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"]
#Get the COG definitions
cog_one_letter, desc_cog_letter, desc_cog_number = COG.cog_definitions()
#Create the output files
for feature in features_to_annotate:
