def test_for_skip_check_sizes():
"""
TT
└A--T <-bridge read
GTA--AT <-bridge contig
012--345 <-contig coord
^ctg_clv
5432--10 <-rev contig coord
| |
76543210 <-rev genome offset coord
01234567 <-genome offset coord
^gnm_offset
"""
cigartuples = [
(S.BAM_CMATCH, 3),
(S.BAM_CREF_SKIP, 2),
(S.BAM_CMATCH, 2),
]
assert calc_genome_offset(cigartuples,
ctg_clv=2,
tail_side='left',
skip_check_size=1) == 5
assert calc_genome_offset(cigartuples, ctg_clv=2, tail_side='left') == 2
def test_for_a_case_derived_from_a_real_one_E1_L_4362_chr16_plus_strand():
"""
mostly just the bases around the clv are copied, the coordinates are
arbitray
AA
AAG-----G┘ AAAA <-bridge read
AAG-----GCTT┘ <-bridge contig
012 34567 <-contig coord
^ctg_clv
AAGXXXXXGCTT
0123456789012 <-genome offset coord
^gnm_offset
"""
cigartuples = [
(S.BAM_CMATCH, 3),
(S.BAM_CREF_SKIP, 5),
(S.BAM_CMATCH, 4),
(S.BAM_CSOFT_CLIP, 4),
]
gnm_offset = 8
assert calc_genome_offset(cigartuples, ctg_clv=3, tail_side='right') == gnm_offset
assert calc_genome_offset(cigartuples, ctg_clv=3, tail_side='right', skip_check_size=1) == 2
def analyze_bridge(contig, read, ref_fa, dd_bridge, bridge_skip_check_size):
"""
:param dd_bridge: holds bridge_evidence for a given contig, here it's just
used to check if hexamer_search has already been done for a given ref_clv
"""
seqname = contig.reference_name
bdg_support = do_bridge(contig, read)
if bdg_support is None: # likely a chimeric contig
return
strand, ctg_clv, tail_len, tail_direction = bdg_support
offset = calc_genome_offset(contig.cigartuples,
ctg_clv,
tail_direction,
skip_check_size=3)
if offset < 0: # meaning the clv is on soft/hard clipped region
return
ref_clv = contig.reference_start + offset
ctg_hex_tuple = gen_hex_tuple(contig, strand, ref_clv, ref_fa, ctg_clv,
dd_bridge)
return seqname, strand, ref_clv, ctg_clv, tail_len, ctg_hex_tuple
def test_for_nonskipped_contig(ctg_cigartuples, ctg_clv, gnm_offset):
"""
TT
└AC <-bridge read
AACG <-bridge contig
01234 <-contig offset coord: different from "contig coord", it doesn't consider clipped regions
^ctg_clv
01234 <-genome offset coord
^gnm_offset
"""
assert calc_genome_offset(ctg_cigartuples, ctg_clv, 'left') == gnm_offset
def test_for_skipped_with_clv_before_a_skip(ctg_cigartuples, ctg_clv,
gnm_offset):
"""
TT
└AC <-bridge read
AACGTA--ATCG <-bridge contig
012345 67890 <-contig offset coord
^
0123456789012 <-genome offset coord
^ctf/gnm_offset
"""
assert calc_genome_offset(ctg_cigartuples, ctg_clv, 'left') == gnm_offset
def test_for_skipped_contig_with_clv_after_a_skip(ctg_cigartuples, ctg_clv,
gnm_offset):
"""
TT
|└AC <-bridge read
CG--ATCGAT <-bridge contig
01 2345678 <-contig offset coord
^ctg_clv
01234567890 <-genome offset coord
^gnm_offset
"""
assert calc_genome_offset(ctg_cigartuples, ctg_clv, 'left') == gnm_offset
def test_for_contig_with_hardclip(ctg_clv, expected_gnm_offset):
