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import click
from ..reduce import merge_coolers
from . import cli
from ._util import parse_field_param
@cli.command()
@click.argument(
"out_path",
type=click.Path(exists=False)
)
@click.argument(
"in_paths",
nargs=-1,
type=click.Path(exists=False)
)
@click.option(
"--chunksize", "-c",
help="Size of the merge buffer in number of pixel table rows.",
type=int,
default=int(20e6),
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(
"--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 merge(out_path, in_paths, chunksize, field, append):
"""
Merge multiple coolers with identical axes.
OUT_PATH : Output file path or URI.
IN_PATHS : Input file paths or URIs of coolers to merge.
**Notes**
Data columns merged:
pixels/bin1_id, pixels/bin2_id, pixels/<value columns>
Data columns preserved:
chroms/name, chroms/length
bins/chrom, bins/start, bins/end
Additional columns in the the input files are not transferred to the output.
"""
# logger = get_logger(__name__)
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
merge_coolers(
out_path,
in_paths,
mergebuf=chunksize,
columns=columns,
dtypes=dtypes,
agg=agg,
mode="a" if append else "w"
)
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