def test_wholeProbeMaps_justAlleleMapsNothingElseMaps(self):
ref_name = "reference"
ref_length = 55
header = create_sam_header(ref_name, ref_length)
flag = 0
cigar = "5S1M50S"
nm = "NM:i:0"
md = "MD:Z:1"
mapq = 60
pos = 1
query_name = "IV=[5,6);"
sequence = "AAAAAAAAAAACGGCTCGCATAGACACGACGACGACACGTACGATCGATCAGTCAT"
sam_string = f"{query_name}\t{flag}\t{ref_name}\t{pos}\t{mapq}\t{cigar}\t*\t0\t0\t{sequence}\t*\t{nm}\t{md}\tAS:i:0\tXS:i:0"
record = pysam.AlignedSegment.fromstring(sam_string, header)
classification = Classification(record=record)
assert classification._whole_query_probe_maps()
def test_wholeProbeMaps_doesNotMapInTheForwardStrand(self):
ref_name = "reference"
ref_length = 55
header = create_sam_header(ref_name, ref_length)
flag = 0
cigar = "29S27M"
nm = "NM:i:0"
md = "MD:Z:27"
mapq = 60
pos = 1
query_name = "IV=[11,21);"
sequence = "AAAAAAAAAAACGGCTCGCATAGACACGACGACGACACGTACGATCGATCAGTCAT"
sam_string = f"{query_name}\t{flag}\t{ref_name}\t{pos}\t{mapq}\t{cigar}\t*\t0\t0\t{sequence}\t*\t{nm}\t{md}\tAS:i:0\tXS:i:0"
record = pysam.AlignedSegment.fromstring(sam_string, header)
classification = Classification(record=record)
assert not classification._whole_query_probe_maps()
def test_wholeProbeMaps_probeStartsAtFirstAlignmentPositionMapsReturnsTrue(
self):
ref_name = "reference"
ref_length = 55
header = create_sam_header(ref_name, ref_length)
flag = 0
cigar = "11S45M"
nm = "NM:i:0"
md = "MD:Z:45"
mapq = 60
pos = 1
query_name = "IV=[11,21);"
sequence = "AAAAAAAAAAACGGCTCGCATAGACACGACGACGACACGTACGATCGATCAGTCAT"
sam_string = f"{query_name}\t{flag}\t{ref_name}\t{pos}\t{mapq}\t{cigar}\t*\t0\t0\t{sequence}\t*\t{nm}\t{md}\tAS:i:0\tXS:i:0"
record = pysam.AlignedSegment.fromstring(sam_string, header)
classification = Classification(record=record)
assert classification._whole_query_probe_maps()
def test_wholeProbeMaps_unmappedRecordReturnsFalse(self):
ref_name = "reference"
ref_length = 55
header = create_sam_header(ref_name, ref_length)
flag = 4
cigar = "*"
nm = ""
md = ""
mapq = 0
pos = 0
query_name = "IV=[11,21);"
ref_name = "*"
sequence = "AAAAAAAAAAACGGCTCGCATAGACACGACGACGACACGTACGATCGATCAGTCAT"
sam_string = f"{query_name}\t{flag}\t{ref_name}\t{pos}\t{mapq}\t{cigar}\t*\t0\t0\t{sequence}\t*\tAS:i:0\tXS:i:0"
record = pysam.AlignedSegment.fromstring(sam_string, header)
classification = Classification(record=record)
assert not classification._whole_query_probe_maps()
def test_isCorrect_deletionInRefOfLastProbeCoreBaseReturnsFalse(self):
ref_name = "reference"
ref_length = 63
header = create_sam_header(ref_name, ref_length)
flag = 0
cigar = "20M1I35M"
nm = "NM:i:1"
md = "MD:Z:55"
mapq = 60
pos = 1
query_name = "IV=[11,21);"
sequence = "AAAAAAAAAAACGGCTCGCATAGACACGACGACGACACGTACGATCGATCAGTCAT"
sam_string = f"{query_name}\t{flag}\t{ref_name}\t{pos}\t{mapq}\t{cigar}\t*\t0\t0\t{sequence}\t*\t{nm}\t{md}\tAS:i:0\tXS:i:0"
record = pysam.AlignedSegment.fromstring(sam_string, header)
probe = Probe(header=ProbeHeader.from_string(query_name),
full_sequence=sequence)
classification = RecallClassification(record=record)
assert not classification.is_correct()
def test_isCorrect_mismatchInBaseAfterCoreProbeEndsReturnsTrue(self):
ref_name = "reference"
ref_length = 64
header = create_sam_header(ref_name, ref_length)
flag = 0
cigar = "56M"
nm = "NM:i:1"
md = "MD:Z:21C34"
mapq = 60
pos = 1
query_name = "IV=[11,21);"
sequence = "AAAAAAAAAAACGGCTCGCATAGACACGACGACGACACGTACGATCGATCAGTCAT"
sam_string = f"{query_name}\t{flag}\t{ref_name}\t{pos}\t{mapq}\t{cigar}\t*\t0\t0\t{sequence}\t*\t{nm}\t{md}\tAS:i:0\tXS:i:0"
record = pysam.AlignedSegment.fromstring(sam_string, header)
probe = Probe(header=ProbeHeader.from_string(query_name),
full_sequence=sequence)
classification = RecallClassification(record=record)
assert classification.is_correct()
def test_isCorrect_probeIsDeletionBaseToRightIsMismatchReturnsFalse(self):
ref_name = "reference"
ref_length = 64
header = create_sam_header(ref_name, ref_length)
flag = 0
cigar = "56M"
nm = "NM:i:1"