"""
TT
└ACG
\\ACGT <-contig
0123456 <-contig offset coord
^ctg_clv
0123 <-genome offset coord
^gnm_offset
"""
ctg_cigartuples = ((S.BAM_CHARD_CLIP, 2), (S.BAM_CMATCH, 3))
assert calc_genome_offset(ctg_cigartuples, ctg_clv,
'left') == expected_gnm_offset
def test_for_contig_with_softclip(ctg_clv, expected_gnm_offset):
"""
TTT
012 <-contig offset coord for tail
└XXX <-contig
345 <-contig offset coord
^ctg_clv
012 <-genome offset coord
^gnm_offset
"""
ctg_cigartuples = ((S.BAM_CSOFT_CLIP, 3), (S.BAM_CMATCH, 3))
assert calc_genome_offset(ctg_cigartuples, ctg_clv,
'left') == expected_gnm_offset
def test_for_a_long_contig_with_deletion(ctg_cigartuples, ctg_clv, gnm_offset):
"""
TT TT TT
|└TC └C └TC <-bridge read
ATCGATCGATCGATCGATCGATCGATCGATC__ATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCG <-bridge contig
0123456789012345678901234567890 123456789012345678901234567890123456789012345 <-bridge offset coord
| 1 2 3 | 4 5 6 7
^ctg_clv (case2)^ ^ctg_clv (case3)
012345678901234567890123456789012345678901234567890123456789012345678901234567 <-genome offset coord
| 1 2 3 | 4 5 6 7
^gnm_offset(case1) ^gnm_offset(case3)
"""
assert calc_genome_offset(ctg_cigartuples, ctg_clv, 'left') == gnm_offset
def test_for_contig_with_two_skips_and_soft_clip_edge_case_2():
"""
AA
C--G┘ AAAA <-bridge read
CG--ATC--GAT┘ <-bridge contig
01 234 56789012 <-contig offset coord
^ctg_clv
0123456789012 <-genome offset coord
^gnm_offset(check the passing for introns)
"""
cigartuples = [
(S.BAM_CMATCH, 2),
(S.BAM_CREF_SKIP, 2),
(S.BAM_CMATCH, 3),
(S.BAM_CREF_SKIP, 2),
(S.BAM_CMATCH, 3),
(S.BAM_CSOFT_CLIP, 4),
]
gnm_offset = 9
assert calc_genome_offset(cigartuples, ctg_clv=5, tail_side='right') == gnm_offset
assert calc_genome_offset(cigartuples, ctg_clv=5, tail_side='right', skip_check_size=1) == 6
assert calc_genome_offset(cigartuples, ctg_clv=5, tail_side='right', skip_check_size=2) == 6
def test_for_contig_with_two_skips_and_soft_clip_with_clv_before_the_skip():
"""
AA
AT┘ AAAA <-bridge read
CG--ATC--GAT┘ <-bridge contig
01 234 5678901 <-contig offset coord
^ctg_clv
0123456789012 <-genome offset coord
^gnm_offset
"""
cigartuples = [
(S.BAM_CMATCH, 2),
(S.BAM_CREF_SKIP, 2),
(S.BAM_CMATCH, 3),
(S.BAM_CREF_SKIP, 2),
(S.BAM_CMATCH, 3),
(S.BAM_CSOFT_CLIP, 4),
]
gnm_offset = 5
assert calc_genome_offset(cigartuples, ctg_clv=3, tail_side='right') == gnm_offset
assert calc_genome_offset(cigartuples, ctg_clv=3, tail_side='right', skip_check_size=1) == 5
assert calc_genome_offset(cigartuples, ctg_clv=3, tail_side='right', skip_check_size=2) == 1
def test_for_a_case_derived_from_a_real_one_E1_L_4362_chr16_plus_strand_v2():
"""
basically the same as above, much a bit more bases are included on both sides
AA
AATAAAG-----G┘ AAAA <-bridge read
AATAAAG-----GCTTGGA┘ <-bridge contig
0123456 78901234 <-contig coord
