.setUp(self)
exon1 ="TCONS_00001425 . gene 1439 1564 . - . ID=g.11422;Name=ORF%20g.11422%20m.11422%20type%3A5prime_partial%20len%3A42%20%28-%29"
exon2 ="TCONS_00001425 . gene 1043 1231 . + . ID=g.11419;Name=ORF%20g.11419%20m.11419%20type%3Acomplete%20len%3A63%20%28%2B%29"
exon3 ="TCONS_00001425 . gene 1 1062 . + . ID=g.11414;Name=ORF%20g.11414%20m.11414%20type%3A5prime_partial%20len%3A354%20%28%2B%29"
self.actual_exon = Exon("Spolyrrhiza9509S001 Cufflinks exon 26722 26764 . - . Parent=TCONS_00001425")
self.actual_trans = Transcript(exon1)
actual_exon1 = "Spolyrrhiza9509S001 Cufflinks exon 24497 24656 . - . Parent=TCONS_00001425"
actual_exon2 = "Spolyrrhiza9509S001 Cufflinks exon 24809 24938 . - . Parent=TCONS_00001425"
actual_exon3 = "Spolyrrhiza9509S001 Cufflinks exon 26237 26599 . - . Parent=TCONS_00001425"
self.actual_exon1 = Exon(actual_exon1)
self.actual_exon2 = Exon(actual_exon2)
self.actual_exon3 = Exon(actual_exon3)
self.exon1 = Transcript(exon1)
self.exon2 = Transcript(exon2)
self.exon3 = Transcript(exon3)
return ret
"""
Tests comparison on RNAseq format
"""
def testTranscriptComparison(self):
self.assertGreater(self.exon2, self.exon1)
self.assertGreater(self.exon3, self.exon1)
self.assertGreater(self.exon2, self.exon3)
self.assertLess(self.exon1, self.exon2)
self.assertLess(self.exon1, self.exon3)
self.assertLess(self.exon3, self.exon2)
self.assertEqual(self.exon1, self.exon1)
def testBaseGetDicFormat(self):
actual = self.actual_exon.getDicFormat()
expected = {"name": "TCONS_00001425", "start": 26722, "stop": 26764}
self.assertEqual(actual, expected)
def testBaseConstructor(self):
self.assertEqual(self.exon1.start, 1439)
self.assertEqual(self.exon1.stop, 1564)
self.assertEqual(self.exon1.getLabel(), "gene")
self.assertEqual(self.exon1.parent, "TCONS_00001425")
self.assertEqual(len(self.exon1), 125)
self.assertEqual(str(self.exon1), "TCONS_00001425 . gene 1439 1564 . - . ID=g.11422;Name=ORF%20g.11422%20m.11422%20type%3A5prime_partial%20len%3A42%20%28-%29")
self.assertEqual(self.exon1.partial, "partial")
self.assertEqual(self.exon1.strand, "-")
def testBadPositions(self):
tester = "TCONS_00001425 . gene 2000 1564 . - . ID=g.11422;Name=ORF%20g.11422%20m.11422%20type%3A5prime_partial%20len%3A42%20%28-%29"
try:
Exon(tester)
self.fail("No exception thrown")
except:
pass
tester = "TCONS_00001425 . gene 1564 1564 . - . ID=g.11422;Name=ORF%20g.11422%20m.11422%20type%3A5prime_partial%20len%3A42%20%28-%29"
try:
Exon(tester)
self.fail("No exception thrown")
except:
pass
def testSetLenth(self):
self.exon1.setLength(2222)
self.assertEqual(len(self.exon1), 2222)
def testSwitchStrand(self):
self.exon1.switchStrand()
self.assertEquals(self.exon1.strand, "+")
def testGetExonDicFormat(self):
temp = self.actual_trans
temp.addExon(self.actual_exon1)
temp.addExon(self.actual_exon2)
temp.addExon(self.actual_exon3)
actual = temp.getExonDicList()
expected = [{"start": 24497, "stop":24656 ,"name": "TCONS_00001425"}, {"start":24809 , "stop": 24938 ,"name": "TCONS_00001425"}, {"start": 26237, "stop": 26599 ,"name": "TCONS_00001425"}]
self.assertEqual(actual, expected)
class GFFLineTest(unittest.TestCase):
