def produce_ttl(dataset, target_dir, gaf_path, ontology_graph):
gafparser = GafParser()
gafparser.config = assocparser.AssocParserConfig(ontology=ontology_graph)
with open(gaf_path) as sg:
lines = sum(1 for line in sg)
ttl_path = os.path.join(
os.path.split(gaf_path)[0], "{}_cam.ttl".format(dataset))
click.echo("Producing ttl: {}".format(ttl_path))
rdf_writer = assoc_rdfgen.TurtleRdfWriter()
transformer = assoc_rdfgen.CamRdfTransform(writer=rdf_writer)
parser_config = assocparser.AssocParserConfig(ontology=ontology_graph)
with open(gaf_path) as gf:
with click.progressbar(
iterable=gafparser.association_generator(file=gf),
length=lines) as associations:
for association in associations:
if "header" not in association or not association["header"]:
transformer.provenance()
transformer.translate(association)
with open(ttl_path, "wb") as ttl:
click.echo("Writing ttl to disk")
rdf_writer.serialize(destination=ttl)
return ttl_path
def produce_gpi(dataset, target_dir, gaf_path, ontology_graph):
gafparser = GafParser()
gafparser.config = assocparser.AssocParserConfig(ontology=ontology_graph)
with open(gaf_path) as sg:
lines = sum(1 for line in sg)
gpi_path = os.path.join(
os.path.split(gaf_path)[0], "{}.gpi".format(dataset))
with open(gaf_path) as gf, open(gpi_path, "w") as gpi:
click.echo("Using {} as the gaf to build gpi with".format(gaf_path))
bridge = gafgpibridge.GafGpiBridge()
gpiwriter = entitywriter.GpiWriter(file=gpi)
gpi_cache = set()
with click.progressbar(
iterable=gafparser.association_generator(file=gf),
length=lines) as associations:
for association in associations:
entity = bridge.convert_association(association)
if entity not in gpi_cache and entity is not None:
# If the entity is not in the cache, add it and write it out
gpi_cache.add(entity)
gpiwriter.write_entity(entity)
return gpi_path
def make_products(dataset, target_dir, gaf_path, products, ontology_graph):
gafparser = GafParser()
gafparser.config = assocparser.AssocParserConfig(
ontology=ontology_graph,
paint=True
)
with open(gaf_path) as sg:
lines = sum(1 for line in sg)
product_files = {
"gpad": open(os.path.join(os.path.split(gaf_path)[0], "{}.gpad".format(dataset)), "w"),
"ttl": open(os.path.join(os.path.split(gaf_path)[0], "{}_cam.ttl".format(dataset)), "wb")
}
if not products["gpad"] and not products["ttl"]:
# Bail if we have no products
return []
# def write_gpi_entity(association, bridge, gpiwriter):
with open(gaf_path) as gf:
# gpi info:
click.echo("Using {} as the gaf to build data products with".format(gaf_path))
if products["ttl"]:
click.echo("Setting up {}".format(product_files["ttl"].name))
rdf_writer = assoc_rdfgen.TurtleRdfWriter(label=os.path.split(product_files["ttl"].name)[1] )
transformer = assoc_rdfgen.CamRdfTransform(writer=rdf_writer)
parser_config = assocparser.AssocParserConfig(ontology=ontology_graph)
if products["gpad"]:
click.echo("Setting up {}".format(product_files["gpad"].name))
gpadwriter = GpadWriter(file=product_files["gpad"])
click.echo("Making products...")
with click.progressbar(iterable=gafparser.association_generator(file=gf), length=lines) as associations:
for association in associations:
if products["ttl"]:
if "header" not in association or not association["header"]:
transformer.provenance()
transformer.translate(association)
if products["gpad"]:
gpadwriter.write_assoc(association)
# post ttl steps
if products["ttl"]:
click.echo("Writing ttl to disk")
rdf_writer.serialize(destination=product_files["ttl"])
# After we run through associations
for f in product_files.values():
f.close()
return [product_files[prod].name for prod in sorted(product_files.keys()) if products[prod]]
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())
