#!/opt/conda/conda-bld/zol_1760213924798/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/bin/python

"""
Program: ZOL
Author: Rauf Salamzade
Kalan Lab
UW Madison, Department of Medical Microbiology and Immunology
"""

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# Copyright (c) 2023-2025, Kalan-Lab
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import os
import sys
from zol import util

prog_set = set(['prepTG', 'fai', 'zol', 'cgc', 'cgcg'])

version = util.get_version()

if __name__ == '__main__':
	args = sys.argv[1:]
	if len(args) == 0 or '--help' == args[0] or '-h' == args[0] or '-v' == args[0] or '--version' == args[0] or not (args[0] in prog_set):
		print("""	
		Program: ZOL
		Version: %s""" % (version))
		print("""
		Author: Rauf Salamzade
		Affiliation: Kalan Lab, UW Madison, Department of Medical Microbiology and Immunology
	
		Wrapper for running main programs of the zol suite within Docker:
		
		- prepTG: prepare/setup a database directory of target genomes to search against using fai.
		- fai: perform targeted detection of query gene cluster(s) in genome database.
		- zol: create a tabular report profiling conservation, evo stats, and annotation for ortholog groups found 
		  across homologous/orthologous gene-cluster instance.
		- cgc: create collapsed gene cluster visual
		- cgcg: create collapsed gene cluster network visual
		
		Usage examples:
		
		./run_ZOL.sh prepTG -i Genomes/ -o prepTG_DB/ -c 10
		./run_ZOL.sh fai -pq query_proteins.faa -tg prepTG_DB/ -o fai_Results/ -c 10
		./run_ZOL.sh zol -i fai_Results/Homologous_GenBanks_Directory/ -o zol_Results/
		./run_ZOL.sh cgc -i zol_Results/ -o cgc_Results/
		./run_ZOL.sh cgcg -i zol_Results/ -o cgcg_Results/
		""")
	else:
		os.system(' '.join([x.replace('"', '\\"').replace("'", "\\'") for x in args]))
