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import os.path as op
import click
from ..parallel import lock
from ..reduce import coarsen_cooler
from ..util import parse_cooler_uri
from . import cli
from ._util import parse_field_param
@cli.command()
@click.argument(
"cool_uri",
metavar="COOL_PATH"
)
@click.option(
"--factor", "-k",
help="Gridding factor. The contact matrix is coarsegrained by grouping "
"each chromosomal contact block into k-by-k element tiles",
type=int,
default=2,
show_default=True,
)
@click.option(
"--nproc", "-n", "-p",
help="Number of processes to use for batch processing chunks of pixels "
"[default: 1, i.e. no process pool]",
default=1,
type=int,
)
@click.option(
"--chunksize", "-c",
help="Number of pixels allocated to each process",
type=int,
default=int(10e6),
show_default=True,
)
@click.option(
"--field",
help="Specify the names of value columns to merge as '<name>'. "
"Repeat the `--field` option for each one. "
"Use '<name>,dtype=<dtype>' to specify the dtype. Include "
"',agg=<agg>' to specify an aggregation function different from 'sum'.",
type=str,
multiple=True,
)
@click.option(
"--out", "-o",
required=True,
help="Output file or URI"
)
@click.option(
"--append", "-a",
is_flag=True,
default=False,
help="Pass this flag to append the output cooler to an existing file "
"instead of overwriting the file."
)
def coarsen(cool_uri, factor, nproc, chunksize, field, out, append):
"""
Coarsen a cooler to a lower resolution.
Works by pooling *k*-by-*k* neighborhoods of pixels and aggregating.
Each chromosomal block is coarsened individually.
COOL_PATH : Path to a COOL file or Cooler URI.
"""
infile, _ = parse_cooler_uri(cool_uri)
outfile, _ = parse_cooler_uri(out)
same_file = op.realpath(infile) == op.realpath(outfile)
if len(field):
field_specifiers = [
parse_field_param(arg, includes_colnum=False) for arg in field
]
columns, _, dtypes, agg = zip(*field_specifiers)
dtypes = {col: dt for col, dt in zip(columns, dtypes) if dt is not None}
agg = {col: f for col, f in zip(columns, agg) if f is not None}
else:
# If no other fields are given, 'count' is implicitly chosen.
# Default aggregation. Dtype will be inferred.
columns, dtypes, agg = ["count"], None, None
coarsen_cooler(
cool_uri,
out,
factor,
chunksize=chunksize,
nproc=nproc,
columns=columns,
dtypes=dtypes,
agg=agg,
lock=lock if same_file else None,
mode="a" if append else "w"
)
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