$ allcools region -h
usage: allcools allc-to-region-count [-h] --allc_path ALLC_PATH
--output_prefix OUTPUT_PREFIX
--chrom_size_path CHROM_SIZE_PATH
--mc_contexts MC_CONTEXTS
[MC_CONTEXTS ...] [--split_strand]
[--region_bed_paths REGION_BED_PATHS [REGION_BED_PATHS ...]]
[--region_bed_names REGION_BED_NAMES [REGION_BED_NAMES ...]]
[--bin_sizes BIN_SIZES [BIN_SIZES ...]]
[--cov_cutoff COV_CUTOFF]
[--save_zero_cov] [--cpu CPU]
optional arguments:
-h, --help show this help message and exit
--split_strand If true, Watson (+) and Crick (-) strands will be
count separately (default: False)
--region_bed_paths REGION_BED_PATHS [REGION_BED_PATHS ...]
Arbitrary genomic regions can be defined in several
BED files to count on. Space separated paths to each
BED files, The fourth column of the BED file should be
unique id of the regions. (default: None)
--region_bed_names REGION_BED_NAMES [REGION_BED_NAMES ...]
Space separated names for each BED file provided in
region_bed_paths. (default: None)
--bin_sizes BIN_SIZES [BIN_SIZES ...]
Fix-size genomic bins can be defined by bin_sizes and
chrom_size_path. Space separated sizes of genome bins,
each size will be count separately. (default: None)
--cov_cutoff COV_CUTOFF
Max cov filter for a single site in ALLC. Sites with
cov > cov_cutoff will be skipped. (default: 9999)
--save_zero_cov If present, save the regions that have 0 cov in
output, only apply to region count but not the
chromosome count. (default: False)
--cpu CPU Number of processes to use in parallel. This function
parallel on region level and will generate a bunch of
small files if cpu > 1. Do not use cpu > 1 for single
cell region count. For single cell data, parallel on
cell level is better. (default: 1)
required arguments:
--allc_path ALLC_PATH, -allc ALLC_PATH
Path to 1 ALLC file (default: None)
--output_prefix OUTPUT_PREFIX, -out OUTPUT_PREFIX
Path prefix of the output region count file. (default:
None)
--chrom_size_path CHROM_SIZE_PATH
Path to UCSC chrom size file. This can be generated
from the genome fasta or downloaded via UCSC
fetchChromSizes tools. All ALLCools functions will
refer to this file whenever possible to check for
chromosome names and lengths, so it is crucial to use
a chrom size file consistent to the reference fasta
file ever since mapping. ALLCools functions will not
change or infer chromosome names. (default: None)
--mc_contexts MC_CONTEXTS [MC_CONTEXTS ...]
Space separated mC context patterns to extract from
ALLC. The context length should be the same as ALLC
file context. Context pattern follows IUPAC nucleotide
code, e.g. N for ATCG, H for ATC, Y for CT. (default:
None)
