def setUpClass(cls):
argv = [
'clinvar_to_evidence_strings.py', '--clinSig', cls.clin_sig,
'--ignore', cls.ignore, '--out', cls.out, '-e', cls.efo_map_file,
'-g', cls.snp_2_gene_file, '--ot-schema', cls.ot_schema_path
]
cls.argparser = utilities.ArgParser(argv)
def main():
parser = utilities.ArgParser(sys.argv)
utilities.check_dir_exists_create(parser.out)
clinvar_to_evidence_strings.launch_pipeline(
parser.out,
efo_mapping_file=parser.efo_mapping_file,
snp_2_gene_file=parser.snp_2_gene_file,
json_file=parser.json_file,
ot_schema=parser.ot_schema)
def main():
parser = utilities.ArgParser(sys.argv)
utilities.check_for_local_schema()
utilities.check_dir_exists_create(parser.out)
clinvar_to_evidence_strings.launch_pipeline(parser.out,
allowed_clinical_significance=parser.clinical_significance,
efo_mapping_file=parser.efo_mapping_file,
snp_2_gene_file=parser.snp_2_gene_file,
json_file=parser.json_file)
print('>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finished <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<')