def main():
arg_parser = argparse.ArgumentParser(
description=
'Compare the sample name in the VCF file and the one specified in the metadata.'
)
arg_parser.add_argument('--metadata-file',
required=True,
dest='metadata_file',
help='EVA Submission Metadata Excel sheet')
arg_parser.add_argument(
'--vcf-dir',
required=True,
dest='vcf_dir',
help='Path to the directory in which submitted files can be found')
arg_parser.add_argument(
'--debug',
action='store_true',
default=False,
help='Set the script to output logging information at debug level',
)
args = arg_parser.parse_args()
log_cfg.add_stdout_handler()
if args.debug:
log_cfg.set_log_level(logging.DEBUG)
# Load the config_file from default location
load_config()
compare_spreadsheet_and_vcf(args.metadata_file, args.vcf_dir)
def _validate_sample_names(self):
overall_differences, results_per_analysis_alias = compare_spreadsheet_and_vcf(
eva_files_sheet=self.eload_cfg['submission']
['metadata_spreadsheet'],
vcf_dir=self._get_dir('vcf'))
for analysis_alias in results_per_analysis_alias:
has_difference, diff_submitted_file_submission, diff_submission_submitted_file = results_per_analysis_alias[
analysis_alias]
self.eload_cfg.set('validation',
'sample_check',
'analysis',
str(analysis_alias),
value={
'difference_exists':
has_difference,
'in_VCF_not_in_metadata':
diff_submitted_file_submission,
'in_metadata_not_in_VCF':
diff_submission_submitted_file
})
self.eload_cfg.set('validation',
'sample_check',
'pass',
value=not overall_differences)