def setup_logging(log_dir, debug):
logfile = os.path.join(log_dir, 'abstar.log')
debug = True if debug > 0 else False
print_debug = True if debug == 2 else False
log.setup_logging(logfile, debug=debug)
global logger
logger = log.get_logger('abstar')
def run_standalone(args):
logfile = args.log if args.log else os.path.join(args.output,
'abcompare.log')
log.setup_logging(logfile)
global logger
logger = log.get_logger('abcompare')
main(args)
def run_standalone(args):
logfile = args.log if args.log else os.path.join(args.output_dir, 'abfinder.log')
log.setup_logging(logfile)
global logger
logger = log.get_logger('abfinder')
main(args)
print_standards_info(standards)
collections = mongodb.get_collections(db, args.collection, prefix=args.collection_prefix)
print_collections_info(collections)
for collection in collections:
indexed = False
print_single_collection(collection)
if args.remove_padding:
print_remove_padding()
mongodb.remove_padding(db, collection)
seq_files = get_sequences(db, collection, args.temp_dir, args)
for standard in standards:
print_single_standard(standard)
scores = run_jobs(seq_files, standard, args)
if args.output_dir:
make_figure(standard.id, scores, collection, args)
if args.update:
if not indexed:
mongodb.index(db, collection, 'seq_id')
indexed = True
update_db(db, standard.id, scores, collection, args)
clean_up(seq_files)
if __name__ == '__main__':
parser = parse_args()
args = parser.parse_args()
logfile = args.log if args.log else os.path.join(args.output_dir, 'abfinder.log')
log.setup_logging(logfile)
logger = log.get_logger('abfinder')
main(args)
def run_standalone(args):
global logger
logger = log.get_logger('demultiplex')
main(args)
def main(args):
for f in list_files(args.input):
experiment = get_experiment(f, args)
wb = load_workbook(f)
ws = wb[wb.get_sheet_names()[0]]
plate_blocks = get_plate_blocks(ws, args)
plural = '' if len(plate_blocks) <= 2 else 's'
logger.info('\nFound {} plate{} in the input file'.format(
len(plate_blocks) - 1, plural))
logger.info('Experiment name: {}\n'.format(experiment))
plates = parse_plates(plate_blocks[1:], args)
write_output(plates, experiment, args)
logger.info('')
if __name__ == '__main__':
args = parse_args()
if args.log is None:
args.log = os.path.join(args.output, 'platemap.log')
log.setup_logging(args.log)
logger = log.get_logger('demultiplex')
main(args)
def run_standalone(args):
logfile = args.log if args.log else os.path.join(args.output, 'abcompare.log')
log.setup_logging(logfile)
global logger
logger = log.get_logger('abcompare')
main(args)