def setUp(self):
ret = unittest.TestCase.setUp(self)
exon1 = "TCONS_00001425 . gene 1439 1564 . - . ID=g.11422;Name=ORF%20g.11422%20m.11422%20type%3A5prime_partial%20len%3A42%20%28-%29"
exon2 = "TCONS_00001425 . gene 1043 1231 . + . ID=g.11419;Name=ORF%20g.11419%20m.11419%20type%3Acomplete%20len%3A63%20%28%2B%29"
exon3 = "TCONS_00001425 . gene 1 1062 . + . ID=g.11414;Name=ORF%20g.11414%20m.11414%20type%3A5prime_partial%20len%3A354%20%28%2B%29"
self.actual_exon = Exon(
"Spolyrrhiza9509S001 Cufflinks exon 26722 26764 . - . Parent=TCONS_00001425"
)
self.actual_trans = Transcript(exon1)
actual_exon1 = "Spolyrrhiza9509S001 Cufflinks exon 24497 24656 . - . Parent=TCONS_00001425"
actual_exon2 = "Spolyrrhiza9509S001 Cufflinks exon 24809 24938 . - . Parent=TCONS_00001425"
actual_exon3 = "Spolyrrhiza9509S001 Cufflinks exon 26237 26599 . - . Parent=TCONS_00001425"
self.actual_exon1 = Exon(actual_exon1)
self.actual_exon2 = Exon(actual_exon2)
self.actual_exon3 = Exon(actual_exon3)
self.exon1 = Transcript(exon1)
self.exon2 = Transcript(exon2)
self.exon3 = Transcript(exon3)
return ret
"""
Tests comparison on RNAseq format
"""
def testTranscriptComparison(self):
self.assertGreater(self.exon2, self.exon1)
self.assertGreater(self.exon3, self.exon1)
self.assertGreater(self.exon2, self.exon3)
self.assertLess(self.exon1, self.exon2)
self.assertLess(self.exon1, self.exon3)
self.assertLess(self.exon3, self.exon2)
self.assertEqual(self.exon1, self.exon1)
def testBaseGetDicFormat(self):
actual = self.actual_exon.getDicFormat()
expected = {"name": "TCONS_00001425", "start": 26722, "stop": 26764}
self.assertEqual(actual, expected)
def testBaseConstructor(self):
self.assertEqual(self.exon1.start, 1439)
self.assertEqual(self.exon1.stop, 1564)
self.assertEqual(self.exon1.getLabel(), "gene")
self.assertEqual(self.exon1.parent, "TCONS_00001425")
self.assertEqual(len(self.exon1), 125)
self.assertEqual(
str(self.exon1),
"TCONS_00001425 . gene 1439 1564 . - . ID=g.11422;Name=ORF%20g.11422%20m.11422%20type%3A5prime_partial%20len%3A42%20%28-%29"
)
self.assertEqual(self.exon1.partial, "partial")
self.assertEqual(self.exon1.strand, "-")
def testBadPositions(self):
tester = "TCONS_00001425 . gene 2000 1564 . - . ID=g.11422;Name=ORF%20g.11422%20m.11422%20type%3A5prime_partial%20len%3A42%20%28-%29"
try:
Exon(tester)
self.fail("No exception thrown")
except:
pass
tester = "TCONS_00001425 . gene 1564 1564 . - . ID=g.11422;Name=ORF%20g.11422%20m.11422%20type%3A5prime_partial%20len%3A42%20%28-%29"
try:
Exon(tester)
self.fail("No exception thrown")
except:
pass
def testSetLenth(self):
self.exon1.setLength(2222)
self.assertEqual(len(self.exon1), 2222)
def testSwitchStrand(self):
self.exon1.switchStrand()
self.assertEquals(self.exon1.strand, "+")
def testGetExonDicFormat(self):
temp = self.actual_trans
temp.addExon(self.actual_exon1)
temp.addExon(self.actual_exon2)
temp.addExon(self.actual_exon3)
actual = temp.getExonDicList()
expected = [{
"start": 24497,
"stop": 24656,
"name": "TCONS_00001425"
}, {
"start": 24809,
"stop": 24938,
"name": "TCONS_00001425"
}, {
"start": 26237,
"stop": 26599,
"name": "TCONS_00001425"
}]
self.assertEqual(actual, expected)
