Merge branch 'ben_dev' into 'master'
Added data preparation, hyperparameter optimisation, benchmarking code and k-mer library visualisation See merge request !3
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- CnnParameterFile.yaml 12 additions, 11 deletionsCnnParameterFile.yaml
- compare_benchmark_performance/compare_accuracy.py 253 additions, 0 deletionscompare_benchmark_performance/compare_accuracy.py
- compare_benchmark_performance/compare_run_times.py 110 additions, 0 deletionscompare_benchmark_performance/compare_run_times.py
- db_building/TrainingRead.py 0 additions, 3 deletionsdb_building/TrainingRead.py
- helper_functions.py 27 additions, 0 deletionshelper_functions.py
- hyperparameter_search/hyperparameter_ranges_cnn_test.yaml 15 additions, 7 deletionshyperparameter_search/hyperparameter_ranges_cnn_test.yaml
- hyperparameter_search/optimize_hyperparams.py 36 additions, 28 deletionshyperparameter_search/optimize_hyperparams.py
- k_mer_design/evolutionary_algorithm_kmers.py 22 additions, 22 deletionsk_mer_design/evolutionary_algorithm_kmers.py
- k_mer_design/make_k_mer_library_figures.py 61 additions, 0 deletionsk_mer_design/make_k_mer_library_figures.py
- nns/Cnn_test.py 6 additions, 2 deletionsnns/Cnn_test.py
- nns/keras_metrics_from_logits.py 21 additions, 8 deletionsnns/keras_metrics_from_logits.py
- run_production_pipeline.sf 7 additions, 0 deletionsrun_production_pipeline.sf
- tools/create_k_folds_for_benchmark.py 84 additions, 0 deletionstools/create_k_folds_for_benchmark.py
- tools/extract_16s_from_gbff.py 45 additions, 17 deletionstools/extract_16s_from_gbff.py
- tools/get_one_barcode.py 114 additions, 23 deletionstools/get_one_barcode.py
- tools/plot_nn_performance.py 41 additions, 37 deletionstools/plot_nn_performance.py
- tools/set_ground_truths_of_reads.py 75 additions, 0 deletionstools/set_ground_truths_of_reads.py
- tools/split_data_in_train_test.py 91 additions, 0 deletionstools/split_data_in_train_test.py
- tools/squigglenet_data_preparation.py 48 additions, 0 deletionstools/squigglenet_data_preparation.py
- tools/visualise_ground_truth_file.py 69 additions, 0 deletionstools/visualise_ground_truth_file.py
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