#Get the coords for all the proteins and store in a dictionary
gene_coords = defaultdict(tuple)
coord_folder = args.data_folders + "/coords/"
for coord_file in os.listdir(coord_folder):
for line in open(coord_folder + coord_file, 'r'):
line = line.rstrip()
contig_id, protein_id, start, stop = line.split("\t")
gene_coords[protein_id] = (contig_id, start, stop)
#Get the annotation information
annotation_folder = args.data_folders + "/annotation"
protein_annotation, function_definitions = \
AnnotationTools.parse_annotation_folder(genome_gene_info.keys(), annotation_folder)
#Print output table
output_file = open(args.output_file, 'w')
#Get the COG definitions
cog_one_letter, desc_cog_letter, desc_cog_number = COG.cog_definitions()
for genome in genome_gene_info:
for protein in genome_gene_info[genome]:
try:
product = protein_annotation[protein]["Product"]
except KeyError:
product = None
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"]
#Get the COG definitions
cog_one_letter, desc_cog_letter, desc_cog_number = COG.cog_definitions()
# Get the coords for all the proteins and store in a dictionary
gene_coords = defaultdict(tuple)
coord_folder = args.data_folders + "/coords/"
for coord_file in os.listdir(coord_folder):
for line in open(coord_folder + coord_file, "r"):
line = line.rstrip()
contig_id, protein_id, start, stop = line.split("\t")
gene_coords[protein_id] = (contig_id, start, stop)
# Get the annotation information
annotation_folder = args.data_folders + "/annotation"
protein_annotation, function_definitions = AnnotationTools.parse_annotation_folder(
genome_gene_info.keys(), annotation_folder
)
# Print output table
output_file = open(args.output_file, "w")
# Get the COG definitions
cog_one_letter, desc_cog_letter, desc_cog_number = COG.cog_definitions()
for genome in genome_gene_info:
for protein in genome_gene_info[genome]:
try:
product = protein_annotation[protein]["Product"]
except KeyError:
product = None