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fix mean_fragsize #332

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merged 3 commits into from
Jul 4, 2023
Merged

fix mean_fragsize #332

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8903e8e
fix mean_fragsize
Phlya Jun 16, 2023
37c4f00
Fix zoomify for variable size bins
Phlya Jun 20, 2023
fc279f3
fix
Phlya Jun 20, 2023
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66 changes: 30 additions & 36 deletions src/cooler/cli/zoomify.py
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Expand Up @@ -34,9 +34,7 @@ def invoke_balance(args, resolutions, outfile):
logger.info(f"Balancing zoom level with bin size {res}")

try:
balance_cmd.main(
args=[uri, *args], prog_name='cooler'
)
balance_cmd.main(args=[uri, *args], prog_name="cooler")
except SystemExit as e:
# exc_info = sys.exc_info()
exit_code = e.code
Expand All @@ -49,32 +47,33 @@ def invoke_balance(args, resolutions, outfile):


@cli.command()
@click.argument(
"cool_uri",
metavar="COOL_PATH"
)
@click.argument("cool_uri", metavar="COOL_PATH")
@click.option(
"--nproc", "-n", "-p",
"--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",
"--chunksize",
"-c",
help="Number of pixels allocated to each process",
type=int,
default=int(10e6),
show_default=True,
)
@click.option(
"--resolutions", "-r",
"--resolutions",
"-r",
help="Comma-separated list of target resolutions. Use suffixes B or N to "
"specify a progression: B for binary (geometric steps of factor 2), N for "
"nice (geometric steps of factor 10 interleaved with steps of 2 and 5). "
"Examples: 1000B=1000,2000,4000,8000,... 1000N=1000,2000,5000,10000,... "
"5000N=5000,10000,25000,50000,... 4DN is an alias for 1000,2000,5000N "
"[default: B]"
"[default: B]",
)
@click.option(
"--balance",
Expand All @@ -88,17 +87,15 @@ def invoke_balance(args, resolutions, outfile):
"To deal with space ambiguity, use quotes to pass multiple arguments, "
"e.g. --balance-args '--nproc 8 --ignore-diags 3'. Note that nproc for "
"balancing must be specified independently of zoomify arguments.",
type=str
type=str,
)
@click.option(
"--base-uri", "-i",
"--base-uri",
"-i",
help="One or more additional base coolers to aggregate from, if needed.",
multiple=True,
)
@click.option(
"--out", "-o",
help="Output file or URI"
)
@click.option("--out", "-o", help="Output file or URI")
@click.option(
"--field",
help="Specify the names of value columns to merge as '<name>'. "
Expand Down Expand Up @@ -164,9 +161,7 @@ def zoomify(
continue
logger.info(f"Balancing zoom level {level}, bin size {res}")
try:
balance_cmd.main(
args=[uri, *balance_args], prog_name='cooler'
)
balance_cmd.main(args=[uri, *balance_args], prog_name="cooler")
except SystemExit as e:
# exc_info = sys.exc_info()
exit_code = e.code
Expand All @@ -178,7 +173,6 @@ def zoomify(
raise e

else:

clr = api.Cooler(cool_uri)
genome_length = clr.chromsizes.values.sum()

Expand All @@ -188,34 +182,34 @@ def zoomify(
maxres = int(ceil(genome_length / HIGLASS_TILE_DIM))
curres = clr.binsize
else:
mean_fragsize = clr.bins()[['end', 'start']][:].diff(axis=1).mean()
mean_fragsize = clr.bins()[["start", "end"]][:].diff(axis=1)["end"].mean()
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maxres = int(ceil(genome_length / mean_fragsize / HIGLASS_TILE_DIM))
curres = 1

# Default is to use a binary geometric progression
if resolutions is None:
resolutions = 'b'
resolutions = "b"

# Parse and expand user-provided resolutions
resolutions, rstring = [], resolutions
for res in [s.strip().lower() for s in rstring.split(",")]:
if 'n' in res or 'b' in res and maxres < curres:
if "n" in res or "b" in res and maxres < curres:
warnings.warn(
"Map is already < 256 x 256. Provide resolutions "
"explicitly if you want to coarsen more."
)
if res == 'n':
r = preferred_sequence(curres, maxres, 'nice')
elif res == 'b':
r = preferred_sequence(curres, maxres, 'binary')
elif res == '4dn':
r = [1000, 2000, *preferred_sequence(5000, maxres, 'nice')]
elif res.endswith('n'):
res = int(res.split('n')[0])
r = preferred_sequence(res, maxres, 'nice')
elif res.endswith('n'):
res = int(res.split('b')[0])
r = preferred_sequence(res, maxres, 'binary')
if res == "n":
r = preferred_sequence(curres, maxres, "nice")
elif res == "b":
r = preferred_sequence(curres, maxres, "binary")
elif res == "4dn":
r = [1000, 2000, *preferred_sequence(5000, maxres, "nice")]
elif res.endswith("n"):
res = int(res.split("n")[0])
r = preferred_sequence(res, maxres, "nice")
elif res.endswith("n"):
res = int(res.split("b")[0])
r = preferred_sequence(res, maxres, "binary")
else:
r = [int(res)]
resolutions.extend(r)
Expand Down