def __init__(self, config=None, group="unknown", dataset="unknown"):
"""
Arguments:
---------
config : a AssocParserConfig object
"""
if config is None:
config = assocparser.AssocParserConfig()
self.config = config
self.report = assocparser.Report(group=group, dataset=dataset)
self.gpi = None
if self.config.gpi_authority_path is not None:
self.gpi = dict()
parser = entityparser.GpiParser()
with open(self.config.gpi_authority_path) as gpi_f:
entities = parser.parse(file=gpi_f)
for entity in entities:
self.gpi[entity["id"]] = {
"symbol": entity["label"],
"name": entity["full_name"],
"synonyms": entitywriter.stringify(entity["synonyms"]),
"type": entity["type"]
}
print("Loaded {} entities from {}".format(len(self.gpi.keys()), self.config.gpi_authority_path))
def load_from_file(BioEntities, path: str):
entities = dict() # type: Dict[Curie, Subject]
try:
gpi_parser = entityparser.GpiParser()
with open(path) as gpi:
for line in gpi:
_, ents = gpi_parser.parse_line(line)
for entity in ents:
# entity will be a well-formed curie
entity_id = Curie.from_str(entity["id"])
entities[entity_id] = Subject(
entity_id, entity["label"], entity["full_name"],
entity["synonyms"], entity["type"],
Curie.from_str(entity["taxon"]["id"]))
except Exception as e:
logger.error("Failed to read GPI file: {}".format(str(e)))
return BioEntities(entities)
def load_from_file(BioEntities, path: str):
entities = dict() # type: Dict[Curie, Subject]
print("loading from {}".format(path))
try:
gpi_parser = entityparser.GpiParser()
with open(path) as gpi:
for line in gpi:
ents = gpi_parser.line_as_entity_subject(line)
if ents is None:
continue
for entity in ents:
entity_id = entity.id
entities[entity_id] = entity
except Exception as e:
logger.error("Failed to read GPI file: {}".format(str(e)))
return BioEntities(entities)
def main():
"""
Wrapper for Assoc Parsing
"""
parser = argparse.ArgumentParser(
description='Wrapper for obographs assocmodel library'
"""
By default, ontologies and assocs are cached locally and synced from a remote sparql endpoint
""",
formatter_class=argparse.RawTextHelpFormatter)
parser.add_argument('-r',
'--resource',
type=str,
required=False,
help='Name of ontology')
parser.add_argument(
'-f',
'--file',
type=str,
required=False,
help='Name of input file for associations - currently GAF is assumed')
parser.add_argument('-F',
'--format',
type=str,
required=False,
help='Format of assoc file. One of GAF, GPAD or HPOA')
parser.add_argument('-o',
'--outfile',
type=str,
required=False,
help='Path to output file')
parser.add_argument('-m',
'--messagefile',
type=str,
required=False,
help='Path to messages (report) markdown file')
parser.add_argument('-t',
'--to',
type=str,
required=False,
help='Output to (tree, dot, ...)')
parser.add_argument(
"--filter-out",
nargs="+",
required=False,
default=[],
metavar="EVIDENCE",
help=
"List of any evidence codes to filter out of the GAF. E.G. --filter-out IEA IMP"
)
parser.add_argument("--filtered-file",
required=False,
default=None,
metavar="FILTERED_FILE",
help="File to write the filtered out evidence GAF to")
parser.add_argument(
'-T',
'--taxon',
nargs='*',
required=False,
help='valid taxon (NCBITaxon ID) - validate against this')
parser.add_argument('--subject_prefix',
nargs='*',
required=False,
help='E.g PomBase - validate against this')
parser.add_argument('--object_prefix',
nargs='*',
required=False,
help='E.g GO - validate against this')
parser.add_argument('-v',
'--verbosity',
default=0,
action='count',
help='Increase output verbosity')
subparsers = parser.add_subparsers(dest='subcommand',
help='sub-command help')
parser_n = subparsers.add_parser('validate', help='Validate associations')
parser_n.set_defaults(function=validate_assocs)
parser_n = subparsers.add_parser('filter', help='Filter associations')
parser_n.set_defaults(function=filter_assocs)
parser_n = subparsers.add_parser('convert', help='Convert associations')
parser_n.set_defaults(function=convert_assocs)
parser_n.add_argument('-t',
'--to',
type=str,
required=True,
help='Format to convert to')
parser_n = subparsers.add_parser('map2slim', help='Map to a subset/slim')
parser_n.set_defaults(function=map2slim)
parser_n.add_argument('-p',
'--properties',
nargs='*',
type=str,
required=False,
help='Properties')
parser_n.add_argument('-s',
'--subset',
type=str,
required=True,
help='subset (e.g. map2slim)')
args = parser.parse_args()
if args.verbosity >= 2:
logging.basicConfig(level=logging.DEBUG)
elif args.verbosity == 1:
logging.basicConfig(level=logging.INFO)
else:
logging.basicConfig(level=logging.WARNING)
logging.info("Welcome!")
