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"]
