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| author | Frederick Muriuki Muriithi | 2022-01-24 15:24:59 +0300 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2022-01-27 10:02:02 +0300 |
| commit | 7bc3d9a11ee1e5a863a01a91abd7510bdbfae54e (patch) | |
| tree | 2592a5db5ac644846e0383062fa2dfabd30e9c8f /gn3/computations | |
| parent | f9dfc61b4fe5d78c6a09adbeafa28a4e5d91c2ad (diff) | |
| download | genenetwork3-7bc3d9a11ee1e5a863a01a91abd7510bdbfae54e.tar.gz | |
Refactor: Remove circular importrefactor-circular-import
The function
`gn3.computation.partial_correlations.correlations_of_all_tissue_traits` was,
before this commit, called inside the
`gn3.db.correlations.build_temporary_tissue_correlations_table`
function, leading to a circular dependency. This commit removes the circular
dependency by rearranging the calls.
Diffstat (limited to 'gn3/computations')
| -rw-r--r-- | gn3/computations/partial_correlations.py | 14 |
1 files changed, 10 insertions, 4 deletions
diff --git a/gn3/computations/partial_correlations.py b/gn3/computations/partial_correlations.py index 9bad12a..4b35c51 100644 --- a/gn3/computations/partial_correlations.py +++ b/gn3/computations/partial_correlations.py @@ -406,6 +406,12 @@ def partial_corrs(# pylint: disable=[R0913] `web.webqtl.correlation.PartialCorrDBPage.__init__` function in GeneNetwork1. """ + symbol_corr_dict, symbol_p_value_dict = correlations_of_all_tissue_traits( + fetch_gene_symbol_tissue_value_dict_for_trait( + (input_trait_symbol,), tissue_probeset_freeze_id, conn), + fetch_gene_symbol_tissue_value_dict_for_trait( + tuple(), tissue_probeset_freeze_id, conn), + method) if database_filename: return partial_correlations_fast( samples, primary_vals, control_vals, database_filename, @@ -414,15 +420,15 @@ def partial_corrs(# pylint: disable=[R0913] species, input_trait_geneid, dataset, return_number, conn) if "literature" in method.lower() else fetch_tissue_correlations( - dataset, input_trait_symbol, tissue_probeset_freeze_id, - method, return_number, conn)), + dataset, symbol_corr_dict, symbol_p_value_dict, + return_number, conn)), method, ("literature" if method.lower() == "sgo literature correlation" else ("tissue" if "tissue" in method.lower() else "genetic"))) trait_database, data_start_pos = fetch_all_database_data( - conn, species, input_trait_geneid, input_trait_symbol, samples, dataset, - method, return_number, tissue_probeset_freeze_id) + conn, species, input_trait_geneid, samples, dataset, method, + symbol_corr_dict, symbol_p_value_dict, return_number) return partial_correlations_normal( primary_vals, control_vals, input_trait_geneid, trait_database, data_start_pos, dataset, method) |