bedfilegenerator

Usage

bip bedfilegenerator [-h] --gene-list GENE_LIST [GENE_LIST ...] --bed-file-name BED_FILE_NAME --output-folder OUTPUT_FOLDER --whole-gene-list WHOLE_GENE_LIST [WHOLE_GENE_LIST ...] [--parsed-gtf-path PARSED_GTF_PATH] [--whole-gene-locs-path WHOLE_GENE_LOCS_PATH] [--cds] [--ref-folder REF_FOLDER]

Options

Option	Alias	Required	Description
-h, --help		No	Show this help message and exit
--gene-list GENE_LIST [GENE_LIST ...]	-g	Yes	Gene names to include.
--bed-file-name BED_FILE_NAME	-b	Yes	Name of the output BED file.
--output-folder OUTPUT_FOLDER	-o	Yes	Folder to save the output BED file.
--whole-gene-list WHOLE_GENE_LIST [...]	-w	Yes	Whole gene names to include.
--parsed-gtf-path PARSED_GTF_PATH	-p	No	Path to Parsed GTF file.
--whole-gene-locs-path WHOLE_GENE_LOCS_PATH	-wglp	No	Path to whole gene locs file.
--cds	-c	No	If used, use CDS features; otherwise use exon features.
--ref-folder REF_FOLDER	-rf	No	Path to the folder for reference