diff --git a/src/rmi_splitter/rmi_splitter.py b/src/rmi_splitter/rmi_splitter.py index 095931c968e54faec72a75a053d4daa89d28a1a8..cd5ab507a406b95c7842ac75047269a8bb4b87f2 100644 --- a/src/rmi_splitter/rmi_splitter.py +++ b/src/rmi_splitter/rmi_splitter.py @@ -305,7 +305,7 @@ def list_reads_number(config): if not adaptator == 'conditions': if int(config[adaptator]['coords']['reads']) > read_number: read_number = int(config[adaptator]['coords']['reads']) - return list(range(0, read_number + 1)) + return read_number + 1 def create_barcode_dictionaries(config, mismatch=None): @@ -962,23 +962,17 @@ def main(argv=None): main function """ - try: - parameters['mismatch'] - except Exception as e: - parse_ntuples_fastqs(fastqs=parameters['inputfiles'], - config=config, - results_path=parameters['outputfolder'], - verbose=parameters['verbose'], - ntuple_param=parameters['ntuple'], - gzed=parameters['gzed']) + if 'mismatch' not in parameters: + parameters['mismatch'] = None else: - parse_ntuples_fastqs(fastqs=parameters['inputfiles'], - config=config, - results_path=parameters['outputfolder'], - verbose=parameters['verbose'], - mismatch=int(parameters['mismatch']), - ntuple_param=parameters['ntuple'], - gzed=parameters['gzed']) + parameters['mismatch'] = int(parameters['mismatch']) + parse_ntuples_fastqs(fastqs=parameters['inputfiles'], + config=config, + results_path=parameters['outputfolder'], + verbose=parameters['verbose'], + mismatch=parameters['mismatch'], + ntuple_param=parameters['ntuple'], + gzed=parameters['gzed']) if __name__ == "__main__": diff --git a/src/rmi_splitter/tests/rmi_splitter_test.py b/src/rmi_splitter/tests/rmi_splitter_test.py index ac2d0be8653dff6eb4a91ac0c10158eb03e706b8..520e7a3246d4f79dfb48ca0248ee55cc9e299df8 100644 --- a/src/rmi_splitter/tests/rmi_splitter_test.py +++ b/src/rmi_splitter/tests/rmi_splitter_test.py @@ -611,7 +611,7 @@ class HandleFastqTest(unittest.TestCase): rmi_splitter.list_reads_number( config=data_test.CONFIG_TOY_PAIRED ), - [0, 1, 2] + 3 ) def test_assign_reads_single(self):