def test_with_skipped_region_for_plus_strand_clv():
"""
AAA <-tail of suffix contig
ACGG--GC┘|| <-suffix contig with skip
0123 456789 <-contig coord
| 1
ctg_clv^ ^init_ctg_idx <-contig coord
...ACGGTTGCGGT... <-genome
789012345678 <-genome coord
1 | |
ref_clv^ ^init_ref_idx
"""
ctg = MagicMock()
ctg.reference_name = 'chr1'
ctg.query_sequence = 'ACGGGCAAA'
ctg.cigartuples = ((S.BAM_CMATCH, 4), (S.BAM_CREF_SKIP, 2),
(S.BAM_CMATCH, 2), (S.BAM_CSOFT_CLIP, 3))
ref_fa = MagicMock()
ref_fa.get_reference_length.return_value = 100
ref_fa.fetch = MagicMock(return_value='TT')
kw = dict(contig=ctg, strand='+', ref_clv=14, ref_fa=ref_fa, ctg_clv=5)
assert extract_seq(**kw) == 'ACGGTTGC'
assert extract_seq(window=3, **kw) == 'TGC'
ref_fa.fetch.assert_called_with('chr1', 11, 13)
def test_hardclip_minus_strand(mock_apautils):
"""
TT
|└CGCACCG <-suffix contig with hardclip
| | /// <-hardclip mask
01234567890 <-contig coord
icb^ ^cc 1
XXCGCACCG... <-genome
3456789012 <-genome coord
| | 1
irb^ ^rc
"""
ctg = MagicMock()
ctg.reference_name = 'chr2'
mock_apautils.infer_query_sequence.return_value = 'TTCGCACCG'
ctg.cigartuples = (
(S.BAM_CSOFT_CLIP, 2),
(S.BAM_CMATCH, 4),
(S.BAM_CHARD_CLIP, 3),
)
ref_fa = MagicMock()
ref_fa.get_reference_length.return_value = 100
kw = dict(contig=ctg, strand='-', ref_clv=5, ref_fa=ref_fa, ctg_clv=2)
assert extract_seq(**kw) == 'CGCACCG'
assert extract_seq(window=1, **kw) == 'C'
assert extract_seq(window=3, **kw) == 'CGC'
def test_with_hardclip_after_clv(mock_apautils):
"""
TT
|└GTGA <-bridge read
ATTCGTGA <-bridge contig (hardcipped), chimeric
// <-hardclip mask
012345678 <-contig coord
icb^ ^cc
...ATTCGTGA...
567890123 <-genome coordinate
| |1
irb^ ^rc
"""
ctg = MagicMock()
ctg.reference_name = 'chr2'
mock_apautils.infer_query_sequence.return_value = 'ATTCGTGA'
ctg.cigartuples = (
(S.BAM_CMATCH, 6),
(S.BAM_CHARD_CLIP, 2),
)
ref_fa = MagicMock()
ref_fa.get_reference_length.return_value = 100
kw = dict(contig=ctg, strand='-', ref_clv=9, ref_fa=ref_fa, ctg_clv=4)
assert extract_seq(**kw) == 'GTGA'
assert extract_seq(window=5, **kw) == 'GTGA'
def test_with_skipped_region_and_insertions_mismatches_for_plus_strand_clv():
"""
G
┬ AAA <-tail of suffix contig
A TA--GCG┘|| <-suffix contig with skip
0 23 456789 <-contig coord
| |x | |
ctg_clv ^ ^init_ctg_idx <-contig coord
...A TTCCGCGXXX... <-genome
7 8901234567 <-genome coord
1 | |
ref_clv^ ^init_ref_idx
"""
ctg = MagicMock()
ctg.reference_name = 'chr3'
ctg.query_sequence = 'AGTAGCGAAA'
ctg.cigartuples = (
