def main():
common.init_logger()
parameters = load_parameters()
samples = common.load_manifest(parameters['manifest_path'])
sample_depths = {}
combined_regions = process_samples(parameters, samples, sample_depths)
normalize_counts(sample_depths, combined_regions)
output_json = create_json(combined_regions)
write_json(parameters, output_json)
def main():
common.init_logger()
parameters = load_parameters()
combined_counts = common.load_combined_json(parameters['counts_path'])
samples = common.load_manifest(parameters['manifest_path'])
count_table = generate_count_table(combined_counts)
count_table = common.filter_counts(parameters['min_count'], count_table)
sample_status = common.extract_case_control_assignments(samples)
common.compare_counts(sample_status, count_table)
common.correct_pvalues(count_table)
output_results(count_table, parameters['output_path'])
logging.info('Done')
def main():
np.random.seed(42)
common.init_logger()
parser = initialize_parser()
subparsers = initialize_subparsers(parser)
locus_command_parser = add_locus_command(subparsers)
locus_command_parser.set_defaults(run_workflow=run_locus_workflow)
motif_command_parser = add_motif_command(subparsers)
motif_command_parser.set_defaults(run_workflow=run_motif_workflow)
args = parser.parse_args()
args.run_workflow(args)
def main():
common.init_logger()
parameters = load_parameters()
combined_counts = common.load_combined_json(parameters['counts_path'])
samples = common.load_manifest(parameters['manifest_path'])
target_regions = None
if parameters['target_regions']:
target_regions = load_target_regions(parameters['target_regions'])
count_table = generate_count_table(combined_counts)
count_table = common.filter_counts(count_table, parameters['min_count'],
target_regions)
logging.info('%i regions left after initial filtering', len(count_table))
sample_status = common.extract_case_control_assignments(samples)
common.compare_counts(parameters['test_params'], sample_status,
count_table)
common.correct_pvalues(count_table)
output_results(count_table, parameters['output_path'])
logging.info('Done')