def get_arguments(program):
""" Get arguments for specified program """
if program == 'species':
args = species_arguments()
elif program == 'genes':
args = gene_arguments()
elif program == 'snps':
args = snp_arguments()
else:
sys.exit("\nError: Unrecognized program: '%s'\n" % program)
utility.add_executables(args)
return args
"Maximum number of genomes to process per species (use all).\nUseful for quick tests"
)
args = vars(parser.parse_args())
return args
def check_args(args):
if not os.path.isdir(args['outdir']):
os.mkdir(args['outdir'])
if not os.path.isdir(args['indir']):
sys.exit(
"\nError: could not locate directory specified by --genomes: %s\n"
% args['indir'])
if not os.path.isfile(args['mapfile']):
sys.exit(
"\nError: could not locate file specified by --mapping: %s\n" %
args['mapfile'])
for program in ['hmmsearch', 'vsearch']:
if not utility.which(program):
error = "\nError: program '%s' not found in your PATH" % program
error += "\nMake sure that you've installed the program and added it's location to your PATH\n"
sys.exit(error)
if __name__ == "__main__":
args = fetch_arguments()
utility.add_executables(args)
check_args(args)
utility.print_copyright()
build_db.run_pipeline(args)