(S.BAM_CMATCH, 1),
(S.BAM_CINS, 1),
(S.BAM_CMATCH, 2),
(S.BAM_CREF_SKIP, 2),
(S.BAM_CMATCH, 3),
(S.BAM_CSOFT_CLIP, 3),
)
ref_fa = MagicMock()
ref_fa.get_reference_length.return_value = 100
ref_fa.fetch.return_value = 'CC'
kw = dict(contig=ctg, strand='+', ref_clv=14, ref_fa=ref_fa, ctg_clv=6)
assert extract_seq(**kw) == 'AGTACCGCG'
ref_fa.fetch.assert_called_once_with('chr3', 10, 12)
assert extract_seq(window=1, **kw) == 'G'
assert extract_seq(window=3, **kw) == 'GCG'
assert extract_seq(window=8, **kw) == 'GTACCGCG'
def test_with_skipped_and_deleted_regions_for_plus_strand_clv():
"""
AAA <-tail of suffix contig
A_TT--GC┘|| <-suffix contig with skip
0 12 345678 <-contig coord
|
ctg_clv^ ^init_ctg_idx <-contig coord
...ACTTAAGCGGT... <-genome
789012345678 <-genome coord
1 | |
ref_clv^ ^init_ref_idx
"""
ctg = MagicMock()
ctg.reference_name = 'chr3'
ctg.query_sequence = 'ATTGCAAA'
ctg.cigartuples = (
(S.BAM_CMATCH, 1),
(S.BAM_CDEL, 1),
(S.BAM_CMATCH, 2),
(S.BAM_CREF_SKIP, 2),
(S.BAM_CMATCH, 2),
(S.BAM_CSOFT_CLIP, 3),
)
ref_fa = MagicMock()
ref_fa.get_reference_length.return_value = 100
ref_fa.fetch.return_value = 'AA'
kw = dict(contig=ctg, strand='+', ref_clv=14, ref_fa=ref_fa, ctg_clv=4)
assert extract_seq(**kw) == 'ATTAAGC'
ref_fa.fetch.assert_called_once_with('chr3', 11, 13)
assert extract_seq(window=5, **kw) == 'TAAGC'
def test_with_5_base_inserted_region_for_plus_strand_clv():
"""
AATCC
┬ AA <-tail of suffix contig
ACGG GCG┘| <-suffix contig with skip
0123 9012 <-contig coord
| |1| |
ctg_clv^ ^init_ctg_idx <-contig coord
...ACGG GCGXXX... <-genome
7890 1234567 <-genome coord
1 | |
ref_clv^ ^init_ref_idx
"""
ctg = MagicMock()
ctg.reference_name = 'chr1'
ctg.query_sequence = 'ACGGAATCCGCGAA'
ctg.cigartuples = (
(S.BAM_CMATCH, 4),
(S.BAM_CINS, 5),
(S.BAM_CMATCH, 3),
(S.BAM_CSOFT_CLIP, 2),
)
ref_fa = MagicMock()
ref_fa.get_reference_length.return_value = 100
kw = dict(contig=ctg, strand='+', ref_clv=13, ref_fa=ref_fa, ctg_clv=11)
assert extract_seq(**kw) == 'ACGGAATCCGCG'
assert extract_seq(window=5, **kw) == 'CCGCG'
def test_hardclip_plust_strand(mock_apautils):
"""
AAA
CGCACCG┘ | <-suffix contig with hardclip
\\\| | | <-hardclip mask
01234567890 <-contig coord
|cc^ ^ice
...XXXACCGTCG... <-genome
234567890123 <-genome coord
| 1 |
rc^ ^ire
"""
ctg = MagicMock()
ctg.reference_name = 'chr2'
mock_apautils.infer_query_sequence.return_value = 'CGCACCGAAA'
ctg.cigartuples = (
(S.BAM_CHARD_CLIP, 3),
(S.BAM_CMATCH, 4),
(S.BAM_CSOFT_CLIP, 3),
)
ref_fa = MagicMock()
