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import click
from .. import fileops
from . import cli
@cli.command()
@click.argument(
"cool_path",
metavar="COOL_PATH"
)
@click.option(
"--long", "-l",
help="Long listing format",
is_flag=True
)
def ls(cool_path, long):
"""
List all coolers inside a file.
"""
from ..api import Cooler
for group_path in fileops.list_coolers(cool_path):
uri = cool_path + "::" + group_path
if long:
binsize = Cooler(uri).binsize
if binsize is None:
s = f"{uri}\t<variable>"
else:
s = f"{uri}\t{binsize:,}"
click.echo(s)
else:
click.echo(uri)
@cli.command()
@click.argument(
"src_uri",
type=str
)
@click.argument(
"dst_uri",
type=str
)
@click.option(
"--overwrite", "-w",
help="Truncate and replace destination file if it already exists.",
is_flag=True,
default=False,
)
def cp(src_uri, dst_uri, overwrite):
"""
Copy a cooler from one file to another or within the same file.
See also: h5copy, h5repack tools from HDF5 suite.
"""
# \b\bArguments:
# SRC_URI : Path to source file or URI to source Cooler group
# DST_URI : Path to destination file or URI to destination Cooler group
# if dst_group in dst and dst_group != '/':
# click.confirm(
# "A group named '{}' already exists in '{}'. Overwrite?".format(
# dst_group, dst_path),
# abort=True)
# del dst[dst_group]
fileops.cp(src_uri, dst_uri, overwrite=overwrite)
@cli.command()
@click.argument(
"src_uri",
type=str
)
@click.argument(
"dst_uri",
type=str
)
@click.option(
"--overwrite", "-w",
help="Truncate and replace destination file if it already exists.",
is_flag=True,
default=False,
)
@click.option(
"--soft", "-s",
help="Creates a soft link rather than a hard link if the source and "
"destination file are the same. Otherwise, creates an external link. "
"This type of link uses a path rather than a pointer.",
is_flag=True,
default=False,
)
def ln(src_uri, dst_uri, overwrite, soft):
"""
Create a hard link to a cooler (rather than a true copy) in the same file.
Also supports soft links (in the same file) or external links (different
files).
"""
fileops.ln(src_uri, dst_uri, overwrite=overwrite, soft=soft)
@cli.command()
@click.argument(
"src_uri",
type=str
)
@click.argument(
"dst_uri",
type=str
)
@click.option(
"--overwrite", "-w",
help="Truncate and replace destination file if it already exists.",
is_flag=True,
default=False,
)
def mv(src_uri, dst_uri, overwrite):
"""
Rename a cooler within the same file.
"""
fileops.mv(src_uri, dst_uri, overwrite=overwrite)
@cli.command()
@click.argument(
"uri",
type=str
)
@click.option(
"-L", "--level",
type=int
)
def tree(uri, level):
"""
Display a file's data hierarchy.
"""
t = fileops.pprint_data_tree(uri, level)
click.echo(t)
@cli.command()
@click.argument(
"uri",
type=str
)
@click.option(
"-L", "--level",
type=int
)
def attrs(uri, level):
"""
Display a file's attribute hierarchy.
"""
t = fileops.pprint_attr_tree(uri, level)
click.echo(t)
|
