parser.add_argument('graph',metavar='graph.gfa',type=argparse.FileType('r'),help='pangenome graph file in GFA format containing the genome that the annotation refers to and the target genome.s')
parser.add_argument('gff',metavar='annotation.gff',type=argparse.FileType('r'),help='annotation file in GFF format containing the annotations to be transfered')
# graph format
parser.add_argument('-P','--paths',help="the genomes are embedded in the GFA file as paths",action='store_true')
parser.add_argument('-W','--walks',help="the genomes are embedded in the GFA file as walks",action='store_true')
# optionnal input file
parser.add_argument('-coord','--segment_coordinates_path',metavar="path/to/files",type=dir_path,default=".",help="path to the files given by the preprocessing of the graph; if not given the program will do the preprocessing; recommended if the program will run several times")
