help="File with the genome list. Format GenomeID, FullName, ShortName", required=True)
parser.add_argument("-a", "--annotation_folder", type=str,
help="Folder with the annotation files from JGI", required=True)
parser.add_argument("-c", "--cluster_file", type=str,
help="Cluster file", required=True)
parser.add_argument("-o", "--output_directory", type=str,
help="Output folder", required=True)
args = parser.parse_args()
#Create the output directory
if not os.path.exists(args.output_directory):
os.makedirs(args.output_directory)
#####Read the genome list
genome_id_dictionary, genome_count = ClusterTools.read_genome_list(args.genome_list_index)
###Read the annotation information
protein_annotation, function_definitions = AnnotationTools.parse_annotation_folder(genome_id_dictionary.keys(), args.annotation_folder)
##Read the cluster information
total_clusters = ClusterTools.get_cluster_information(args.cluster_file)
##Print log file
logfile = open(args.output_directory + "/logfile.txt", 'w')
##Total number of clusters
logfile.write("Total number of analyzed clusters: %d" % len(total_clusters) + "\n")
features_to_annotate = ["COG", "KO", "PFAM", "Product"]
