class RegionFilter(Filter):
intervaltree = None
region_names = []
@classmethod
def customize_parser(cls, parser: argparse.ArgumentParser):
parser.add_argument("--region_filter",
"-R",
action=RegionArgParser,
default=[])
def __init__(self, args: argparse.Namespace) -> "RegionFilter":
super().__init__(args)
self.intervaltree = IntervalTree()
if hasattr(args, "region_filter"):
self.region_names = args.region_filter
for name in args.region_filter:
regions = REGIONS[name].regions
for location in regions:
# convert to 0-based, half open coordinates
self.intervaltree.add(
Interval(location.start - 1, location.end))
def __repr__(self):
name = f"{self.__class__.__name__}"
if self.region_names:
name += " on " + ", ".join(self.region_names)
else:
name += " (inactive)"
return name
def __call__(self, record: Record) -> Union[Record, None]:
# this logic added so that it easier to add debug code
retain = True
if record.affected_end < record.affected_start:
# this is a insert - 0 length feature
retain = not self.intervaltree.overlaps_point(
record.affected_start)
else:
# SNV or MNV (del) - size 1 and above
retain = not self.intervaltree.overlaps(record.affected_start,
record.affected_end)
if retain:
return record
else:
return None
class CloseToIndelFilter(Filter):
intervaltree = None
dist = 0
def __init__(self, args: argparse.Namespace) -> "CloseToIndelFilter":
super().__init__(args)
self.intervaltree = IntervalTree()
if hasattr(args,
"close_to_indel_filter") and args.close_to_indel_filter:
reader = Reader(args.input_file)
dist = args.indel_window_size
self.dist = dist
for record in reader:
if not record.is_snv():
if record.affected_end < record.affected_start:
# this is an insertion, we only have the start site
self.intervaltree.addi(
begin=record.affected_start - dist,
end=record.affected_start + dist,
)
else:
self.intervaltree.addi(
begin=record.affected_start - dist,
end=record.affected_end + dist,
)
args.input_file.seek(0)
def __repr__(self) -> str:
name = f"{self.__class__.__name__}"
if self.dist:
name += f" (Window {self.dist})"
else:
name += " (inactive)"
return name
@classmethod
def customize_parser(cls, parser: argparse.ArgumentParser) -> None:
parser.add_argument(
"--close_to_indel_filter",
"-I",
action="store_true",
default=False,
help=
"Mask out single nucleotide variants that are too close to indels",
)
parser.add_argument(
"--indel_window_size",
type=int,
default=5,
help=
"Window around indel to mask out (mask this number of bases upstream/downstream from the indel. Requires -I option to selected)", # noqa: E501
)
def __call__(self, record: Record) -> Union[Record, None]:
retain = True
if record.is_snv():
# we are masking SNVs, only the affected_start is relevant since this is a size 1 feature
retain = not self.intervaltree.overlaps_point(
record.affected_start)
return record if retain else None