ref_fa.get_reference_length.return_value = 100
kw = dict(contig=ctg, strand='+', ref_clv=8, ref_fa=ref_fa, ctg_clv=6)
assert extract_seq(**kw) == 'CGCACCG'
assert extract_seq(window=1, **kw) == 'G'
assert extract_seq(window=3, **kw) == 'CCG'
def test_with_indel_and_skipped_regions_and_mismatches_for_plus_strand_clv():
"""
TC
┬ AA <-tail of suffix contig
A---CC GTA__GC┘| <-suffix contig with skip
0 12 567 8901 <-contig coord
x x |1
x ctg_clv^ ^init_ctg_idx <-contig coord
...ACTGTC GAATTGC... <-genome
789012 345678901 <-genome coord
1 | |
ref_clv^ ^init_ref_idx
"""
ctg = MagicMock()
ctg.reference_name = 'chr3'
ctg.query_sequence = 'ACCTCGTAGCAA'
ctg.cigartuples = (
(S.BAM_CMATCH, 1),
(S.BAM_CREF_SKIP, 3),
(S.BAM_CMATCH, 2),
(S.BAM_CINS, 2),
(S.BAM_CMATCH, 3),
(S.BAM_CDEL, 2),
(S.BAM_CMATCH, 2),
(S.BAM_CSOFT_CLIP, 2),
)
ref_fa = MagicMock()
ref_fa.get_reference_length.return_value = 100
ref_fa.fetch.return_value = 'CTG'
kw = dict(contig=ctg, strand='+', ref_clv=19, ref_fa=ref_fa, ctg_clv=9)
assert extract_seq(**kw) == 'ACTGCCTCGTAGC'
ref_fa.fetch.assert_called_once_with('chr3', 8, 11)
assert extract_seq(window=10, **kw) == 'GCCTCGTAGC'
def test_extract_seq_for_minus_strand_clv_supported_by_suffix():
"""
TTT <-tail of suffix contig
└ACATC <-suffix contig
012345678 <-contig coord
icb^ ^ctg_clv
...567890129... <-genome coord
irb^ ^ref_clv
"""
strand = '-'
ref_clv = 8
ctg_clv = 3
ref_fa = MagicMock()
contig = MagicMock()
contig.query_sequence = 'TTTACATCG'
contig.cigartuples = (
(S.BAM_CSOFT_CLIP, 3),
(S.BAM_CMATCH, 6),
)
args = contig, strand, ref_clv, ref_fa, ctg_clv
assert extract_seq(*args) == 'ACATCG'
assert extract_seq(*args, window=1) == 'A'
assert extract_seq(*args, window=2) == 'AC'
assert extract_seq(*args, window=3) == 'ACA'
assert extract_seq(*args, window=4) == 'ACAT'
def test_with_2_base_insertion():
"""
GA
TTT ┬ <-tail of suffix contig
||└AC TCG <-suffix contig
01234 5678 <-contig coord
ici^ ^ctg_clv
XXXXX XXX <-genome
45678 9012... <-genome coord
| 1
^ref_clv/iri
"""
ctg = MagicMock()
ctg.reference_name = 'chr1'
ctg.query_sequence = 'TTTACGATCG'
ctg.cigartuples = (
(S.BAM_CSOFT_CLIP, 3),
(S.BAM_CMATCH, 2),
(S.BAM_CINS, 2),
(S.BAM_CMATCH, 3),
)
ref_fa = MagicMock()
ref_fa.get_reference_length.return_value = 100
kw = dict(contig=ctg, strand='-', ref_clv=7, ref_fa=ref_fa, ctg_clv=3)
assert extract_seq(**kw) == 'ACGATCG'
assert extract_seq(window=2, **kw) == 'AC'
assert extract_seq(window=3, **kw) == 'ACG'
def test_with_skipped_region():
"""
TTT <-tail of suffix contig
