p.add_option(
"--term",
help="Write the parents and children of this query term",
)
opts, args = p.parse_args()
if len(args) != 1:
sys.exit(p.print_help())
(obo_file, ) = args
def description(rec):
level = "level-{:>02}".format(rec.level)
description = "{} [{}]".format(rec.name, rec.namespace)
if rec.is_obsolete:
description += " obsolete"
alt_ids = ",".join(rec.alt_ids)
return "\t".join((rec.item_id, level, description, alt_ids))
g = GODag(obo_file, prt=None)
header = "\t".join(("#id", "level", "name", "alt_ids"))
print(header)
for rec in sorted(set(g.values()), key=lambda x: x.item_id):
print(description(rec))
# run a test case
if opts.term:
rec = g.query_term(opts.term, verbose=True)
g.draw_lineage([rec], verbose=True)
" from the obo file specified in args",
action="store_true")
p.add_option("--term",
dest="term",
help="write the parents and children"
"of the query term",
action="store",
type="string",
default=None)
p.add_option("--gml",
action="store_true",
help="Write GML output (for Cytoscape) [default: %default]")
opts, args = p.parse_args()
if not len(args):
obo_file = "gene_ontology.1_2.obo"
else:
obo_file = args[0]
assert os.path.exists(obo_file), "file %s not found!" % obo_file
g = GODag(obo_file)
if opts.desc:
g.write_dag()
# run a test case
if opts.term is not None:
rec = g.query_term(opts.term, verbose=True)
g.draw_lineage([rec], gml=opts.gml)
dest='draw_parents',
help="Do not draw parents of the query term")
p.add_option("--disable-draw-children",
action="store_false",
dest='draw_children',
help="Do not draw children of the query term")
p.set_defaults(draw_parents=True)
p.set_defaults(draw_children=True)
opts, args = p.parse_args()
if not len(args):
obo_file = "go-basic.obo"
else:
obo_file = args[0]
assert os.path.exists(obo_file), "file %s not found!" % obo_file
g = GODag(obo_file)
if opts.desc:
g.write_dag()
# run a test case
if opts.term is not None:
rec = g.query_term(opts.term, verbose=True)
g.draw_lineage([rec], engine=opts.engine,
gml=opts.gml,
draw_parents=opts.draw_parents,
draw_children=opts.draw_children)
if __name__ == '__main__':
import optparse
p = optparse.OptionParser("%prog [obo_file]")
p.add_option("--description", dest="desc",
help="write term descriptions to stdout"
" from the obo file specified in args", action="store_true")
p.add_option("--term", dest="term", help="write the parents and children"
"of the query term", action="store", type="string",
default=None)
p.add_option("--gml", action="store_true",
help="Write GML output (for Cytoscape) [default: %default]")
opts, args = p.parse_args()
if not len(args):
obo_file = "gene_ontology.1_2.obo"
else:
obo_file = args[0]
assert os.path.exists(obo_file), "file %s not found!" % obo_file
g = GODag(obo_file)
if opts.desc:
g.write_dag()
# run a test case
if opts.term is not None:
rec = g.query_term(opts.term, verbose=True)
g.draw_lineage([rec], gml=opts.gml)
)
p.set_defaults(draw_parents=True)
p.set_defaults(draw_children=True)
opts, args = p.parse_args()
if not args:
obo_file = "go-basic.obo"
else:
obo_file = args[0]
assert os.path.exists(obo_file), "file %s not found!" % obo_file
g = GODag(obo_file)
if opts.desc:
g.write_dag()
# run a test case
if opts.term is not None:
rec = g.query_term(opts.term, verbose=True)
g.draw_lineage(
[rec],
dpi=opts.dpi,
engine=opts.engine,
gml=opts.gml,
output=opts.output,
draw_parents=opts.draw_parents,
draw_children=opts.draw_children,
)
import optparse
p = optparse.OptionParser("%prog [obo_file]")
p.add_option("--description", dest="desc",
help="write term descriptions to stdout" \
" from the obo file specified in args", action="store_true")
p.add_option("--term", dest="term", help="write the parents and children" \
"of the query term", action="store", type="string", default=None)
(options, args) = p.parse_args()
if not len(args):
obo_file = None
else:
obo_file = args[0]
assert os.path.exists(obo_file), "file %s not found!" % obo_file
if obo_file is None:
g = GODag()
else:
g = GODag(obo_file)
if options.desc:
g.write_dag()
# run a test case
if options.term is not None:
rec = g.query_term(options.term, verbose=True)
g.draw_lineage(rec, dpi=50, verbose=True)
p.add_option(
"--term",
help="Write the parents and children of this query term",
)
opts, args = p.parse_args()
if len(args) != 1:
sys.exit(p.print_help())
(obo_file, ) = args
def description(record):
level = "level-{:>02}".format(record.level)
desc = "{} [{}]".format(record.name, record.namespace)
if record.is_obsolete:
desc += " obsolete"
alt_ids = ",".join(record.alt_ids)
return "\t".join((record.item_id, level, desc, alt_ids))
g = GODag(obo_file, prt=None)
header = "\t".join(("#id", "level", "name", "alt_ids"))
print(header)
for rec in sorted(set(g.values()), key=lambda x: x.item_id):
print(description(rec))
# run a test case
if opts.term:
rec = g.query_term(opts.term, verbose=True)
g.draw_lineage([rec])
import optparse
p = optparse.OptionParser("%prog [obo_file]")
p.add_option("--description", dest="desc",
help="write term descriptions to stdout" \
" from the obo file specified in args", action="store_true")
p.add_option("--term", dest="term", help="write the parents and children" \
"of the query term", action="store", type="string", default=None)
(options, args) = p.parse_args()
if not len(args):
obo_file = None
else:
obo_file = args[0]
assert os.path.exists(obo_file), "file %s not found!" % obo_file
if obo_file is None:
g = GODag()
else:
g = GODag(obo_file)
if options.desc:
g.write_dag()
# run a test case
if options.term is not None:
rec = g.query_term(options.term, verbose=True)
g.draw_lineage([rec], verbose=True)