def handle(self, *args, **options):
updated = []
update_failed = []
if not options["skip_gencode"]:
# Download latest version first, and then add any genes from old releases not included in the latest release
# Old gene ids are used in the gene constraint table and other datasets, as well as older sequencing data
update_gencode(31, reset=True)
update_gencode(29)
update_gencode(28)
update_gencode(27)
update_gencode(19)
updated.append('gencode')
if not options["skip_omim"]:
if not options["omim_key"]:
raise CommandError(
"Please provide --omim-key or use --skip-omim")
try:
update_records(OmimReferenceDataHandler(options["omim_key"]))
updated.append('omim')
except Exception as e:
logger.error("unable to update omim: {}".format(e))
update_failed.append('omim')
for source, data_handler in REFERENCE_DATA_SOURCES.items():
if not options["skip_{}".format(source)]:
try:
if data_handler:
update_records(data_handler())
elif source == "hpo":
update_hpo()
updated.append(source)
except Exception as e:
logger.error("unable to update {}: {}".format(source, e))
update_failed.append(source)
logger.info("Done")
if updated:
logger.info("Updated: {}".format(', '.join(updated)))
if update_failed:
logger.info("Failed to Update: {}".format(
', '.join(update_failed)))
def handle(self, *args, **options):
updated = []
update_failed = []
if not options["skip_gencode"]:
# Download latest version first, and then add any genes from old releases not included in the latest release
# Old gene ids are used in the gene constraint table and other datasets, as well as older sequencing data
update_gencode(29, reset=True)
update_gencode(28)
update_gencode(27)
update_gencode(19)
updated.append('gencode')
if not options["skip_omim"]:
if not options["omim_key"]:
raise CommandError("Please provide --omim-key or use --skip-omim")
try:
update_records(OmimReferenceDataHandler(options["omim_key"]))
updated.append('omim')
except Exception as e:
logger.error("unable to update omim: {}".format(e))
update_failed.append('omim')
for source, data_handler in REFERENCE_DATA_SOURCES.items():
if not options["skip_{}".format(source)]:
try:
if data_handler:
update_records(data_handler())
elif source == "hpo":
update_hpo()
updated.append(source)
except Exception as e:
logger.error("unable to update {}: {}".format(source, e))
update_failed.append(source)
logger.info("Done")
if updated:
logger.info("Updated: {}".format(', '.join(updated)))
if update_failed:
logger.info("Failed to Update: {}".format(', '.join(update_failed)))
def handle(self, *args, **options):
if not options["skip_gencode"]:
# download v19 and then v27 and then v28 because there are 1000+ gene and transcript ids in v19 that
# gencode retired by the time of v28, but that are used in the gene constraint table and other datasets
# and also ~100 genes and transcripts that were retired between v27 and v28
update_gencode(19, reset=True)
update_gencode(27)
update_gencode(28)
if not options["skip_dbnsfp_gene"]:
update_dbnsfp_gene()
if not options["skip_gene_constraint"]:
try:
update_gene_constraint()
except Exception as e:
logger.error("unable to update gene constraint: {}".format(e))
if not options["skip_omim"]:
if not options["omim_key"]:
raise CommandError(
"Please provide --omim-key or use --skip-omim")
try:
update_omim(omim_key=options["omim_key"])
except Exception as e:
logger.error("unable to update omim: {}".format(e))
if not options["skip_hpo"]:
try:
update_hpo()
except Exception as e:
logger.error(
"unable to update human phenotype ontology: {}".format(e))
if not options["skip_gtex"]:
try:
update_gtex()
except Exception as e:
logger.error("unable to update gtex: {}".format(e))