||└GT--C <-suffix contig with skip
01234 56 <-contig coord
icb^ ^ctg_clv <-contig coord
...XXXGTTGC... <-genome
5678901234 <-genome coord
| | 1
irb^ ^ref_clv/iri
"""
ctg = MagicMock()
ctg.reference_name = 'chr2'
ctg.query_sequence = 'TTTGTC'
ctg.cigartuples = ((S.BAM_CSOFT_CLIP, 3), (S.BAM_CMATCH, 2),
(S.BAM_CREF_SKIP, 2), (S.BAM_CMATCH, 1))
ref_fa = MagicMock()
ref_fa.get_reference_length.return_value = 100
ref_fa.fetch = MagicMock(return_value='TG')
kw = dict(contig=ctg, strand='-', ref_clv=8, ref_fa=ref_fa, ctg_clv=3)
assert extract_seq(**kw) == 'GTTGC'
ref_fa.fetch.assert_called_with('chr2', 10, 12)
# **kw needs go after window for py34 syntax
assert extract_seq(window=1, **kw) == 'G'
assert extract_seq(window=3, **kw) == 'GTT'
assert extract_seq(window=4, **kw) == 'GTTG'
def test_extract_seq_for_bridge_with_deletion():
"""
AA
CG┘ <-bridge read
GAC__TCGTC <-bridge contig
012 345678 <-contig coord
| ||x
| |^cc ^ice
...GACGGTCCTC... <-genome
56789012345 <-genome coord
1| |
^rc ^rce
"""
ctg = MagicMock()
ctg.reference_name = 'chr2'
ctg.query_sequence = 'GACTCGTC'
ctg.cigartuples = (
(S.BAM_CMATCH, 3),
(S.BAM_CDEL, 2),
(S.BAM_CMATCH, 5),
)
ref_fa = MagicMock()
ref_fa.get_reference_length.return_value = 100
kw = dict(contig=ctg, strand='+', ref_clv=15, ref_fa=ref_fa, ctg_clv=5)
assert extract_seq(**kw) == 'GACTCG'
def test_extract_seq_for_bridge_with_insertion():
"""
AG AA <-inserted bases
┬ GT┘ <-bread read
GA CGGTCGC <-bridge contig
01 45678901 <-contig coord
x 1| |
x cc^ ^ice
...GT CGGTCGC... <-genome
56 78901234 <-genome coord
| |
rc^ ^ire
"""
ctg = MagicMock()
ctg.reference_name = 'chr2'
ctg.query_sequence = 'GAAGCGGTCGC'
ctg.cigartuples = (
(S.BAM_CMATCH, 2),
(S.BAM_CINS, 2),
(S.BAM_CMATCH, 7)
)
ref_fa = MagicMock()
ref_fa.get_reference_length.return_value = 100
kw = dict(contig=ctg, strand='+', ref_clv=10, ref_fa=ref_fa, ctg_clv=7)
assert extract_seq(**kw) == 'GAAGCGGT'
def test_extract_seq_with_skip_before_and_after_ctg_clv():
"""
AA
GT┘ <-bridge read
G--AGT-GC <-bridge contig
0 123 456 <-contig coord
ctg_clv^ ^ice
...GACAGTTGC... <-genome
5678901234 <-genome coord
1 |
ref_clv^ ^ire
"""
ctg = MagicMock()
ctg.reference_name = 'chr2'
ctg.query_sequence = 'GAGTGC'
ctg.cigartuples = (
(S.BAM_CMATCH, 1),
(S.BAM_CREF_SKIP, 2),
(S.BAM_CMATCH, 3),
(S.BAM_CREF_SKIP, 1),
(S.BAM_CMATCH, 2),
)
ref_fa = MagicMock()
ref_fa.get_reference_length.return_value = 100
ref_fa.fetch.return_value = 'AC'
kw = dict(contig=ctg, strand='+', ref_clv=10, ref_fa=ref_fa, ctg_clv=3)
