def create_classifier_with_two_entries(cls: Type) -> Type[Classifier]:
flag = 0
cigar = "56M"
nm = "NM:i:0"
md = "MD:Z:56"
mapq = 60
pos = 1
query_header = ProbeHeader(interval=ProbeInterval(12, 17))
sequence = "AAAAAAAAAAACGGCTCGCATAGACACGACGACGACACGTACGATCGATCAGTCAT"
ref_header = ProbeHeader(
chrom="GC00000422_2",
sample="CFT073",
pos=603,
interval=ProbeInterval(25, 32),
svtype="PH_SNPs",
gt_conf=89.5987,
)
header = create_sam_header(str(ref_header), 64)
contents = str(header) + "\n"
record1 = pysam.AlignedSegment.fromstring(
f"{query_header}\t{flag}\t{ref_header}\t{pos}\t{mapq}\t{cigar}\t*\t0\t0\t{sequence}\t*\t{nm}\t{md}\tAS:i:43\tXS:i:32",
header,
)
contents += record1.to_string() + "\n"
flag = 2048
cigar = "43M"
nm = "NM:i:1"
md = "MD:Z:21T21"
mapq = 0
pos = 5
query_header = ProbeHeader(chrom="3", pos=14788, interval=ProbeInterval(21, 22))
sequence = "CGCGAAAGCCCTGACCATCTGCACCGTGTCTGACCACATCCGC"
header = create_sam_header(str(ref_header), 57)
record2 = pysam.AlignedSegment.fromstring(
f"{query_header}\t{flag}\t{ref_header}\t{pos}\t{mapq}\t{cigar}\t*\t0\t0\t{sequence}\t*\t{nm}\t{md}\tAS:i:43\tXS:i:32",
header,
)
contents += record2.to_string() + "\n"
sam = create_tmp_sam(contents)
return cls(sam)
class TestRecallMasker:
@patch.object(
Probe, "get_interval", return_value=ProbeInterval(3, 4)
)
@patch.object(Probe, "chrom", return_value="chrom1", new_callable=PropertyMock)
@patch.object(Probe, "pos", return_value=45, new_callable=PropertyMock)
def test_getIntervalWhereProbeAlignsToTruth_probeOfLengthOneReturnsIntervalOfLengthOne(
self, *mock
):
actual = RecallMasker.get_interval_where_probe_aligns_to_truth(Classification())
expected = Interval(45, 46, "chrom1")
assert actual == expected
@patch.object(
Probe, "get_interval", return_value=ProbeInterval(3, 5)
)
@patch.object(Probe, "chrom", return_value="chrom1", new_callable=PropertyMock)
@patch.object(Probe, "pos", return_value=45, new_callable=PropertyMock)
def test_getIntervalWhereProbeAlignsToTruth_probeOfLengthTwoReturnsIntervalOfLengthTwo(
self, *mock
):
actual = RecallMasker.get_interval_where_probe_aligns_to_truth(Classification())
expected = Interval(45, 47, "chrom1")
assert actual == expected
@patch.object(
Probe, "get_interval", return_value=ProbeInterval(3, 3)
)
@patch.object(Probe, "chrom", return_value="chrom1", new_callable=PropertyMock)
@patch.object(Probe, "pos", return_value=45, new_callable=PropertyMock)
def test_getIntervalWhereProbeAlignsToTruth_probeOfLengthZeroReturnsNullInterval(
self, *mock
):
actual = RecallMasker.get_interval_where_probe_aligns_to_truth(Classification())
expected = Interval(45, 45, "chrom1")
assert actual == expected
def create_incorrect_primary_sam_record() -> pysam.AlignedSegment:
flag = 0
cigar = "56M"
nm = "NM:i:1"
md = "MD:Z:12T43"
mapq = 60
pos = 1
query_header = ProbeHeader(interval=ProbeInterval(12, 13))
ref_header = ProbeHeader(
chrom="GC00000422_2",
sample="CFT073",
pos=603,
interval=ProbeInterval(25, 32),
svtype="PH_SNPs",
gt_conf=89.5987,
)
sequence = "AAAAAAAAAAACGGCTCGCATAGACACGACGACGACACGTACGATCGATCAGTCAT"
header = create_sam_header(str(ref_header), 64)
record = pysam.AlignedSegment.fromstring(
f"{query_header}\t{flag}\t{ref_header}\t{pos}\t{mapq}\t{cigar}\t*\t0\t0\t{sequence}\t*\t{nm}\t{md}\tAS:i:43\tXS:i:32",
header,
)
return record
def create_correct_supplementary_sam_record() -> pysam.AlignedSegment:
flag = 2048
cigar = "43M"
nm = "NM:i:1"
md = "MD:Z:19T23"
mapq = 0
pos = 5
query_header = ProbeHeader(chrom="3", pos=14788, interval=ProbeInterval(21, 22))
ref_header = ProbeHeader(
chrom="GC00000422_2",
sample="CFT073",
pos=603,
interval=ProbeInterval(25, 32),
svtype="PH_SNPs",
gt_conf=89.5987,
)
sequence = "CGCGAAAGCCCTGACCATCTGCACCGTGTCTGACCACATCCGC"
header = create_sam_header(str(ref_header), 57)
record = pysam.AlignedSegment.fromstring(
f"{query_header}\t{flag}\t{ref_header}\t{pos}\t{mapq}\t{cigar}\t*\t0\t0\t{sequence}\t*\t{nm}\t{md}\tAS:i:43\tXS:i:32",
header,
)
return record