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))
"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))
