diff --git a/README.md b/README.md index 9946f59..4c1ca22 100644 --- a/README.md +++ b/README.md @@ -137,48 +137,46 @@ usage: deepbinner classify [-s START_MODEL] [-e END_MODEL] [--scan_size SCAN_SIZ [--score_diff SCORE_DIFF] [--require_both] [--batch_size BATCH_SIZE] [--intra_op_parallelism_threads INTRA_OP_PARALLELISM_THREADS] [--inter_op_parallelism_threads INTER_OP_PARALLELISM_THREADS] - [--device_count DEVICE_COUNT] [--omp_num_threads OMP_NUM_THREADS] - [--verbose] [-h] + [--device_count DEVICE_COUNT] [--omp_num_threads OMP_NUM_THREADS] [--verbose] + [-h] input Classify fast5 reads Positional: - input One of the following: a single fast5 file, a directory of fast5 - files (will be searched recursively) or a tab-delimited file of - training data + input One of the following: a single fast5 file, a directory of fast5 files + (will be searched recursively) or a tab-delimited file of training + data Models (at least one is required): -s START_MODEL, --start_model START_MODEL - Model trained on the starts of reads + Model trained on the starts of reads -e END_MODEL, --end_model END_MODEL - Model trained on the ends of reads + Model trained on the ends of reads Barcoding: - --scan_size SCAN_SIZE This much of a read's start/end signal will examined for barcode - signals (default: 6144) - --score_diff SCORE_DIFF For a read to be classified, there must be this much difference - between the best and second-best barcode scores (default: 0.5) - --require_both When classifying reads using two models (read start and read end) - require both barcode calls to match to make the final call - (default: False) + --scan_size SCAN_SIZE This much of a read's start/end signal will examined for barcode + signals (default: 6144) + --score_diff SCORE_DIFF For a read to be classified, there must be this much difference + between the best and second-best barcode scores (default: 0.5) + --require_both When classifying reads using two models (read start and read end) + require both barcode calls to match to make the final call (default: + a call on either the read start or read end is sufficient) Performance: - --batch_size BATCH_SIZE Neural network batch size (default: 256) + --batch_size BATCH_SIZE Neural network batch size (default: 256) --intra_op_parallelism_threads INTRA_OP_PARALLELISM_THREADS - TensorFlow's intra_op_parallelism_threads config option (default: - 12) + TensorFlow's intra_op_parallelism_threads config option (default: 12) --inter_op_parallelism_threads INTER_OP_PARALLELISM_THREADS - TensorFlow's inter_op_parallelism_threads config option (default: - 1) - --device_count DEVICE_COUNT TensorFlow's device_count config option (default: 1) + TensorFlow's inter_op_parallelism_threads config option (default: 1) + --device_count DEVICE_COUNT TensorFlow's device_count config option (default: 1) --omp_num_threads OMP_NUM_THREADS - OMP_NUM_THREADS environment variable value (default: 12) + OMP_NUM_THREADS environment variable value (default: 12) Other: - --verbose Include the output probabilities for all barcodes in the results - (default: just show the final barcode call) - -h, --help Show this help message and exit + --verbose Include the output probabilities for all barcodes in the results + (default: just show the final barcode call) + -h, --help Show this help message and exit ``` @@ -232,38 +230,36 @@ usage: deepbinner realtime --in_dir IN_DIR --out_dir OUT_DIR [-s START_MODEL] [- Sort fast5 files during sequencing Required: - --in_dir IN_DIR Directory where sequencer deposits fast5 files - --out_dir OUT_DIR Directory to output binned fast5 files + --in_dir IN_DIR Directory where sequencer deposits fast5 files + --out_dir OUT_DIR Directory to output binned fast5 files Models (at least one is required): -s START_MODEL, --start_model START_MODEL - Model trained on the starts of reads + Model trained on the starts of reads -e END_MODEL, --end_model END_MODEL - Model trained on the ends of reads + Model trained on the ends of reads Barcoding: - --scan_size SCAN_SIZE This much of a read's start/end signal will examined for barcode - signals (default: 6144) - --score_diff SCORE_DIFF For a read to be classified, there must be this much difference - between the best and second-best barcode scores (default: 0.5) - --require_both When classifying reads using two models (read start and read end) - require both barcode calls to match to make the final call - (default: False) + --scan_size SCAN_SIZE This much of a read's start/end signal will examined for barcode + signals (default: 6144) + --score_diff SCORE_DIFF For a read to be classified, there must be this much difference + between the best and second-best barcode scores (default: 0.5) + --require_both When classifying reads using two models (read start and read end) + require both barcode calls to match to make the final call (default: + a call on either the read start or read end is sufficient) Performance: - --batch_size BATCH_SIZE Neural network batch size (default: 256) + --batch_size BATCH_SIZE Neural network batch size (default: 256) --intra_op_parallelism_threads INTRA_OP_PARALLELISM_THREADS - TensorFlow's intra_op_parallelism_threads config option (default: - 12) + TensorFlow's intra_op_parallelism_threads config option (default: 12) --inter_op_parallelism_threads INTER_OP_PARALLELISM_THREADS - TensorFlow's inter_op_parallelism_threads config option (default: - 1) - --device_count DEVICE_COUNT TensorFlow's device_count config option (default: 1) + TensorFlow's inter_op_parallelism_threads config option (default: 1) + --device_count DEVICE_COUNT TensorFlow's device_count config option (default: 1) --omp_num_threads OMP_NUM_THREADS - OMP_NUM_THREADS environment variable value (default: 12) + OMP_NUM_THREADS environment variable value (default: 12) Other: - -h, --help Show this help message and exit + -h, --help Show this help message and exit ``` diff --git a/deepbinner/deepbinner.py b/deepbinner/deepbinner.py index 7efef01..482cb80 100644 --- a/deepbinner/deepbinner.py +++ b/deepbinner/deepbinner.py @@ -125,7 +125,8 @@ def classify_and_realtime_options(group): barcode_args.add_argument('--require_both', action='store_true', help='When classifying reads using two models (read start and read ' 'end) require both barcode calls to match to make the final ' - 'call') + 'call (default: a call on either the read start or read end is ' + 'sufficient)') perf_args = group.add_argument_group('Performance') perf_args.add_argument('--batch_size', type=int, required=False, default=256,