assert extract_seq(**kw) == 'GACAGT'
ref_fa.fetch.assert_called_once_with('chr2', 6, 8)
def test_hardclip_spanning_clv_from_after_edgecase_3(mock_apautils):
"""
AAA
GTT┘ <-bridge read
A-GGTTGCA <-bridge contig
| | ///// <-hardclip mask
0 12345678 <-contig coord
cc^ ^ice
...ACGGTTGCA... <-genome
7890123456 <-genome coord
1 | |
rc^ ^ie
"""
ctg = MagicMock()
ctg.reference_name = 'chr1'
mock_apautils.infer_query_sequence.return_value = 'AGGTTGCA'
ctg.cigartuples = (
(S.BAM_CMATCH, 1),
(S.BAM_CREF_SKIP, 1),
(S.BAM_CMATCH, 2),
(S.BAM_CHARD_CLIP, 5),
)
ref_fa = MagicMock()
ref_fa.get_reference_length.return_value = 100
ref_fa.fetch = MagicMock(return_value='C')
kw = dict(contig=ctg, strand='+', ref_clv=12, ref_fa=ref_fa, ctg_clv=4)
assert extract_seq(**kw) == 'ACGGTT'
def test_extract_seq_for_bridge_with_multiple_skips_before_clv():
"""
AA
TA┘ <-bridge read
G-C--CTAGC <-bridge contig
0 1 234567 <-contig coord
||| x ^cc^ice
...GACTGGTAGC... <-genome
56789012345 <-genome coord
1 | |
rc^ ^ire
"""
ctg = MagicMock()
ctg.reference_name = 'chr2'
ctg.query_sequence = 'GCCTAGC'
ctg.cigartuples = (
(S.BAM_CMATCH, 1),
(S.BAM_CREF_SKIP, 1),
(S.BAM_CMATCH, 1),
(S.BAM_CREF_SKIP, 2),
(S.BAM_CMATCH, 5)
)
ref_fa = MagicMock()
ref_fa.get_reference_length.return_value = 100
ref_fa.fetch.side_effect = list(reversed(['A', 'TG'])) # from Right => Left
kw = dict(contig=ctg, strand='+', ref_clv=12, ref_fa=ref_fa, ctg_clv=4)
assert extract_seq(**kw) == 'GACTGCTA'
def test_with_two_skipped_regions_and_a_mismatch():
"""
TTT <-tail of suffix contig
||└GT--CAG-AC <-suffix contig with skip
01234 567 890 <-contig coord
init_ctg_clv^ ^cc x <-contig coord
...XXXGTTGCGGCAC... <-genome
56789012345678 <-genome coord
| 1
^ref_clv/iri
"""
ctg = MagicMock()
ctg.reference_name = 'chr2'
ctg.query_sequence = 'TTTGTCAGAC'
ctg.cigartuples = (
(S.BAM_CSOFT_CLIP, 3),
(S.BAM_CMATCH, 2),
(S.BAM_CREF_SKIP, 2),
(S.BAM_CMATCH, 3),
(S.BAM_CREF_SKIP, 1),
(S.BAM_CMATCH, 2),
)
ref_fa = MagicMock()
ref_fa.get_reference_length.return_value = 100
ref_fa.fetch.side_effect = ['TG', 'C']
kw = dict(contig=ctg, strand='-', ref_clv=8, ref_fa=ref_fa, ctg_clv=3)
assert extract_seq(**kw) == 'GTTGCAGCAC'
assert ref_fa.fetch.call_count == 2
ref_fa.fetch.assert_has_calls([call('chr2', 10, 12), call('chr2', 15, 16)])
def test_with_hardclip_spanning_clv_from_before_edgecase_3(mock_apautils):
"""
TT
└GTGA <-bridge read
GTGA <-bridge contig (hardcipped), chimeric
/ <-hardclip mask
012345678 <-contig coord
^icb/cc
...GTGA...
