ALLCools._allc_to_bigwig
Contents
ALLCools._allc_to_bigwig¶
This file is modified from methylpy https://github.com/yupenghe/methylpy
Module Contents¶
- _allc_to_bedgraph(allc_path, out_prefix, chrom_size_path, remove_additional_chrom=False, bin_size=50)[source]¶
Simply calculate cov and mc_rate for fixed genome bins. No mC context filter.
- _bedgraph_to_bigwig(input_file, chrom_size_path, path_to_wigtobigwig, remove_bedgraph=True)[source]¶
- allc_to_bigwig(allc_path, output_prefix, chrom_size_path, mc_contexts, split_strand=False, bin_size=50, remove_additional_chrom=False, region=None, cov_cutoff=9999, path_to_wigtobigwig='', remove_temp=True, cpu=1)[source]¶
Generate bigwig file(s) from 1 ALLC file.
- Parameters
allc_path – {allc_path_doc}
output_prefix – Output prefix of the bigwig file(s)
chrom_size_path – {chrom_size_path_doc}
mc_contexts – {mc_contexts_doc}
split_strand – {split_strand_doc}
bin_size – Minimum bin size of bigwig file
remove_additional_chrom – {remove_additional_chrom_doc}
region – {region_doc}
cov_cutoff – {cov_cutoff_doc}
path_to_wigtobigwig – Path to wigtobigwig to allow allcools to find it
remove_temp – debug parameter, whether to remove the temp file or not
cpu – Number of cores to use