ALLCools.sandbox.motif.motif_scan
Contents
ALLCools.sandbox.motif.motif_scan¶
Module Contents¶
- _count_data_to_xarray(total_data: dict, allc_series)[source]¶
total_data: key is ALLC path, value is series of motif cov/mc count sum from all regions of that ALLC
- _count_single_cmotif_bin_on_multiple_allc(cmotif_dict_path, allc_paths, region, count_binary, context_to_pattern)[source]¶
- allc_motif_scan(allc_table, output_path, mc_contexts, c_motif_dir, count_binary=True, cpu=1)[source]¶
Scan a list of ALLC files using a C-Motif database. C-Motif Database, can be generated via ‘allcools generate-cmotif-database’ Save the integrated multi-dimensional array into netCDF4 format using xarray.
- Parameters
allc_table – {allc_table_doc}
mc_contexts –
c_motif_dir – A directory contains list of .msg files, each file records a dict, position is key, value is tuple of motif direction and id
output_path –
count_binary – Only use this for single cell allc, instead of sum mC or cov directly, will transfer mC and cov into [0, 1] when there is not ambiguity.
cpu – {cpu_basic_doc}