Implemented the public method generate_pheval_result() into the code base. Looks to be a large PR but did some refactoring of the naming of variables to be consistent with PhEval:
config.yaml -> refactored score_order to sort_order for consistency with variable naming in PhEval. This is for specifying the order in which the results should be sorted for ranking. I know this is subject to change if we get rid of the runner config.
config_parser.py -> refactored score_order to sort_order for consistency with variable naming in PhEval.
post_process.py -> refactored score_order to sort_order for consistency with variable naming in PhEval.
post_process_results_format.py -> removed methods create_pheval_gene_result_from_exomiser() and create_pheval_variant_result_from_exomiser() as they called private methods. Implemented the single command generate_pheval_result() from PhEval.
test_post_process_results_format.py -> removed tests for create_pheval_gene_result_from_exomiser() and create_pheval_variant_result_from_exomiser(). Ultimately these tests were testing PhEval method functionality,
test_run.py -> refactored score_order to sort_order for consistency with variable naming in PhEval.
Implemented the public method
generate_pheval_result()into the code base. Looks to be a large PR but did some refactoring of the naming of variables to be consistent with PhEval:config.yaml-> refactoredscore_ordertosort_orderfor consistency with variable naming in PhEval. This is for specifying the order in which the results should be sorted for ranking. I know this is subject to change if we get rid of the runner config.config_parser.py-> refactoredscore_ordertosort_orderfor consistency with variable naming in PhEval.post_process.py-> refactoredscore_ordertosort_orderfor consistency with variable naming in PhEval.post_process_results_format.py-> removed methodscreate_pheval_gene_result_from_exomiser()andcreate_pheval_variant_result_from_exomiser()as they called private methods. Implemented the single commandgenerate_pheval_result()from PhEval.test_post_process_results_format.py-> removed tests forcreate_pheval_gene_result_from_exomiser()andcreate_pheval_variant_result_from_exomiser(). Ultimately these tests were testing PhEval method functionality,test_run.py-> refactoredscore_ordertosort_orderfor consistency with variable naming in PhEval.