| ^ctg_clv
AATAAAGXXXXXGCTTGGA
01234567890123456789 <-genome offset coord
1 ^gnm_offset
"""
cigartuples = [
(S.BAM_CMATCH, 7),
(S.BAM_CREF_SKIP, 5),
(S.BAM_CMATCH, 7),
(S.BAM_CSOFT_CLIP, 4),
]
gnm_offset = 12
assert calc_genome_offset(cigartuples, ctg_clv=7, tail_side='right') == gnm_offset
assert calc_genome_offset(cigartuples, ctg_clv=7, tail_side='right', skip_check_size=1) == 6
def test_for_contig_with_clv_in_hardclip_spanning_clv():
"""
TT
└ACG
CGACGTA <-contig
\\\ | <-hardclip mask
01234567 <-contig coord
76543210 <-rev contig coord
^ctg_clv
|01234 <-genome offset coord
76543210 <-rev genome offset coord
^gnm_offset
"""
ctg_cigartuples = (
(S.BAM_CHARD_CLIP, 3),
(S.BAM_CMATCH, 4),
)
expected_gnm_offset = -1
assert calc_genome_offset(ctg_cigartuples, ctg_clv=2,
tail_side='left') == expected_gnm_offset
# just shift ctg_clv to the left a bit more
assert calc_genome_offset(ctg_cigartuples, ctg_clv=1,
tail_side='left') == -2
def init_ref_beg(ref_clv, cigartuples, ctg_clv):
"""
Initialize the beginning index in genome coordinate by calculating the
offset from left, using `calc_genome_offset`
"""
# TODO: left may not matter in such case
offset = calc_genome_offset(cigartuples, ctg_clv, 'left')
# ref_clv = contig.reference_start + offset, so
# ref_clv - offset = contig.reference_start,
# so still needs to subtract clipped region, which isn't in reference_start
cgr = cigartuples[0]
if cgr[0] == S.BAM_CSOFT_CLIP or cgr[0] == S.BAM_CHARD_CLIP:
offset += cgr[1]
return ref_clv - offset
def test_for_skipped_contig_with_clv_right_before_the_skip():
"""
AA
AT┘ <-bridge read
CGAT--CGAT <-bridge contig
0123 45678 <-contig offset coord
^ctg_clv
01234567890 <-genome offset coord
^gnm_offset
"""
cigartuples = [
(S.BAM_CMATCH, 4),
(S.BAM_CREF_SKIP, 2),
(S.BAM_CMATCH, 4)
]
gnm_offset = 3
assert calc_genome_offset(cigartuples, ctg_clv=3, tail_side='right') == gnm_offset
def test_for_bridge_support_on_suffix_contig_edgecase():
"""
AA
CGTACT┘| <-bridge read
012345678
|||AAA |
ATGACGT┘ | | <-suffix contig
0123456789012 <-contig offset coord
| ^ctg_clv
0123456789012 <-genome offset coord
^gnm_offset
"""
ctg_cigartuples = ((S.BAM_CMATCH, 7), (S.BAM_CSOFT_CLIP, 3))
expected_gnm_offset = 9
assert calc_genome_offset(ctg_cigartuples, ctg_clv=9,
tail_side='right') == expected_gnm_offset
def test_skip_check():
"""
AA
G--A┘ <-bridge read
CG--ATC <-bridge contig
01 2345 <-contig offset coord
^ctg_clv
01234567 <-genome offset coord
^gnm_offset
"""
cigartuples = [
(S.BAM_CMATCH, 2),
(S.BAM_CREF_SKIP, 2),
(S.BAM_CMATCH, 3),
]
gnm_offset = 1
assert calc_genome_offset(cigartuples, ctg_clv=2, tail_side='right', skip_check_size=1) == gnm_offset
def test_for_contig_with_clv_after_insertion_so_tail_side_does_not_matter(
ctg_clv, tail_side, expected_gnm_offset):
"""
TT AA <-bridge read tail
