def test_is_a_right_tail_suffix_read_for_forward_suffix_contig_with_suffix_read_tail_len_equal_to_suffix_contig_tail_len(
):
"""
CGCAAA # suffix read
AAA
ATCGC┘ | # suffix contig
012345678 # contig coord
^ctg_clv
...ATCGCTGC...
234567890 # genome coord
ref_clv^ 1
"""
mock_read = MagicMock()
mock_read.query_sequence = 'CGCAAA'
mock_read.reference_end = 8
mock_read.cigartuples = [
(S.BAM_CMATCH, 5),
]
mock_contig = MagicMock()
mock_contig.is_reverse = False
mock_contig.query_sequence = 'ATCGCAAA'
mock_contig.cigartuples = [
(S.BAM_CMATCH, 5),
(S.BAM_CSOFT_CLIP, 3),
]
assert is_a_suffix_read(mock_read, mock_contig, ctg_clv=4) == 3
def test_is_a_left_tail_suffix_read_for_reverse_suffix_contig_with_suffix_read_tail_len_equal_to_suffix_contig_tail_len(
):
"""
TTTATC # suffix read
TTT
| └ATCGCTAC # suffix contig in r2c alignment
012345678901 # contig coord in r2c alignment
| # flip
|AAA
GTAGCGAT┘ | # suffix contig in c2g alignment
012345678901 # contig coord in c2g alignment
ctg_clv^ 1
109876543210 # rev contig coord, corresponding to contig coord in r2c alignment
1 |ctg_clv
...GTAGCGATCGT... # genome
234567890123 # genome coord
ref_clv^1
"""
mock_read = MagicMock()
mock_read.query_sequence = 'TTTATC'
mock_read.reference_start = 0
mock_read.cigartuples = [
(S.BAM_CMATCH, 5),
]
mock_contig = MagicMock()
mock_contig.is_reverse = True
mock_contig.query_sequence = 'GTAGCGGCGATAAA'
mock_contig.infer_query_length.return_value = 11
mock_contig.cigartuples = [
(S.BAM_CMATCH, 5),
(S.BAM_CSOFT_CLIP, 3),
]
assert is_a_suffix_read(mock_read, mock_contig, ctg_clv=7) == 3
def test_is_a_left_tail_suffix_read_for_forward_suffix_contig_with_suffix_read_tail_len_equal_to_suffix_contig_tail_len(
):
"""
TTTATC # suffix read
TTT
|└ATCGC # suffix contig
012345678 # contig coord
^ctg_clv
234567890 # genome coord
^ref_clv
"""
mock_read = MagicMock()
mock_read.query_sequence = 'TTTATC'
mock_read.reference_start = 0
mock_read.cigartuples = [
(S.BAM_CMATCH, 5),
]
mock_contig = MagicMock()
mock_contig.is_reverse = False
mock_contig.query_sequence = 'TTTATCGC'
mock_contig.cigartuples = [
(S.BAM_CSOFT_CLIP, 3),
(S.BAM_CMATCH, 5),
]
assert is_a_suffix_read(mock_read, mock_contig, ctg_clv=3) == 3
def test_is_a_right_tail_suffix_read_for_reverse_suffix_contig_with_suffix_read_tail_len_equal_to_suffix_contig_tail_len(
):
"""
CGCAAA # suffix read
AAA
GCGATCGC┘ | # suffix contig in r2c alignment
012345678901 # contig coord in r2c alignment
| 1 # flip
TTTGCGTACGC # suffix contig in c2g alignment
012345678901 # contig coord in c2g alignment
ctg_clv^ 1
109876543210 # rev contig coord, corresponding to contig coord in r2c alignment
1 |
...GCGTACGC... # genome
23456789 # genome coord
^ref_clv
"""
mock_read = MagicMock()
mock_read.query_sequence = 'CGCAAA'
mock_read.reference_end = 11
mock_read.cigartuples = [
(S.BAM_CMATCH, 5),
]
mock_contig = MagicMock()
mock_contig.is_reverse = True
mock_contig.query_sequence = 'TTTGCGTACGC'
mock_contig.infer_query_length.return_value = 11
mock_contig.cigartuples = [
(S.BAM_CSOFT_CLIP, 3),
(S.BAM_CMATCH, 8),
]
assert is_a_suffix_read(mock_read, mock_contig, ctg_clv=3) == 3
def test_is_not_a_suffix_read_for_forward_suffix_contig():
"""
ATC # suffix read
TTT|
└ATCGC # suffix contig
01234567
^ctg_clv
"""
mock_read = MagicMock()
mock_read.reference_start = 3
mock_read.query_sequence = 'ATC'
mock_read.cigartuples = [
(S.BAM_CMATCH, 3),
]
mock_contig = MagicMock()
mock_contig.is_reverse = False
mock_contig.query_sequence = 'TTTATCGC'
mock_contig.cigartuples = [
(S.BAM_CSOFT_CLIP, 3),
(S.BAM_CMATCH, 5),
]
assert is_a_suffix_read(mock_read, mock_contig, ctg_clv=3) is None
def test_is_not_a_suffix_read_for_reverse_suffix_contig():
"""
CGC # suffix read
|AAA
ATCGC┘ # suffix contig
01234567
^ctg_clv
"""
mock_read = MagicMock()
mock_read.query_sequence = 'CGC'
mock_read.reference_end = 5
mock_read.cigartuples = [
(S.BAM_CMATCH, 3),
]
mock_contig = MagicMock()
mock_contig.is_reverse = True
mock_contig.query_sequence = 'ATCGCAAA'
mock_contig.infer_query_length.return_value = 8
mock_contig.cigartuples = [
(S.BAM_CMATCH, 5),
(S.BAM_CSOFT_CLIP, 3),
]
assert is_a_suffix_read(mock_read, mock_contig, ctg_clv=4) is None