def test_rev_complement(self):
string = "AGTCGTGCAGNGTCGAAGTGCAACAGTGC"
self.assertEqual(TranscriptChecker.rev_complement(string),
"GCACTGTTGCACTTCGACNCTGCACGACT")
string = "agtcGTGCAGNGTCGAAGTGCAACAgtgc"
self.assertEqual(TranscriptChecker.rev_complement(string),
"gcacTGTTGCACTTCGACNCTGCACgact")
def test_sequence_reversed(self):
model = Transcript()
model.chrom, model.start, model.end, model.strand = "Chr5", 1001, 1500, "+"
model.add_exon((1001, 1500))
model.id, model.parent = "foo.1", "foo"
model.finalize()
seq = self.fasta.fetch("Chr5", 1001 - 1, 1500)
self.assertEqual(len(seq), len(model))
model = TranscriptChecker(model, seq, strand_specific=True)
model.reverse_strand()
fasta = "".join(model.fasta.split("\n")[1:])
self.assertEqual(model.strand, "-")
self.assertEqual(fasta, TranscriptChecker.rev_complement(seq))
def test_rev_complement(self):
string = "AGTCGTGCAGNGTCGAAGTGCAACAGTGC"
self.assertEqual(TranscriptChecker.rev_complement(string),
"GCACTGTTGCACTTCGACNCTGCACGACT")
