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Clarify help text
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@rrwick
rrwick committed Jun 18, 2018
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82 changes: 39 additions & 43 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -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
```


Expand Down Expand Up @@ -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
```


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3 changes: 2 additions & 1 deletion deepbinner/deepbinner.py
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Expand Up @@ -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,
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