map_block2chromSegment

Map mutation blocks to predicted chromatin segment regions.

Optional Arguments:

  • -h, –help: Show this help message and exit

Required Arguments:

  • -in_BSpos IN_SORTEDBLOCK_FILE, –in_sortedBlock_file IN_SORTEDBLOCK_FILE: Bpb3 exported mutation block summary position file in BED format and sorted by chromosome and position

  • -out_folder OUT_FILE_FOLDER, –out_file_folder OUT_FILE_FOLDER: Export file folder

  • -in_chrSeg IN_CHROMSEGMENT_FOLDER, –in_chromSegment_folder IN_CHROMSEGMENT_FOLDER: File folder path of chromatin segment files

Optional Arguments with Default Values:

  • -in_prefStr, –in_prefix_string4chromSegment_file: Prefix string for chromatin segment file names. Default=combined*merged.bed.gz

  • -is_change, –change_name: Whether to change the 4th column of name by reducing its length. Columns 1, 2, 3 are chr, start_pos, and end_pos, but column 4 is the id information. Default=False, does not change id information. If this option is used, the program will split the name by “:” and only take the first two elements for exporting a new id name.

  • -in_cutoff IN_DMR_MINIMUM_CUTOFF, –in_dmr_minimum_cutoff IN_DMR_MINIMUM_CUTOFF: Minimum cutoff values for selecting blocks or mrs to export. Default=None, which means no minimum cutoff for exporting data or there is no 9th column (p-value or other values can be used to filter by minimum cutoff) in the dataframe.

  • -isMorB IS_MR_OR_BLOCKS, –is_MR_or_Blocks IS_MR_OR_BLOCKS: Is input bed position files are MR (methylation regions chr#:mr#) or mutation blocks block_#_chr_start_end. 0 for MR, 1 for Blocks. Default=0 is MR.