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 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