def test_set_info(self):
transcript = Transcript(strand='-', start=10000, end=19600)
transcript.exons = [Exon('1-2'), Exon('3-4'), Exon('5-6')]
transcript.cdna_length = 8100
transcript.prot_length = 1200
transcript.set_info()
assert transcript.info == '-/9.6kb/3/8.1kb/1200'
def test_finalize(self):
transcript = Transcript(strand='+', coding_start=16, coding_end=53)
transcript.exons = [Exon('10-20'), Exon('30-40'), Exon('50-60')]
transcript.finalize()
assert transcript.cdna_length == 30
assert transcript.prot_length == 5
assert transcript.start == 10
assert transcript.end == 60
transcript = Transcript(strand='-', coding_start=55, coding_end=15)
transcript.exons = [Exon('50-60'), Exon('30-40'), Exon('10-20')]
transcript.finalize()
assert transcript.cdna_length == 30
assert transcript.prot_length == 6
assert transcript.start == 10
assert transcript.end == 60
def test_add(self):
transcript = Transcript(id='xyz',
chrom='11',
strand='+',
start=130,
end=580)
transcript.exons = [Exon('100-200'), Exon('300-400'), Exon('500-600')]
self.tdb_writer.add(transcript)
assert self.tdb_writer._records['11'][0] == [
'xyz', '11', '100-200,300-400,500-600', 130, 580
]