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| author | Frederick Muriuki Muriithi | 2022-05-06 15:35:57 +0300 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2022-05-06 15:35:57 +0300 |
| commit | d04241d0e49a50d9aa775042fffe5a7d8cfaf551 (patch) | |
| tree | 7577b1dd72eed9e32670d9240a632b27831e1417 /gn3/computations | |
| parent | 081bd53222a40a610257c3d67e9186c09da49106 (diff) | |
| download | genenetwork3-d04241d0e49a50d9aa775042fffe5a7d8cfaf551.tar.gz | |
Hook up pcorrs with target traits computations
Enable the endpoint to actually compute partial correlations with selected
target traits rather than against an entire dataset.
Fix some issues caused by recent refactor that broke pcorrs against a dataset
Diffstat (limited to 'gn3/computations')
| -rw-r--r-- | gn3/computations/partial_correlations.py | 20 |
1 files changed, 11 insertions, 9 deletions
diff --git a/gn3/computations/partial_correlations.py b/gn3/computations/partial_correlations.py index 0041684..07c73db 100644 --- a/gn3/computations/partial_correlations.py +++ b/gn3/computations/partial_correlations.py @@ -555,9 +555,9 @@ def trait_for_output(trait): } return {key: val for key, val in trait.items() if val is not None} -def check_for_common_errors(conn, primary_trait_name, control_trait_names): +def check_for_common_errors( + conn, primary_trait_name, control_trait_names, threshold): """Check for common errors""" - threshold = 0 corr_min_informative = 4 non_error_result = {"status": "success"} @@ -671,8 +671,10 @@ def partial_correlations_with_target_db(# pylint: disable=[R0913, R0914, R0911] functionality into smaller functions that do fewer things. """ + threshold = 0 + check_res = check_for_common_errors( - conn, primary_trait_name, control_trait_names) + conn, primary_trait_name, control_trait_names, threshold) if check_res.get("status") == "error": return error_check_results @@ -680,7 +682,7 @@ def partial_correlations_with_target_db(# pylint: disable=[R0913, R0914, R0911] input_trait_geneid = primary_trait.get("geneid", 0) input_trait_symbol = primary_trait.get("symbol", "") input_trait_mouse_geneid = translate_to_mouse_gene_id( - species, input_trait_geneid, conn) + check_res["species"], input_trait_geneid, conn) tissue_probeset_freeze_id = 1 db_type = primary_trait["db"]["dataset_type"] @@ -744,8 +746,8 @@ def partial_correlations_with_target_db(# pylint: disable=[R0913, R0914, R0911] database_filename = get_filename(conn, target_db_name, TEXTDIR) _total_traits, all_correlations = partial_corrs( conn, check_res["common_primary_control_samples"], - check_res["fixed_primary_values"], check_res["fixed_control_vals"], - len(check_res["fixed_primary_vals"]), check_res["species"], + check_res["fixed_primary_values"], check_res["fixed_control_values"], + len(check_res["fixed_primary_values"]), check_res["species"], input_trait_geneid, input_trait_symbol, tissue_probeset_freeze_id, method, {**target_dataset, "dataset_type": target_dataset["type"]}, database_filename) @@ -764,7 +766,7 @@ def partial_correlations_with_target_db(# pylint: disable=[R0913, R0914, R0911] return __by_partial_corr_p_value__ add_lit_corr_and_tiss_corr = compose( - partial(literature_correlation_by_list, conn, species), + partial(literature_correlation_by_list, conn, check_res["species"]), partial( tissue_correlation_by_list, conn, input_trait_symbol, tissue_probeset_freeze_id, method)) @@ -801,7 +803,7 @@ def partial_correlations_with_target_db(# pylint: disable=[R0913, R0914, R0911] "results": { "primary_trait": trait_for_output(primary_trait), "control_traits": tuple( - trait_for_output(trait) for trait in cntrl_traits), + trait_for_output(trait) for trait in check_res["control_traits"]), "correlations": tuple( trait_for_output(trait) for trait in trait_list), "dataset_type": target_dataset["type"], @@ -818,7 +820,7 @@ def partial_correlations_with_target_traits( """ threshold = 0 check_res = check_for_common_errors( - conn, primary_trait_name, control_trait_names) + conn, primary_trait_name, control_trait_names, threshold) if check_res.get("status") == "error": return error_check_results |