0123 <-genome coordinate
|1
^irb/rc
"""
ctg = MagicMock()
ctg.reference_name = 'chr2'
mock_apautils.infer_query_sequence.return_value = 'GTGA'
ctg.cigartuples = (
(S.BAM_CHARD_CLIP, 1),
(S.BAM_CMATCH, 3),
)
ref_fa = MagicMock()
ref_fa.get_reference_length.return_value = 100
kw = dict(contig=ctg, strand='-', ref_clv=0, ref_fa=ref_fa, ctg_clv=0)
assert extract_seq(**kw) == 'GTGA'
def test_with_three_skipped_region_and_mismatches_for_plus_strand_clv():
"""
AA <-tail of suffix contig
A---CC-GTA--GC┘| <-suffix contig with skip
0|||12|345||678 <-contig coord
|||x | x || |
|||x ctg_clv^ ^init_ctg_idx <-contig coord
...ACTGTCAGAATTGCX... <-genome
789012345678901 <-genome coord
1 |2|
ref_clv^ ^init_ref_idx
"""
ctg = MagicMock()
ctg.reference_name = 'chr3'
ctg.query_sequence = 'ACCGTAGCAA'
ctg.cigartuples = (
(S.BAM_CMATCH, 1),
(S.BAM_CREF_SKIP, 3),
(S.BAM_CMATCH, 2),
(S.BAM_CREF_SKIP, 1),
(S.BAM_CMATCH, 3),
(S.BAM_CREF_SKIP, 2),
(S.BAM_CMATCH, 2),
(S.BAM_CSOFT_CLIP, 2),
)
ref_fa = MagicMock()
ref_fa.get_reference_length.return_value = 100
ref_fa.fetch.side_effect = ['TT', 'A', 'CTG']
kw = dict(contig=ctg, strand='+', ref_clv=20, ref_fa=ref_fa, ctg_clv=7)
assert extract_seq(**kw) == 'ACTGCCAGTATTGC'
assert ref_fa.fetch.call_count == 3
ref_fa.fetch.assert_has_calls(
[call('chr3', 17, 19),
call('chr3', 13, 14),
call('chr3', 8, 11)])
ref_fa = MagicMock()
ref_fa.get_reference_length.return_value = 100
ref_fa.fetch.side_effect = ['TT', 'A']
kw.update(ref_fa=ref_fa)
assert extract_seq(window=9, **kw) == 'CAGTATTGC'
assert ref_fa.fetch.call_count == 2
def test_extract_seq_for_minus_strand_clv_supported_by_link():
"""
ACATC <-link contig
01234 <-contig coord
...89012... <-genome coord
^ref_clv
"""
strand = '-'
ref_clv = 8
ctg_clv = 0
ref_fa = MagicMock()
contig = MagicMock()
contig.query_sequence = 'ACATCG'
contig.cigartuples = ((S.BAM_CMATCH, 6), )
args = contig, strand, ref_clv, ref_fa, ctg_clv
assert extract_seq(*args) == 'ACATCG'
assert extract_seq(*args, window=1) == 'A'
assert extract_seq(*args, window=2) == 'AC'
assert extract_seq(*args, window=3) == 'ACA'
assert extract_seq(*args, window=4) == 'ACAT'
def test_hardclip_before_clv(mock_apautils):
"""
AA
TC┘ <-bridge read
CGCATTCGTCG <-bridge contig (hardcipped, could be chimeric https://www.biostars.org/p/109333/)
\\\| | <-hardclip mask
012345678901 <-contig coord
|cc^ ^ice
...XXXATTCGTCG... <-genome
234567890123 <-genome coord
| 1 |
rc^ ^ire
"""
ctg = MagicMock()
ctg.reference_name = 'chr2'
mock_apautils.infer_query_sequence.return_value = 'CGCATTCGTCG'
ctg.cigartuples = ((S.BAM_CHARD_CLIP, 3), (S.BAM_CMATCH, 8))
ref_fa = MagicMock()
ref_fa.get_reference_length.return_value = 100
kw = dict(contig=ctg, strand='+', ref_clv=8, ref_fa=ref_fa, ctg_clv=6)
