map_block2genome
=================


.. contents::
    :local:

Map mutation blocks to genomic regions.

Optional Arguments:

- `-h, --help`: Show this help message and exit

Required Arguments:

- `-inSBfile 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
- `-inGRfile IN_GENOMEREGION_FILE, --in_genomeRegion_file IN_GENOMEREGION_FILE`: A list of genome region files which contains TSS, TES, gene, position, et al
- `-inRGfile IN_REFERENCEGENOME_FILE, --in_referenceGenome_file IN_REFERENCEGENOME_FILE`: Sorted reference genome refFlat file in BED format

Optional Arguments with Default Values:

- `-outFold, --out_file_folder`: Output file folder name
- `-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.