handle = args.resource
# Ontology Factory
ofactory = OntologyFactory()
logging.info("Creating ont object from: {} {}".format(handle, ofactory))
ont = ofactory.create(handle)
logging.info("ont: {}".format(ont))
func = args.function
# Upper case all evidence codes
args.filter_out = [code.upper() for code in args.filter_out]
# set configuration
filtered_evidence_file = open(args.filtered_file,
"w") if args.filtered_file else None
config = assocparser.AssocParserConfig(
valid_taxa=args.taxon,
ontology=ont,
class_idspaces=args.object_prefix,
entity_idspaces=args.subject_prefix,
filter_out_evidence=args.filter_out,
filtered_evidence_file=filtered_evidence_file)
p = None
fmt = None
if args.format is None:
fmt = 'gaf'
else:
fmt = args.format.lower()
# TODO: use a factory
if fmt == 'gaf':
p = GafParser()
elif fmt == 'gpad':
p = GpadParser()
elif fmt == 'hpoa':
p = HpoaParser()
elif fmt == "gpi":
p = entityparser.GpiParser()
func = validate_entity
p.config = config
outfh = None
if args.outfile is not None:
two_mb = 2097152
outfh = open(args.outfile, "w", buffering=two_mb)
func(ont, args.file, outfh, p, args)
if filtered_evidence_file:
filtered_evidence_file.close()
if outfh is not None:
outfh.close()
if args.messagefile is not None:
mfh = open(args.messagefile, "w")
mfh.write(p.report.to_markdown())
mfh.close()
else:
print(p.report.to_markdown())
def main():
"""
Wrapper for Assoc Parsing
"""
parser = argparse.ArgumentParser(description='Wrapper for obographs assocmodel library'
"""
By default, ontologies and assocs are cached locally and synced from a remote sparql endpoint
""",
formatter_class=argparse.RawTextHelpFormatter)
parser.add_argument('-r', '--resource', type=str, required=False,
help='Name of ontology')
parser.add_argument('-f', '--file', type=str, required=False,
help='Name of input file for associations - currently GAF is assumed')
parser.add_argument('-F', '--format', type=str, required=False,
help='Format of assoc file. One of GAF, GPAD or HPOA')
parser.add_argument('-o', '--outfile', type=str, required=False,
help='Path to output file')
parser.add_argument("--report-md", type=str, required=False, dest="report_md",
help="Path to report markdown file")
parser.add_argument("--report-json", type=str, required=False, dest="report_json",
help="Path to report JSON file")
parser.add_argument('-t', '--to', type=str, required=False,
help='Output to (tree, dot, ...)')
