def test_fetch_seq_bound_larger_than_chr_length_coordinate_by_chr_length(
self):
chrm = 'GL000192.1' # len: 547496
clv = 547493
beg, end = gen_coords(clv, '-', window=6)
calc_beg = 547493
calc_end = 547499
self.assertEqual((beg, end), (calc_beg, calc_end))
expected = 'ttc' # the last 3 bases of GL000192.1
def test_fetch_seq_based_on_KLEAT_clv_minus_strand_chr9_GNAQ(self):
chrm = '9'
# reported by KLEAT, converted to 0-based, corresponding to a T, the
# last base of its 3'UTR
clv = 80335189 - 1
self.assertEqual(fetch_seq(self.refseq, chrm, clv, clv + 1), 'T')
beg, end = gen_coords(clv, '-', window=6)
self.assertEqual((beg, end), (clv, clv + 6))
self.assertEqual(fetch_seq(self.refseq, chrm, beg, end), 'TTTTAT')
def test_fetch_seq_based_on_KLEAT_clv_minus_strand_chr2_NFE2L2(self):
chrm = '2'
# reported by KLEAT, converted to 0-based, corresponding to a T, the
# last base of its 3'UTR
clv = 178095802 - 1
self.assertEqual(fetch_seq(self.refseq, chrm, clv, clv + 1), 'G')
beg, end = gen_coords(clv, '-', window=10)
self.assertEqual((beg, end), (clv, clv + 10))
self.assertEqual(fetch_seq(self.refseq, chrm, beg, end),
'GCCACTTTAT')
def test_fetch_seq_based_on_KLEAT_clv_plus_strand_chr12_DRAM1(self):
"""based on hg19"""
chrm = '12'
# this is a coord reported by KLEAT, it's 1-based, so -1 to make it
# 0-based, and it points to the end of 3'UTR, where there is a hexamer
# right to the upstream of it, see included screenshot in the repo
clv = 102316878 - 1
# 'a' is the last base on 3'UTR
self.assertEqual(fetch_seq(self.refseq, chrm, clv, clv + 1), 'a')
beg, end = gen_coords(clv, '+', window=6)
self.assertEqual((beg, end), (clv - 6 + 1, clv + 1))
self.assertEqual(fetch_seq(self.refseq, chrm, beg, end), 'aataaa')
def test_fetch_seq_bound_negative_coordinate_by_0(self):
chrm = 'GL000192.1'
clv = 3
beg, end = gen_coords(clv, '+', window=6)
calc_beg = -2 # clv - 6 + 1
calc_end = 4 # clv + 1
self.assertEqual((beg, end), (calc_beg, calc_end))
expected = 'GAAT' # the first 4 bases of GL000192.1
self.assertEqual(fetch_seq(self.refseq, chrm, beg, end), expected)
# assert beginning is bound by 0
self.assertEqual(fetch_seq(self.refseq, chrm, 0, end), expected)