def main(): """Print a GO term's lower-level hierarchy.""" import argparse prs = argparse.ArgumentParser(__doc__, formatter_class=argparse.ArgumentDefaultsHelpFormatter) prs.add_argument('go_ids', type=str, nargs='*', help='GO Term, e.g. GO:0070458') prs.add_argument('--o', default=None, type=str, help="Specifies the name of the output file") prs.add_argument('--no_indent', default=False, help="Do not indent GO terms", action='store_true') prs.add_argument('--obo', default="go-basic.obo", type=str, help="Location and name of the obo file") prs.add_argument('--dash_len', default=1, type=int, help="Printed width of the dashes column") prs.add_argument('--max_depth', default=None, type=int, help="max depth for printing relative to GO Term") prs.add_argument('--num_child', default=None, action='store_true', help="Print count of total number of children for each GO") prs.add_argument('--short', default=False, action='store_true', help="If a branch has already been printed, do not re-print." "Print '===' instead of dashes to note the point of compression") args = prs.parse_args() obo_dag = GODag(obo_file=args.obo) file_out = sys.stdout if args.o is None else open(args.o, 'w') lenprt = args.dash_len if not args.no_indent else None if args.go_ids: for go_id in args.go_ids: obo_dag.write_hier( go_id, file_out, len_dash=lenprt, max_depth=args.max_depth, num_child=args.num_child, short_prt=args.short) else: obo_dag.write_hier_all( file_out, len_dash=lenprt, max_depth=args.max_depth, num_child=args.num_child, short_prt=args.short) if args.o is not None: file_out.close() sys.stdout.write(" WROTE: {}\n".format(args.o))
default=False, action='store_true', help="If a branch has already been printed, do not re-print." "Print '===' instead of dashes to note the point of compression") args = p.parse_args() obo_dag = GODag(obo_file=args.obo) file_out = sys.stdout if args.o is None else open(args.o, 'w') lenprt = args.dash_len if not args.no_indent else None if args.go_ids: for go_id in args.go_ids: obo_dag.write_hier(go_id, file_out, len_dash=lenprt, max_depth=args.max_depth, num_child=args.num_child, short_prt=args.short) else: obo_dag.write_hier_all(file_out, len_dash=lenprt, max_depth=args.max_depth, num_child=args.num_child, short_prt=args.short) if args.o is not None: file_out.close() sys.stdout.write(" WROTE: {}\n".format(args.o))
def main(): """Print a GO term's lower-level hierarchy.""" import argparse prs = argparse.ArgumentParser( __doc__, formatter_class=argparse.ArgumentDefaultsHelpFormatter) prs.add_argument('go_ids', type=str, nargs='*', help='GO Term, e.g. GO:0070458') prs.add_argument('--o', default=None, type=str, help="Specifies the name of the output file") prs.add_argument('--no_indent', default=False, help="Do not indent GO terms", action='store_true') prs.add_argument('--obo', default="go-basic.obo", type=str, help="Location and name of the obo file") prs.add_argument('--dash_len', default=1, type=int, help="Printed width of the dashes column") prs.add_argument('--max_depth', default=None, type=int, help="max depth for printing relative to GO Term") prs.add_argument( '--num_child', default=None, action='store_true', help="Print count of total number of children for each GO") prs.add_argument( '--short', default=False, action='store_true', help="If a branch has already been printed, do not re-print." "Print '===' instead of dashes to note the point of compression") args = prs.parse_args() obo_dag = GODag(obo_file=args.obo) file_out = sys.stdout if args.o is None else open(args.o, 'w') lenprt = args.dash_len if not args.no_indent else None if args.go_ids: for go_id in args.go_ids: obo_dag.write_hier(go_id, file_out, len_dash=lenprt, max_depth=args.max_depth, num_child=args.num_child, short_prt=args.short) else: obo_dag.write_hier_all(file_out, len_dash=lenprt, max_depth=args.max_depth, num_child=args.num_child, short_prt=args.short) if args.o is not None: file_out.close() sys.stdout.write(" WROTE: {}\n".format(args.o))
help="If a branch has already been printed, do not re-print." "Print '===' instead of dashes to note the point of compression") args = p.parse_args() obo_dag = GODag(obo_file=args.obo) file_out = sys.stdout if args.o is None else open(args.o, 'w') lenprt = args.dash_len if not args.no_indent else None if args.go_ids: for go_id in args.go_ids: obo_dag.write_hier( go_id, file_out, len_dash=lenprt, max_depth=args.max_depth, num_child=args.num_child, short_prt=args.short) else: obo_dag.write_hier_all( file_out, len_dash=lenprt, max_depth=args.max_depth, num_child=args.num_child, short_prt=args.short) if args.o is not None: file_out.close() sys.stdout.write(" WROTE: {}\n".format(args.o))