def test_windows(self):
"""Test WindowSelector.windows()."""
window = WindowSelector(self.test_ws_config())
candidates = {0: 2, 2: 4, 3: 11, 8: 3}
self.assertEqual(list(window.windows(candidates, 'ref', 0)), [
range_pb2.Range(reference_name='ref', start=-4, end=6),
range_pb2.Range(reference_name='ref', start=4, end=12)
])
def windows(self, candidate_pos, ref_name, ref_offset):
""""Process candidate positions to determine windows for local assembly.
Following filters are applied:
- Candidate position with low number of supporting reads is ignored.
- Candidate position with too many of supporting reads is ignored.
Windows are within range of
[min(pos) - self.config.min_windows_distance,
max(pos) + self.config.min_windows_distance)
Args:
candidate_pos: A dictionary with ref_pos as key and number of supporting
reads as its value.
ref_name: Reference name, used in setting the output
genomics.range.reference_name value.
ref_offset: Start offset for reference position.
Yields:
A genomics.range record. Note: only start and end fields are
populated.
"""
start_pos = end_pos = -1
for pos in sorted(candidate_pos):
if candidate_pos[pos] < self.config.min_num_supporting_reads:
continue
if candidate_pos[pos] > self.config.max_num_supporting_reads:
continue
if start_pos == -1:
start_pos = pos
end_pos = pos
elif pos > end_pos + self.config.min_windows_distance:
yield range_pb2.Range(reference_name=ref_name,
start=start_pos + ref_offset -
self.config.min_windows_distance,
end=end_pos + ref_offset +
self.config.min_windows_distance)
start_pos = pos
end_pos = pos
else:
end_pos = pos
if start_pos != -1:
yield range_pb2.Range(reference_name=ref_name,
start=start_pos + ref_offset -
self.config.min_windows_distance,
end=end_pos + ref_offset +
self.config.min_windows_distance)
def make_range(chrom, start, end):
"""Returns a nucleus.genomics.v1.Range.
Args:
chrom: str. The chromosome name.
start: int. The start position (0-based, inclusive) of this range.
end: int. The end position (0-based, exclusive) of this range.
Returns:
A nucleus.genomics.v1.Range.
"""
return range_pb2.Range(reference_name=chrom, start=start, end=end)
def make_range(chrom, start, end):
"""Creates a genomics.Range object chr:start-end.
Args:
chrom: The chromosome name as a string.
start: The start position (0-based, inclusive, integer) of this range.
end: The end position (0-based, exclusive, integer) of this range.
Returns:
A third_party.nucleus.protos.Range.
"""
return range_pb2.Range(reference_name=chrom, start=start, end=end)
def read_range(read):
"""Creates a Range proto from the alignment of Read.
Args:
read: nucleus.genomics.v1.Read. The read to calculate the range for.
Returns:
A nucleus.genomics.v1.Range for read.
"""
range_pb = range_pb2.Range()
utils_cpp.read_range(read, range_pb)
return range_pb
def read_range(read, use_cached_read_end=True):
"""Creates a Range proto from the alignment of Read.
Args:
read: nucleus.genomics.v1.Read. The read to calculate the range for.
use_cached_read_end: If True, use the `cached_end` stored in Read instead of
recalculating.
Returns:
A nucleus.genomics.v1.Range for read.
"""
range_pb = range_pb2.Range()
utils_cpp.read_range(read,
range_pb,
use_cached_read_end=use_cached_read_end)
return range_pb