def test_fetch_seq_for_circular_DNA_when_beginning_is_negative():
"""
AATTCCGG
012345678
"""
assert fetch_seq(REF_FA, seqname='chrM', beg=-1, end=1) == 'GA'
assert fetch_seq(REF_FA, seqname='chrM', beg=-2, end=3) == 'GGAAT'
def test_fetch_seq_for_circular_DNA_with_positive_beginning_and_ending_less_than_contig_length():
"""
AATTCCGG
012345678
"""
assert fetch_seq(REF_FA, seqname='chrM', beg=0, end=8) == 'AATTCCGG'
assert fetch_seq(REF_FA, seqname='chrM', beg=2, end=6) == 'TTCC'
def test_fetch_seq_for_circular_DNA_when_ending_is_beyond_contig_length():
"""
AATTCCGG
012345678
"""
assert fetch_seq(REF_FA, seqname='chrM', beg=6, end=11) == 'GGAAT'
assert fetch_seq(REF_FA, seqname='chrM', beg=7, end=9) == 'GA'
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)
def test_fetch_seq_for_circular_DNA_when_both_beg_and_end_are_less_than_0():
"""
this happens when the assembled contig cross the starting point of a circular DNA
┬ ┬
AATTCCGGAC AATTCCGGAC AATTCCGGAC
0123456789 0123456789 0123456789
"""
assert fetch_seq(REF_FA, seqname='MT', beg=-1, end=1) == 'CA'
assert fetch_seq(REF_FA, seqname='MT', beg=-3, end=-1) == 'GA'
assert fetch_seq(REF_FA, seqname='MT', beg=-2, end=-1) == 'A'
assert fetch_seq(REF_FA, seqname='MT', beg=-3, end=0) == 'GAC'
assert fetch_seq(REF_FA, seqname='MT', beg=-2, end=0) == 'AC'
def do_skip(ref_b, cigar_val, ref_fa, seqname, ref_clv):
"""
Handle BAM CREF_SKIP CIGAR
"""
ref_e = ref_b + cigar_val
if ref_b <= ref_clv:
if ref_e > ref_clv:
seq_to_add = fetch_seq(ref_fa, seqname, ref_clv, ref_e)
else: # still before clv
seq_to_add = ''
else:
seq_to_add = fetch_seq(ref_fa, seqname, ref_b, ref_e)
next_ref_b = ref_e
return next_ref_b, seq_to_add
def do_skip(ref_e, cigar_val, ref_fa, seqname, ref_clv):
"""
:param ref_e: reference end index
:param ref_fa: a pysam.libcalignmentfile.AlignmentFile instance for reference genome
:param ref_clv: cleavage site in reference genome coordinate
"""
ref_b = ref_e - cigar_val
if ref_e >= ref_clv:
if ref_b < ref_clv:
seq_to_add = fetch_seq(ref_fa, seqname, ref_b, ref_clv + 1)
else:
seq_to_add = ''
else:
seq_to_add = fetch_seq(ref_fa, seqname, ref_b, ref_e)
next_ref_e = ref_b
return next_ref_e, seq_to_add
def test_chr12_DRAM_plus_strand(self):
chrom = '12'
clv = 102316878 - 1
# confirm the corresponding seq in hg19
self.assertEqual(
fetch_seq(self.refseq, '12', 102316872, 102316872 + 6),
'aataaa')
self.assertEqual(
search_ref_genome(self.refseq, chrom, clv, '+', 50),
('AATAAA', 16, 102316872))
def test_chr19_AKT2_minus_strand(self):
chrom = '19'
clv = 40737005 - 1
# confirm the corresponding seq in hg19
self.assertEqual(
fetch_seq(self.refseq, chrom, 40737011 + 1 - 6, 40737011 + 1),
'TTTATT')
self.assertEqual(
search_ref_genome(self.refseq, chrom, clv, '-', 50),
('AATAAA', 16, 40737011))
def test_fetch_seq_for_circular_DNA_when_ending_beg_is_larger_than_end():
"""
AATTCCGG
01234567890
"""
assert fetch_seq(REF_FA, seqname='chrM', beg=8, end=1) == 'A'
assert fetch_seq(REF_FA, seqname='chrM', beg=8, end=2) == 'AA'
assert fetch_seq(REF_FA, seqname='chrM', beg=8, end=7) == 'AATTCCG'
assert fetch_seq(REF_FA, seqname='chrM', beg=9, end=1) == ''
assert fetch_seq(REF_FA, seqname='chrM', beg=9, end=2) == 'A'
assert fetch_seq(REF_FA, seqname='chrM', beg=9, end=3) == 'AT'
assert fetch_seq(REF_FA, seqname='chrM', beg=9, end=3) == 'AT'
def search_ref_genome(refseq, chrom, clv, strand, window=50):
"""
Different from search, this function search hexamer on reference genome
:param refseq: an object returned by pysam.FastaFile, see TestSearch for
its usage
:param clv: 0-based. suppposed to be the 1-based coordinate of last base of
3' UTR (e.g. output by KLEAT) - 1. converted to 0-based because pysam is
0-based.
