def test_case2(self):
# case 2: longer < 2 x len shorter and < 50% shorter overlaps longer, trim both
starts_ends = [(5000, 5999), (5900, 6401)]
alignments = [
TruthAlignment(MockAlignment(start, end, end - start))
for start, end in starts_ends
]
filtered = [(f.start, f.end)
for f in TruthAlignment._filter_alignments(
alignments, full_region, min_length=401)]
expected = [(5000, 5900), (5999, 6401)]
if filtered != expected:
raise AssertionError('got {}, expected {}'.format(
filtered, expected))
filtered = [(f.start, f.end)
for f in TruthAlignment._filter_alignments(
alignments, full_region, min_length=899)]
expected = [(5000, 5900)]
if filtered != expected:
raise AssertionError('got {}, expected {}'.format(
filtered, expected))
filtered = [(f.start, f.end)
for f in TruthAlignment._filter_alignments(
alignments, full_region, min_length=1000)]
expected = []
if filtered != expected:
raise AssertionError('got {}, expected {}'.format(
filtered, expected))
def test_case3(self):
# case 3: longer >= 2 x len shorter and < 50% shorter overlaps longer, remove shorter
starts_ends = [(7000, 8000), (7501, 8000)]
expected = [(7000, 8000)]
alignments = [
TruthAlignment(MockAlignment(start, end, end - start))
for start, end in starts_ends
]
filtered = [
(f.start, f.end)
for f in TruthAlignment._filter_alignments(alignments, full_region)
]
if filtered != expected:
raise AssertionError('got {}, expected {}'.format(
filtered, expected))
# case 3 (contained): shorter contained within longer, shorter should be removed
starts_ends = [(0, 1000), (100, 200)]
expected = [(0, 1000)]
alignments = [
TruthAlignment(MockAlignment(start, end, end - start))
for start, end in starts_ends
]
filtered = [
(f.start, f.end)
for f in TruthAlignment._filter_alignments(alignments, full_region)
]
if filtered != expected:
raise AssertionError('got {}, expected {}'.format(
filtered, expected))
def test_labels_trimmed_back(self):
# we should have two alignments which partially overlap
# (318288, 417741)
# (417732, 422799)
# in this case, the first is >2 x longer than the second, so we trim back the second
# check resulting positions and labels are non-overlapping
alignments = TruthAlignment.bam_to_alignments(__truth_bam__,
__ref_name__,
start=318288,
end=422799)
assert alignments[0].start == 318288
assert alignments[0].end == 417741
assert alignments[1].start == 417732
assert alignments[1].end == 422799
filtered_alignments = TruthAlignment.filter_alignments(alignments)
assert filtered_alignments[0].start == 318288
assert filtered_alignments[0].end == 417741
assert filtered_alignments[1].start == 417741
assert filtered_alignments[1].end == 422799
p1_positions, p1_labels = filtered_alignments[
0].get_positions_and_labels()
p2_positions, p2_labels = filtered_alignments[
1].get_positions_and_labels()
assert p1_positions[0]['major'] == filtered_alignments[0].start
assert p1_positions[-1]['major'] == filtered_alignments[0].end - 1
assert p2_positions[0]['major'] == filtered_alignments[1].start
assert p2_positions[-1]['major'] == filtered_alignments[1].end - 1
def test_case4(self):
# case 4: longer >= 2 x len shorter and < 50% shorter overlaps longer, trim shorter
starts_ends = [(3000, 4000), (3800, 4299)]
expected = [(3000, 4000), (4000, 4299)]
alignments = [TruthAlignment(MockAlignment(start, end, end-start)) for start, end in starts_ends]
filtered = [(f.start, f.end) for f in TruthAlignment.filter_alignments(alignments, min_length=298)]
if filtered != expected:
raise AssertionError('got {}, expected {}'.format(filtered, expected))
def test_case1(self):
# case 1: longer < 2 x len shorter and >= 50% of shorter overlaps longer both should be removed
starts_ends = [(2000, 2999), (2500, 3000)]
expected = []
alignments = [TruthAlignment(MockAlignment(start, end, end-start)) for start, end in starts_ends]
filtered = [(f.start, f.end) for f in TruthAlignment.filter_alignments(alignments)]
if filtered != expected:
raise AssertionError('got {}, expected {}'.format(filtered, expected))
def test_many(self):
starts_ends = [(0, 1000), (100, 200),
(3000, 4000), (3800, 4299),
(7000, 8000), (7501, 8000),
