def read_ontologies(filenames):
global options
ontology_by_name = {}
for fn in filenames:
# The way to get ontology names from .obo is a bit flaky, so use
# the given file basename to identify the ontologies.
bn = os.path.basename(fn)
bn = bn.replace(".obo","")
assert bn not in ontology_by_name, "Error: ontology '%s' appears multiple times!"
try:
with open(fn) as f:
try:
all_terms, term_by_id = parse_obo(f)
ontology_by_name[bn] = (all_terms, term_by_id)
except Exception, e:
print >> sys.stderr, "ERROR: failed to parse %s: %s" % (fn, e)
print >> sys.stderr, """
########################################
#
# Warning: could not parse ontology
# %s.
# Matches will not be performed against
# this ontology.
#
########################################""" % bn
except IOError, e:
print >> sys.stderr, "Error: failed to read %s: %s" % (fn, e)
return None
def read_bridge(filename):
# the "bridge" format is just a subset of the full OBO format;
# read in normally
try:
with open(filename) as f:
all_terms, term_by_id = parse_obo(f, include_nameless=True)
except Exception, e:
print >> sys.stderr, "Warning: failed to read \"bridge\" %s: %s" % (filename, e)
print >> sys.stderr, " Mappings will not be applied."
return {}