└A┘ <-bridge read, for visual convenience two cases for different tail sides are merged with only one base shown
| # blank line to separate the bridge read the insertion
AGC <-inserted sequence
456 <-contig offset coord for inserted sequence
┬
ATCG GT <-contig
0123 789 <-contig offset coord
^ctg_clv
0123 456 <-genome offset coord
^gnm_offset
"""
ctg_cigartuples = ((S.BAM_CMATCH, 4), (S.BAM_CINS, 3), (S.BAM_CMATCH, 2))
assert calc_genome_offset(ctg_cigartuples, ctg_clv,
tail_side) == expected_gnm_offset
def test_for_contig_with_clv_before_insertion_so_tail_side_does_not_matter(
ctg_clv, tail_side, expected_gnm_offset):
"""
TT AA <-bridge read tail
└C┘ <-bridge read
| # blank line to separate the bridge read the insertion
|AGC <-inserted sequence
|456 <-contig offset coord for inserted sequence
| ┬
ATCG GT <-contig
0123 789 <-contig offset coord
^ctg_clv
0123 456 <-genome offset coord
^gnm_offset
"""
ctg_cigartuples = ((S.BAM_CMATCH, 4), (S.BAM_CINS, 3), (S.BAM_CMATCH, 2))
assert calc_genome_offset(ctg_cigartuples, ctg_clv,
tail_side) == expected_gnm_offset
def test_for_contig_with_3_base_insertion_with_clv_after_the_insertion(
ctg_clv, expected_gnm_offset):
"""
TT <-bridge read tail
└GT <-bridge read
| # blank line to separate the bridge read the insertion
AGC| <-inserted sequence
456| <-contig offset coord for inserted sequence
┬ |
ATCG GT <-contig
0123 78 <-contig offset coord
^ctg_clv
0123 45 <-genome offset coord
^gnm_offset
"""
ctg_cigartuples = ((S.BAM_CMATCH, 3), (S.BAM_CINS, 3), (S.BAM_CMATCH, 2))
assert calc_genome_offset(ctg_cigartuples, ctg_clv,
'left') == expected_gnm_offset
def test_for_contig_with_3_base_insertion_with_clv_inside_the_insertion_and_clv_is_in_the_middle_of_insertion(
ctg_clv, expected_gnm_offset):
"""
TT <-bridge read tail
└G <-bridge read
| # blank line to separate the bridge read the insertion
AGC <-inserted sequence
456 <-contig offset coord for inserted sequence
ctg_clv^|
|┬
ATCG GT <-contig
0123 789 <-contig offset coord
0123 456 <-genome offset coord
^gnm_offset
"""
ctg_cigartuples = ((S.BAM_CMATCH, 4), (S.BAM_CINS, 3), (S.BAM_CMATCH, 2))
assert calc_genome_offset(ctg_cigartuples, ctg_clv,
'left') == expected_gnm_offset
def test_for_contig_with_1_base_insertion_with_clv_after_insertion(
ctg_clv, expected_gnm_offset):
"""
TT
└AC <-bridge read
| # blank line to separate the bridge read the insertion
G| <-inserted sequence
4| <-contig offset coord for inserted sequence
┬|
ATCG AC <-contig
0123 56 <-contig offset coord
^ctg_clv
0123 45 <-genome offset coord
^gnm_offset
see parameters in the decorator for various ctg_clv
"""
ctg_cigartuples = ((S.BAM_CMATCH, 4), (S.BAM_CINS, 1), (S.BAM_CMATCH, 2))
assert calc_genome_offset(ctg_cigartuples, ctg_clv,
'left') == expected_gnm_offset
def test_for_contig_with_one_base_insertion_with_clv_before_insertion(
ctg_clv, tail_side, expected_gnm_offset):
"""
TT AA
