$ allcools table-to-allc -h
usage: allcools table-to-allc [-h] --input_path INPUT_PATH --output_prefix
OUTPUT_PREFIX [--sep SEP] [--header HEADER]
[--chunk_size CHUNK_SIZE] [--chrom CHROM]
[--pos POS] [--strand STRAND]
[--context CONTEXT] [--mc MC] [--uc UC]
[--cov COV] [--mc_frac MC_FRAC]
[--pseudo_count PSEUDO_COUNT]
[--fasta_path FASTA_PATH]
[--num_upstream_bases NUM_UPSTREAM_BASES]
[--num_downstream_bases NUM_DOWNSTREAM_BASES]
[--add_chr] [--no_sort]
optional arguments:
-h, --help show this help message and exit
--sep SEP character to separate columns in the table (default: )
--header HEADER Whether the table contains header line or not
(default: None)
--chunk_size CHUNK_SIZE
chunk_size to perform conversion (default: 100000)
--chrom CHROM the chromosome column number, 0-based index (default:
0)
--pos POS the position column number, 0-based index (default: 1)
--strand STRAND the strand column number, 0-based index. If not
provided, will infer automatically based on the
fasta_path (default: None)
--context CONTEXT the cytosine context column number, 0-based index. If
not provided, will inter automatically based on the
fasta_path (default: None)
--mc MC the methylated cytosine count column number, 0-based
index. (default: None)
--uc UC the unmethylated cytosine count column number, 0-based
index. (default: None)
--cov COV the total cytosine coverage count column number,
0-based index. (default: None)
--mc_frac MC_FRAC the methylation fraction column number, 0-based index.
(default: None)
--pseudo_count PSEUDO_COUNT
Use this pseudo_count number as the total cytosine
coverage count, if the "cov" column is missing and
"mc_frac" column is provided. (default: 1)
--fasta_path FASTA_PATH
the genome FASTA file path, required if either
"strand" or "context" column is missing. (default:
None)
--num_upstream_bases NUM_UPSTREAM_BASES
number of up stream bases to include when get cytosine
context. (default: 0)
--num_downstream_bases NUM_DOWNSTREAM_BASES
number of down stream bases to include when get
cytosine context. (default: 2)
--add_chr whether add "chr" before the chromosome name.
(default: False)
--no_sort whether sort the ALLC table after conversion.
(default: True)
required arguments:
--input_path INPUT_PATH
input path of the table (default: None)
--output_prefix OUTPUT_PREFIX
output prefix of the ALLC table (default: None)
