find_enhancer_target_genes
==========================


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Find enhancers and their target genes that overlap with mutation blocks associated with a selected gene.

Optional Arguments:

- `-h, --help`: Show the help message and exit.

Required Arguments:

- `-inEnhancerF IN_ENHANCER_FILE_FOLDER, --in_enhancer_file_folder IN_ENHANCER_FILE_FOLDER`: File folder containing enhancer files. Assumes all files end with \*.bed. This folder should contain the enhancer files used for analysis.

- `-inDDSFile IN_DDS_FILE, --in_DDS_file IN_DDS_FILE`: File name of the DDS (Disease-Enhancer-Target gene) final exported ranked gene list. This file contains the ranked gene list generated by the DDS analysis.
- `-inGene IN_SELECTED_GENE, --in_selected_gene IN_SELECTED_GENE`: Gene name in the DDS export file to be searched for overlapping with enhancers. Specify the gene name for which you want to find enhancer-target gene associations.
- `-outFolder OUT_FOLDER, --out_folder OUT_FOLDER`: Output file folder name. Specify the folder where the output files will be saved.

Optional Arguments with Default Values:

- `-isAll, --is_all_blocks`: Whether to use all blocks or only enhancer-associated blocks for the enhancer-gene search. Default: enhancer-only blocks. If this option is used, only the blocks associated with enhancers will be considered for the enhancer-gene search.