args = parser.parse_args()
#Create output directory
if not os.path.exists(args.output_directory):
os.makedirs(args.output_directory)
os.makedirs(args.output_directory + "/nucleotide")
os.makedirs(args.output_directory + "/protein")
os.makedirs(args.output_directory + "/genome")
os.makedirs(args.output_directory + "/annotation")
os.makedirs(args.output_directory + "/coords")
#Read the genome list and create a dictionary with the information, and the total genome count
genome_dictionary, total_genome_count = GenomeData.read_genome_list(args.genome_list)
#Read the source option, and process the genome data
processed_genomes = 0
if args.genome_source == "jgi":
processed_genomes = GenomeData.parse_jgi_dump(genome_dictionary, args.input_folder, args.output_directory)
if args.genome_source == "img_single":
processed_genomes = GenomeData.parse_single_img(genome_dictionary, args.input_folder, args.output_directory)
print "Done processing %d genomes" % total_genome_count
print "A total of %d genomes were found in the input folder" % processed_genomes