parser.add_argument("--filter-out", nargs="+", required=False, default=[], metavar="EVIDENCE",
help="List of any evidence codes to filter out of the GAF. E.G. --filter-out IEA IMP")
parser.add_argument("--filtered-file", required=False, default=None, metavar="FILTERED_FILE",
help="File to write the filtered out evidence GAF to")
parser.add_argument('-T', '--taxon', nargs='*', required=False,
help='valid taxon (NCBITaxon ID) - validate against this')
parser.add_argument('--subject_prefix', nargs='*', required=False,
help='E.g PomBase - validate against this')
parser.add_argument('--object_prefix', nargs='*', required=False,
help='E.g GO - validate against this')
parser.add_argument("-I", "--gaferencer-file", type=argparse.FileType('r'), required=False,
help="Output from Gaferencer run on a set of GAF annotations")
parser.add_argument('-v', '--verbosity', default=0, action='count',
help='Increase output verbosity')
parser.add_argument("--allow_paint", required=False, action="store_const", const=True,
help="Allow IBAs in parser")
parser.add_argument("-g", "--gpi", type=str, required=False, default=None,
help="GPI file")
parser.add_argument("-l", "--rule", action="append", required=None, default=[], dest="rule_set",
help="Set of rules to be run. Default is no rules to be run, with the exception \
of gorule-0000027 and gorule-0000020. See command line documentation in the \
ontobio project or readthedocs for more information")
subparsers = parser.add_subparsers(dest='subcommand', help='sub-command help')
parser_n = subparsers.add_parser('validate', help='Validate associations')
parser_n.set_defaults(function=validate_assocs)
parser_n = subparsers.add_parser('filter', help='Filter associations')
parser_n.set_defaults(function=filter_assocs)
parser_n = subparsers.add_parser('convert', help='Convert associations')
parser_n.set_defaults(function=convert_assocs)
parser_n.add_argument('-t', '--to', type=str, required=True, choices=["GAF", "GPAD", "gaf", "gpad"],
help='Format to convert to')
parser_n.add_argument("-n", "--format-version", dest="version", type=str, required=False, default=None,
help="Version for the file format. GAF default is 2.1, GPAD default is 1.2")
parser_n = subparsers.add_parser('map2slim', help='Map to a subset/slim')
parser_n.set_defaults(function=map2slim)
parser_n.add_argument('-p', '--properties', nargs='*', type=str, default=['subClassOf', 'BFO:0000050'],
help='Properties')
parser_n.add_argument('-s', '--subset', type=str, required=True,
help='subset (e.g. map2slim)')
args = parser.parse_args()
if args.verbosity >= 2:
logging.basicConfig(level=logging.DEBUG)
elif args.verbosity == 1:
logging.basicConfig(level=logging.INFO)
else:
logging.basicConfig(level=logging.WARNING)
logging.info("Welcome!")
# Ontology Factory
ont = None
if args.resource is not None:
ofactory = OntologyFactory()
logging.info("Creating ont object from: {} {}".format(args.resource, ofactory))
ont = ofactory.create(args.resource)
logging.info("ont: {}".format(ont))
func = args.function
# Upper case all evidence codes
args.filter_out = [code.upper() for code in args.filter_out]
gaferences = None
if args.gaferencer_file:
gaferences = gaference.build_annotation_inferences(json.load(args.gaferencer_file))
rule_set = args.rule_set
if rule_set == ["all"]:
rule_set = assocparser.RuleSet.ALL
# set configuration
filtered_evidence_file = open(args.filtered_file, "w") if args.filtered_file else None
config = assocparser.AssocParserConfig(
valid_taxa=args.taxon,
ontology=ont,
class_idspaces=args.object_prefix,
entity_idspaces=args.subject_prefix,
filter_out_evidence=args.filter_out,
filtered_evidence_file=filtered_evidence_file,
annotation_inferences=gaferences,
paint=args.allow_paint,
gpi_authority_path=args.gpi,
rule_set=rule_set
)
p = None
fmt = None
if args.format is None:
fmt = 'gaf'
else:
fmt = args.format.lower()
# TODO: use a factory
if fmt == 'gaf':
p = GafParser(config=config, dataset=args.file)
elif fmt == 'gpad':
p = GpadParser(config=config)
elif fmt == 'hpoa':
p = HpoaParser(config=config)
elif fmt == "gpi":
p = entityparser.GpiParser()
func = validate_entity
outfh = None
if args.outfile is not None:
two_mb = 2097152
outfh = open(args.outfile, "w", buffering=two_mb)
func(ont, args.file, outfh, p, args)
if filtered_evidence_file:
filtered_evidence_file.close()
if outfh is not None:
outfh.close()
if args.report_md is not None:
report_md = open(args.report_md, "w")
report_md.write(p.report.to_markdown())
report_md.close()
if args.report_json is not None:
report_json = open(args.report_json, "w")
report_json.write(json.dumps(p.report.to_report_json(), indent=4))
report_json.close()
if not (args.report_md or args.report_json):
print(p.report.to_markdown())