(2000, 2999), (2500, 3000),
(5000, 5999), (5900, 6401),]
alignments = [TruthAlignment(MockAlignment(start, end, end-start)) for start, end in starts_ends]
filtered = [(f.start, f.end) for f in TruthAlignment.filter_alignments(alignments, min_length=1)]
expected = [(0, 1000), (3000, 4000), (4000, 4299), (5000, 5900), (5999, 6401), (7000, 8000)]
if filtered != expected:
raise AssertionError('got {}, expected {}'.format(filtered, expected))
starts_ends_m = starts_ends + [(0, 5000)]
alignments = [TruthAlignment(MockAlignment(start, end, end-start)) for start, end in starts_ends_m]
filtered = [(f.start, f.end) for f in TruthAlignment.filter_alignments(alignments, min_length=1)]
expected = [(0, 5000), (5000, 5900), (5999, 6401), (7000, 8000)]
if filtered != expected:
raise AssertionError('got {}, expected {}'.format(filtered, expected))
starts_ends_m = starts_ends + [(0, 5200)]
alignments = [TruthAlignment(MockAlignment(start, end, end-start)) for start, end in starts_ends_m]
filtered = [(f.start, f.end) for f in TruthAlignment.filter_alignments(alignments, min_length=1)]
expected = [(0, 5200), (5200, 5900), (5999, 6401), (7000, 8000)]
if filtered != expected:
raise AssertionError('got {}, expected {}'.format(filtered, expected))
starts_ends_m = starts_ends + [(0, 10000)]
alignments = [TruthAlignment(MockAlignment(start, end, end-start)) for start, end in starts_ends_m]
filtered = [(f.start, f.end) for f in TruthAlignment.filter_alignments(alignments, min_length=1)]
expected = [(0, 10000)]
if filtered != expected:
raise AssertionError('got {}, expected {}'.format(filtered, expected))
def test_labels_trimmed_back(self):
# we should have two alignments which partially overlap
# (318288, 417741)
# (417732, 422799)
# in this case, the first is >2 x longer than the second, so we trim back the second
# check resulting positions and labels are non-overlapping
alignments = TruthAlignment.bam_to_alignments(
__truth_bam__, Region(__ref_name__, start=318288, end=422799))
self.assertEqual(alignments[0][0].start, 318288)
self.assertEqual(alignments[0][0].end, 417741)
self.assertEqual(alignments[1][0].start, 417741)
self.assertEqual(alignments[1][0].end, 422799)
def bams_to_training_samples(self,
truth_bam,
bam,
region,
reference=None,
read_fraction=None):
"""Prepare training data chunks.
:param truth_bam: .bam file of truth aligned to ref to generate labels.
:param bam: input .bam file.
:param region: `Region` obj.
the reference will be parsed.
:param reference: reference `.fasta`, should correspond to `bam`.
:returns: tuple of `Sample` objects.
.. note:: Chunks might be missing if `truth_bam` is provided and
regions with multiple mappings were encountered.
"""
ref_rle = self.process_ref_seq(region.ref_name, reference)
# filter truth alignments to restrict ourselves to regions of the ref where the truth
# in unambiguous
alignments = TruthAlignment.bam_to_alignments(truth_bam,
region.ref_name,
start=region.start,
end=region.end)
filtered_alignments = TruthAlignment.filter_alignments(
alignments, start=region.start, end=region.end)
if len(filtered_alignments) == 0:
self.logger.info(
"Filtering removed all alignments of truth to ref from {}.".
format(region))
samples = []
for aln in filtered_alignments:
mock_compr = self.max_hp_len > 1 and not self.is_compressed
truth_pos, truth_labels = aln.get_positions_and_labels(
ref_compr_rle=ref_rle,
mock_compr=mock_compr,
is_compressed=self.is_compressed,
rle_dtype=True)
aln_samples = self.bam_to_sample(bam,
Region(region.ref_name, aln.start,
aln.end),
ref_rle,
read_fraction=read_fraction)
for sample in aln_samples:
# Create labels according to positions in pileup
pad = (encoding[_gap_],
1) if len(truth_labels.dtype) > 0 else encoding[_gap_]
padder = itertools.repeat(pad)
position_to_label = defaultdict(
padder.__next__,
zip([tuple(p) for p in truth_pos],
[a for a in truth_labels]))
padded_labels = np.fromiter(
(position_to_label[tuple(p)] for p in sample.positions),
dtype=truth_labels.dtype,
count=len(sample.positions))
sample = sample._asdict()
sample['labels'] = padded_labels
samples.append(Sample(**sample))
return tuple(samples)