return: a tuple of (hexamer, hexamer id (indicates strength), 0-based hexamer location)
"""
beg, end = gen_coords(clv, strand, window)
seq = apautils.fetch_seq(refseq, chrom, beg, end)
# -1 as it's 0-based
res = search_hexamer(seq, strand, beg, end - 1)
return res
def test_fetch_seq_for_circular_DNA_when_both_beg_and_end_are_larger_than_seq_len():
"""
this happens when the assembled contig cross the starting point of a circular DNA
┬ ┬
AATTCCGGAC AATTCCGGAC AATTCCGGAC
0123456789 0123456789 0123456789
"""
assert fetch_seq(REF_FA, seqname='MT', beg=0, end=10) == 'AATTCCGGAC'
assert fetch_seq(REF_FA, seqname='MT', beg=10, end=11) == 'A'
assert fetch_seq(REF_FA, seqname='MT', beg=10, end=12) == 'AA'
assert fetch_seq(REF_FA, seqname='MT', beg=10, end=13) == 'AAT'
assert fetch_seq(REF_FA, seqname='MT', beg=10, end=14) == 'AATT'
assert fetch_seq(REF_FA, seqname='MT', beg=11, end=11) == ''
assert fetch_seq(REF_FA, seqname='MT', beg=11, end=12) == 'A'
assert fetch_seq(REF_FA, seqname='MT', beg=11, end=13) == 'AT'
assert fetch_seq(REF_FA, seqname='MT', beg=12, end=11) == 'TTCCGGACA'
assert fetch_seq(REF_FA, seqname='MT', beg=12, end=12) == ''
assert fetch_seq(REF_FA, seqname='MT', beg=12, end=13) == 'T'
assert fetch_seq(REF_FA, seqname='MT', beg=21, end=21) == ''
assert fetch_seq(REF_FA, seqname='MT', beg=21, end=23) == 'AT'
def test_fetch_seq_for_circular_DNA_when_ending_beg_is_larger_than_end_set_seq_len_is_ten_for_convenience():
"""
┬ ┬
AATTCCGGAC AATTCCGGAC AATTCCGGAC
0123456789 0123456789 0123456789
"""
assert fetch_seq(REF_FA, seqname='MT', beg=8, end=1) == 'ACA'
assert fetch_seq(REF_FA, seqname='MT', beg=8, end=2) == 'ACAA'
assert fetch_seq(REF_FA, seqname='MT', beg=10, end=1) == 'A'
assert fetch_seq(REF_FA, seqname='MT', beg=10, end=2) == 'AA'
assert fetch_seq(REF_FA, seqname='MT', beg=10, end=3) == 'AAT'
assert fetch_seq(REF_FA, seqname='MT', beg=10, end=4) == 'AATT'
assert fetch_seq(REF_FA, seqname='MT', beg=11, end=1) == ''
assert fetch_seq(REF_FA, seqname='MT', beg=11, end=2) == 'A'
assert fetch_seq(REF_FA, seqname='MT', beg=11, end=3) == 'AT'
assert fetch_seq(REF_FA, seqname='MT', beg=21, end=1) == ''
assert fetch_seq(REF_FA, seqname='MT', beg=21, end=3) == 'AT'
def test_fetch_seq_for_linear_DNA_when_ending_is_beyond_contig_length():
assert fetch_seq(REF_FA, seqname='chr_mock1', beg=6, end=11) == 'GG'
assert fetch_seq(REF_FA, seqname='chr_mock1', beg=7, end=9) == 'G'
def test_fetch_seq_for_linear_DNA_when_beginning_is_negative():
assert fetch_seq(REF_FA, seqname='chr_mock1', beg=-1, end=1) == 'A'
assert fetch_seq(REF_FA, seqname='chr_mock1', beg=-2, end=3) == 'AAT'
def test_fetch_seq_for_linear_DNA_with_positive_beginning_and_ending_less_than_contig_length():
assert fetch_seq(REF_FA, seqname='chr_mock1', beg=0, end=8) == 'AATTCCGG'
assert fetch_seq(REF_FA, seqname='chr_mock1', beg=2, end=6) == 'TTCC'