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| author | Frederick Muriuki Muriithi | 2021-12-13 15:56:01 +0300 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2021-12-13 15:56:01 +0300 |
| commit | 131394ac737aac7e6fced7cfb07f9e9d538b9506 (patch) | |
| tree | 82c8a9dae60c4f8466ee6ea49fb0f6ba09817a30 | |
| parent | 07c94ab13460a2289b386f3a164954ac7920e28c (diff) | |
| download | genenetwork3-131394ac737aac7e6fced7cfb07f9e9d538b9506.tar.gz | |
Run partial correlations against chosen database
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Run the partial correlations against the database that the user selects, and
not the one from which the primary trait is. This was a bug in the code.
| -rw-r--r-- | gn3/computations/partial_correlations.py | 10 |
1 files changed, 9 insertions, 1 deletions
diff --git a/gn3/computations/partial_correlations.py b/gn3/computations/partial_correlations.py index 719c605..bda6ba2 100644 --- a/gn3/computations/partial_correlations.py +++ b/gn3/computations/partial_correlations.py @@ -640,12 +640,20 @@ def partial_correlations_entry(# pylint: disable=[R0913, R0914, R0911] "any associated Tissue Correlation Information."), "error_type": "Tissue Correlation"} + target_dataset = retrieve_trait_dataset( + ("Temp" if "Temp" in target_db_name else + ("Publish" if "Publish" in target_db_name else + "Geno" if "Geno" in target_db_name else "ProbeSet")), + {"db": {"dataset_name": target_db_name}, "trait_name": "_"}, + threshold, + conn) + database_filename = get_filename(conn, target_db_name, TEXTDIR) _total_traits, all_correlations = partial_corrs( conn, common_primary_control_samples, fixed_primary_vals, fixed_control_vals, len(fixed_primary_vals), species, input_trait_geneid, input_trait_symbol, tissue_probeset_freeze_id, - method, primary_trait["db"], database_filename) + method, {**target_dataset, "dataset_type": target_dataset["type"]}, database_filename) def __make_sorter__(method): |