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 = GenomeData.read_genome_list( args.genome_list_index) ###Read the annotation information protein_annotation, function_definitions = \ AnnotationData.parse_annotation_folder(genome_id_dictionary.keys(), args.annotation_folder) ##Read the cluster information total_clusters = AnnotationData.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")
parser.add_argument("-o", "--output_directory", type=str, help="Output folder", required=True) 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
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 = GenomeData.read_genome_list(args.genome_list_index) ###Read the annotation information protein_annotation, function_definitions = \ AnnotationData.parse_annotation_folder(genome_id_dictionary.keys(), args.annotation_folder) ##Read the cluster information total_clusters = AnnotationData.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"]