└C┘ <-bridge read, for visual convenience two cases for different tail sides are merged with only one base shown
| # blank line to separate the bridge read the insertion
| G <-inserted sequence
| 4 <-contig offset coord for inserted sequence
| ┬
ATCG AC <-contig
0123 56 <-contig offset coord
^ctg_clv
0123 45 <-genome offset coord
^gnm_offset
see parameters in the decorator for various ctg_clv
"""
ctg_cigartuples = ((S.BAM_CMATCH, 4), (S.BAM_CINS, 1), (S.BAM_CMATCH, 2))
assert calc_genome_offset(ctg_cigartuples, ctg_clv,
tail_side) == expected_gnm_offset
def test_clv_inside_insertion(ctg_clv, tail_side, skip_check_size,
expected_gnm_offset):
"""
TT AA <-bridge read tail
└A┘ <-bridge read, for visual convenience two cases for different tail sides are merged with only one base shown
| # blank line to separate the bridge read the insertion
AGC <-inserted sequence
345 <-contig offset coord for inserted sequence
ctg_clv^|
|┬
AT-G GT <-contig
01 2 678 <-contig offset coord
0123 456 <-genome offset coord
^gnm_offset
"""
ctg_cigartuples = ((S.BAM_CMATCH, 2), (S.BAM_CREF_SKIP, 1),
(S.BAM_CMATCH, 1), (S.BAM_CINS, 3), (S.BAM_CMATCH, 2))
assert calc_genome_offset(ctg_cigartuples, ctg_clv, tail_side,
skip_check_size) == expected_gnm_offset
def test_for_contig_with_two_skips_with_clv_right_before_the_skip():
"""
AA
TC┘ <-bridge read
CG--ATC--GAT <-bridge contig
01 234 5678 <-contig offset coord
^ctg_clv
0123456789012 <-genome offset coord
^gnm_offset
"""
cigartuples = [
(S.BAM_CMATCH, 2),
(S.BAM_CREF_SKIP, 2),
(S.BAM_CMATCH, 3),
(S.BAM_CREF_SKIP, 2),
(S.BAM_CMATCH, 3),
]
gnm_offset = 6
assert calc_genome_offset(cigartuples, ctg_clv=4, tail_side='right') == gnm_offset
def test_for_contig_with_two_skips_and_soft_clip_edge_case_1():
"""
AA
TC┘ AAAA <-bridge read
CG--ATC--GAT┘ <-bridge contig
01 234 56789012 <-contig offset coord
^ctg_clv
0123456789012 <-genome offset coord
^gnm_offset
"""
cigartuples = [
(S.BAM_CMATCH, 2),
(S.BAM_CREF_SKIP, 2),
(S.BAM_CMATCH, 3),
(S.BAM_CREF_SKIP, 2),
(S.BAM_CMATCH, 3),
(S.BAM_CSOFT_CLIP, 4),
]
gnm_offset = 6
assert calc_genome_offset(cigartuples, ctg_clv=4, tail_side='right') == gnm_offset
def init_ref_end(ref_clv, cigartuples, ctg_clv, ctg_seq):
"""
Initialize the end index in genome coordinate by calculating the offset
from right, using `calc_genome_offset`
comparing to the minus corresponding function, there is one additional
argument neeed, i.e. `ctg_seq`
:param ctg_seq: should include soft/hardclipped region if it's clipped
"""
cigartuples = list(reversed(cigartuples))
ctg_clv = len(ctg_seq) - ctg_clv # from_the_right
# TODO: left may not matter in such case
offset = calc_genome_offset(cigartuples, ctg_clv, 'left')
# note ref_clv = contig.reference_start + offset
cgr = cigartuples[0]
if cgr[0] == S.BAM_CSOFT_CLIP or cgr[0] == S.BAM_CHARD_CLIP:
offset += cgr[1]
return ref_clv + offset