assert extract_seq(**kw) == 'CGCATTC'
assert extract_seq(window=1, **kw) == 'C'
assert extract_seq(window=2, **kw) == 'TC'
assert extract_seq(window=3, **kw) == 'TTC'
assert extract_seq(window=4, **kw) == 'ATTC'
assert extract_seq(window=5, **kw) == 'CATTC'
def test_hardclip_after_clv(mock_apautils):
"""
AAA
GTT┘ <-bridge read
A-GGTTGCAGA <-bridge contig
| | | |/// <-hardclip mask
0 1234567890 <-contig coord
ctg_clv^ ^ice <-contig coord
...ACGGTTGCAGA... <-genome
789012345678 <-genome coord
1 | |
ref_clv^ ^init_fe
"""
ctg = MagicMock()
ctg.reference_name = 'chr1'
mock_apautils.infer_query_sequence.return_value = 'AGGTTGCAGA'
ctg.cigartuples = ((S.BAM_CMATCH, 1), (S.BAM_CREF_SKIP, 1),
(S.BAM_CMATCH, 6), (S.BAM_CHARD_CLIP, 3))
ref_fa = MagicMock()
ref_fa.get_reference_length.return_value = 100
ref_fa.fetch = MagicMock(return_value='C')
kw = dict(contig=ctg, strand='+', ref_clv=12, ref_fa=ref_fa, ctg_clv=4)
assert extract_seq(**kw) == 'ACGGTT'
ref_fa.fetch.assert_called_with('chr1', 8, 9)
assert extract_seq(window=1, **kw) == 'T'
assert extract_seq(window=2, **kw) == 'TT'
assert extract_seq(window=3, **kw) == 'GTT'
assert extract_seq(window=4, **kw) == 'GGTT'
assert extract_seq(window=5, **kw) == 'CGGTT'
def test_extract_seq_for_plus_strand_clv_supported_by_link():
"""
ATCGAC <-link contig
012345 <-contig coord
^ctg_clv
...789012... <-genome coord
1 ^ref_clv
"""
strand = '+'
ref_clv = 12
ctg_clv = 5
ref_fa = MagicMock()
contig = MagicMock()
contig.query_sequence = 'ATCGAC'
contig.cigartuples = ((S.BAM_CMATCH, 6), )
args = contig, strand, ref_clv, ref_fa, ctg_clv
assert extract_seq(*args) == 'ATCGAC'
assert extract_seq(*args, window=1) == 'C'
assert extract_seq(*args, window=2) == 'AC'
assert extract_seq(*args, window=3) == 'GAC'
assert extract_seq(*args, window=4) == 'CGAC'
def test_with_two_skipped_region_for_plus_strand_clv():
"""
AAA <-tail of suffix contig
A-TT--GC┘|| <-suffix contig with skip
0 12 345678 <-contig coord
|
ctg_clv^ ^init_ctg_idx <-contig coord
...ACTTAAGCGGT... <-genome
789012345678 <-genome coord
1 | |
ref_clv^ ^init_ref_idx
"""
ctg = MagicMock()
ctg.reference_name = 'chr3'
ctg.query_sequence = 'ATTGCAAA'
ctg.cigartuples = (
(S.BAM_CMATCH, 1),
(S.BAM_CREF_SKIP, 1),
(S.BAM_CMATCH, 2),
(S.BAM_CREF_SKIP, 2),
(S.BAM_CMATCH, 2),
(S.BAM_CSOFT_CLIP, 3),
)
ref_fa = MagicMock()
ref_fa.get_reference_length.return_value = 100
ref_fa.fetch.side_effect = ['AA', 'C']
kw = dict(contig=ctg, strand='+', ref_clv=14, ref_fa=ref_fa, ctg_clv=4)
assert extract_seq(**kw) == 'ACTTAAGC'
assert ref_fa.fetch.call_count == 2
ref_fa.fetch.assert_has_calls([call('chr3', 11, 13), call('chr3', 8, 9)])
# use a new mock, couldn't make ref_fa.reset_mock() work
ref_fa = MagicMock()
