refactor path parsing functions

argparse_dicts.py

coa_detection/build_coa_db.py

coa_detection/coa_argparse_dicts.py

coa_detection/run_inference.py

coa_detection/train_coa_nn.py

db_building/build_db.py

db_building/collect_examples.py

helper_functions.py

hyperparameter_search/optimize_hyperparams.py

inference/ReadManager.py

inference/ReadTable.py

inference/analyse_abundance_results.py

inference/run_inference.py

inference/run_inference_evaluation.py

path_parsing_functions.py

run_production_pipeline.py

threshold_search/optimize_thresholds.py

threshold_search/run_logit_inference.py

tools/filter_fast5_reads.py

tools/get_stratified_sample.py