run_qc.py

#!/usr/bin/env python

import sys
import argparse

def get_program():
	if len(sys.argv) == 1 or sys.argv[1] in ['-h', '--help']:
		print('MAGpurify: Identify and remove incorrectly binned contigs from metagenome-assembled genomes')
		print('')
		print('Usage: run_qc.py <command> [options]')
		print('')
		print('Commands:')
		print('    phylo-markers: find taxonomic discordant contigs using db of phylogenetic marker genes')
		print('    clade-markers: find taxonomic discordant contigs using db of clade-specific marker genes')
		print('      conspecific: find contigs that fail to align to closely related genomes')
		print('       tetra-freq: find contigs with outlier tetranucleotide frequency')
		print('       gc-content: find contigs with outlier gc content')
		print('     known-contam: find contigs that match a database of known contaminants')
		print('        clean-bin: remove identified contigs from bin')
		print('')
		print('Note: use run_qc.py <command> -h to view usage for a specific command')
		quit()
	elif sys.argv[1] not in ['phylo-markers', 'clade-markers', 'conspecific',
	                         'tetra-freq', 'gc-content', 'known-contam', 'clean-bin']:
		sys.exit("\nError: Unrecognized command: '%s'\n" % sys.argv[1])
		quit()
	else:
		return sys.argv[1]

if __name__ == "__main__":
	
	program = get_program()
	
	if program == 'phylo-markers':
		from magpurify import uscmg
		uscmg.main()

	if program == 'clade-markers':
		from magpurify import csmg
		csmg.main()

	if program == 'conspecific':
		from magpurify import conspecific
		conspecific.main()

	if program == 'tetra-freq':
		from magpurify import tetra
		tetra.main()

	if program == 'gc-content':
		from magpurify import gc
		gc.main()

	if program == 'known-contam':
		from magpurify import contam
		contam.main()

	if program == 'clean-bin':
		from magpurify import clean
		clean.main()