ref_fa.get_reference_length.return_value = 100
ref_fa.fetch.return_value = 'AA'
kw.update(ref_fa=ref_fa)
assert extract_seq(window=3, **kw) == 'AGC'
assert ref_fa.fetch.call_count == 1
def test_extract_seq_for_plus_strand_clv_supported_by_suffix():
"""
AA <-tail of suffix contig
ATCGAC┘ <-suffix contig
012345 <-contig coord
...789012... <-genome coord
^ref_clv
"""
strand = '+'
ctg_clv = 5
ref_clv = 12
ref_fa = MagicMock()
contig = MagicMock()
contig.query_sequence = 'ATCGACAA'
contig.cigartuples = ((S.BAM_CMATCH, 6), (S.BAM_CSOFT_CLIP, 2))
args = contig, strand, ref_clv, ref_fa, ctg_clv
assert extract_seq(*args) == 'ATCGAC'
assert extract_seq(*args, window=1) == 'C'
assert extract_seq(*args, window=2) == 'AC'
assert extract_seq(*args, window=3) == 'GAC'
assert extract_seq(*args, window=4) == 'CGAC'
def gen_hex_tuple(contig, strand, ref_clv, ref_fa, ctg_clv, dd_bridge):
# TODO: the returning of None is pretty ugly, to refactor
seqname = contig.reference_name
clv_key = apautils.gen_clv_key_tuple_with_ctg_clv(seqname, strand, ref_clv,
ctg_clv)
if dd_bridge['hexamer_tuple'][clv_key] is None: # do search
hex_src_seq = extract_seq(contig, strand, ref_clv, ref_fa, ctg_clv)
ctg_hex_tuple = search(strand, ref_clv, hex_src_seq)
if ctg_hex_tuple is None:
ctg_hex_tuple = ('NA', -1, -1)
else:
ctg_hex_tuple = None
return ctg_hex_tuple
def test_extract_seq_with_ending_softclip(self):
"""
AA
GGG┘|
012345 <-contig coord
234567 <-genome coord
"""
contig = MagicMock()
contig.query_sequence = 'GGGAA'
contig.cigartuples = ((S.BAM_CMATCH, 3), (S.BAM_CSOFT_CLIP, 2))
assert extract_seq(contig,
strand='+',
ref_clv=7,
ref_fa=MagicMock(),
ctg_clv=2) == 'GGG'
def test_extract_seq_with_ending_softclip(self, mock_apautils):
"""
AA
GGG┘|
012345 <-contig coord
234567 <-genome coord
"""
contig = MagicMock()
mock_apautils.infer_query_sequence.return_value = 'GGGAA'
contig.cigartuples = ((S.BAM_CMATCH, 3), (S.BAM_CHARD_CLIP, 2))
assert extract_seq(contig,
strand='+',
ref_clv=7,
ref_fa=MagicMock(),
ctg_clv=2) == 'GGG'
def test_extract_seq_with_starting_softclip(self):
"""
TT
└CAA
012345 <-contig coord
678901 <-genome coord
"""
strand = '-'
contig = MagicMock()
contig.query_sequence = 'TTCCA'
contig.cigartuples = ((S.BAM_CSOFT_CLIP, 2), (S.BAM_CMATCH, 4))
assert extract_seq(contig,
strand,
ref_clv=8,
ref_fa=MagicMock(),
ctg_clv=2) == 'CCA'
def test_extract_seq_with_starting_softclip(self, mock_apautils):
"""
TT
└CAA
012345 <-contig coord
678901 <-genome coord
"""
strand = '-'
contig = MagicMock()
mock_apautils.infer_query_sequence.return_value = 'TTCCA'
contig.cigartuples = ((S.BAM_CHARD_CLIP, 2), (S.BAM_CMATCH, 4))
assert extract_seq(contig,
strand,
ref_clv=8,
ref_fa=MagicMock(),
ctg_clv=2) == 'CCA'