md = "MD:Z:12T43"
mapq = 60
pos = 6
query_name = "IV=[12,12);"
sequence = "AAAAAAAAAAACGGCTCGCATAGACACGACGACGACACGTACGATCGATCAGTCAT"
sam_string = f"{query_name}\t{flag}\t{ref_name}\t{pos}\t{mapq}\t{cigar}\t*\t0\t0\t{sequence}\t*\t{nm}\t{md}\tAS:i:0\tXS:i:0"
record = pysam.AlignedSegment.fromstring(sam_string, header)
probe = Probe(header=ProbeHeader.from_string(query_name),
full_sequence=sequence)
classification = RecallClassification(record=record)
assert not classification.is_correct()
def test_wholeProbeMaps_probeEndsOnLastBaseOfAlignmentReturnsTrue(self):
ref_name = "reference"
ref_length = 59
header = create_sam_header(ref_name, ref_length)
flag = 0
cigar = "33M35S"
nm = "NM:i:0"
md = "MD:Z:33"
mapq = 60
pos = 6
query_name = "IV=[23,33);"
sequence = (
"AAAAAAAAAAAAAAAAAAAAAAACGGCTCGCATAGACACGACGACGACACGTACGATCGATCAGTCAT"
)
sam_string = f"{query_name}\t{flag}\t{ref_name}\t{pos}\t{mapq}\t{cigar}\t*\t0\t0\t{sequence}\t*\t{nm}\t{md}\tAS:i:0\tXS:i:0"
record = pysam.AlignedSegment.fromstring(sam_string, header)
classification = Classification(record=record)
assert classification._whole_query_probe_maps()
def test_assessment_mismatchInLastCoreProbeBase(self):
ref_name = "reference"
ref_length = 64
header = create_sam_header(ref_name, ref_length)
flag = 0
cigar = "56M"
nm = "NM:i:1"
md = "MD:Z:20C35"
mapq = 60
pos = 1
query_name = "IV=[11,21);"
sequence = "AAAAAAAAAAACGGCTCGCATAGACACGACGACGACACGTACGATCGATCAGTCAT"
sam_string = f"{query_name}\t{flag}\t{ref_name}\t{pos}\t{mapq}\t{cigar}\t*\t0\t0\t{sequence}\t*\t{nm}\t{md}\tAS:i:0\tXS:i:0"
record = pysam.AlignedSegment.fromstring(sam_string, header)
probe = Probe(header=ProbeHeader.from_string(query_name),
full_sequence=sequence)
classification = PrecisionClassification(record=record)
expected = 0.9
actual = classification.assessment()
assert actual == expected
def test_assessment_probeIsDeletionBasesEitherSideMatch(self):
ref_name = "reference"
ref_length = 64
header = create_sam_header(ref_name, ref_length)
flag = 0
cigar = "56M"
nm = "NM:i:0"
md = "MD:Z:56"
mapq = 60
pos = 6
query_name = "IV=[12,12);"
sequence = "AAAAAAAAAAACGGCTCGCATAGACACGACGACGACACGTACGATCGATCAGTCAT"
sam_string = f"{query_name}\t{flag}\t{ref_name}\t{pos}\t{mapq}\t{cigar}\t*\t0\t0\t{sequence}\t*\t{nm}\t{md}\tAS:i:0\tXS:i:0"
record = pysam.AlignedSegment.fromstring(sam_string, header)
probe = Probe(header=ProbeHeader.from_string(query_name),
full_sequence=sequence)
classification = PrecisionClassification(record=record)
expected = 1.0
actual = classification.assessment()
assert actual == expected
def test_isCorrect_probesMatchPerfectlyReturnsTrue(self):
ref_name = "reference"
ref_length = 59
header = create_sam_header(ref_name, ref_length)
flag = 0
cigar = "33M35S"
nm = "NM:i:0"
md = "MD:Z:33"
mapq = 60
pos = 6
query_name = "IV=[23,33);"
sequence = (
"AAAAAAAAAAAAAAAAAAAAAAACGGCTCGCATAGACACGACGACGACACGTACGATCGATCAGTCAT"
)
sam_string = f"{query_name}\t{flag}\t{ref_name}\t{pos}\t{mapq}\t{cigar}\t*\t0\t0\t{sequence}\t*\t{nm}\t{md}\tAS:i:0\tXS:i:0"
record = pysam.AlignedSegment.fromstring(sam_string, header)
probe = Probe(header=ProbeHeader.from_string(query_name),
full_sequence=sequence)
classification = RecallClassification(record=record)
assert classification.is_correct()
def test_assessment_probesMatchPerfectlyInRCWithTotallyWrongFlanks(self):
ref_name = "reference"
ref_length = 59
header = create_sam_header(ref_name, ref_length)
flag = 16
cigar = "53S5M10S"
nm = "NM:i:0"
md = "MD:Z:4"
mapq = 60
pos = 6
query_name = "IV=[10,15);"
sequence = (
"AAAAAAAAAAAAAAAAAAAAAAACGGCTCGCATAGACACGACGACGACACGTACGATCGATCAGTCAT"
)
sam_string = f"{query_name}\t{flag}\t{ref_name}\t{pos}\t{mapq}\t{cigar}\t*\t0\t0\t{sequence}\t*\t{nm}\t{md}\tAS:i:0\tXS:i:0"
record = pysam.AlignedSegment.fromstring(sam_string, header)
probe = Probe(header=ProbeHeader.from_string(query_name),
full_sequence=sequence)
classification = PrecisionClassification(record=record)
expected = 1.0
actual = classification.assessment()
assert actual == expected
