def make_ramp(strand, sign=1):
transfrags = []
chrom = 'chr1'
start = 1000
end = 1220
change_expr = 0.0
base_expr = 0.0
# "flat" part of expression landscape
expr = 1.0
for i in xrange(0, 50):
t = Transfrag(chrom=chrom, strand=strand,
_id='T1.%d' % i, sample_id='S%d' % i,
expr=expr, is_ref=False,
exons=[Exon(start, end)])
transfrags.append(t)
change_expr += expr
base_expr += expr
# "changing" area
i = 0
expr = 10.0
for pos in range(1100, 1120):
left, right = (start, pos) if sign < 0 else (pos, end)
t = Transfrag(chrom=chrom, strand=strand,
_id='T2.%d' % i, sample_id='S%d' % i,
expr=expr, is_ref=False,
exons=[Exon(left, right)])
transfrags.append(t)
change_expr += expr
i += 1
return chrom, start, end, strand, change_expr, base_expr, transfrags
def test_splices():
t = Transfrag(chrom='chrTest',
strand=Strand.POS,
exons=[Exon(0, 10), Exon(20, 30),
Exon(40, 50)])
splice_sites = frozenset(t.itersplices())
assert len(splice_sites) == 4
assert splice_sites == frozenset((10, 20, 30, 40))
def test_introns():
t = Transfrag(chrom='chrTest',
strand=Strand.POS,
exons=[Exon(0, 10), Exon(20, 30),
Exon(40, 50)])
introns = list(t.iterintrons())
assert len(introns) == 2
assert introns[0] == (10, 20)
assert introns[1] == (30, 40)
