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| author | Frederick Muriuki Muriithi | 2021-10-26 09:17:52 +0300 |
|---|---|---|
| committer | BonfaceKilz | 2021-11-04 12:45:57 +0300 |
| commit | d6e392c2488421ae04b4ffd5de26be40ed86a9b3 (patch) | |
| tree | 268cb6b58030ec773040b4906c407b6571edfab5 | |
| parent | 42dee16ec8a7d7620367dd31481999bfca9313db (diff) | |
| download | genenetwork3-d6e392c2488421ae04b4ffd5de26be40ed86a9b3.tar.gz | |
Complete `correlations_of_all_tissue_traits`
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Complete the implementation of the `correlations_of_all_tissue_traits`
function by providing a call to a non-implemented function.
| -rw-r--r-- | gn3/db/correlations.py | 22 |
1 files changed, 18 insertions, 4 deletions
diff --git a/gn3/db/correlations.py b/gn3/db/correlations.py index cae8080..f43b8a5 100644 --- a/gn3/db/correlations.py +++ b/gn3/db/correlations.py @@ -265,7 +265,6 @@ def fetch_tissue_probeset_xref_info( results or tuple(), (tuple(), {}, {}, {}, {}, {}, {})) -def correlations_of_all_tissue_traits() -> Tuple[dict, dict]: def fetch_gene_symbol_tissue_value_dict_for_trait( gene_name_list: Tuple[str, ...], probeset_freeze_id: int, conn: Any) -> dict: @@ -282,12 +281,25 @@ def fetch_gene_symbol_tissue_value_dict_for_trait( return fetch_gene_symbol_tissue_value_dict(xref_info[0], xref_info[2], conn) return {} +def correlations_of_all_tissue_traits( + trait_symbol: str, probeset_freeze_id: int, + method: str, conn: Any) -> Tuple[dict, dict]: + """ + Computes and returns the correlation of all tissue traits. + This is a migration of the - `web.webqtl.correlation.CorrelationPage.calculateCorrOfAllTissueTrait` + `web.webqtl.correlation.correlationFunction.calculateCorrOfAllTissueTrait` function in GeneNetwork1. """ - raise Exception("Unimplemented!!!") - return ({}, {}) + primary_trait_symbol_value_dict = fetch_gene_symbol_tissue_value_dict_for_trait( + (trait_symbol,), probeset_freeze_id, conn) + primary_trait_value = primary_trait_symbol_value_dict.vlaues()[0] + symbol_value_dict = fetch_gene_symbol_tissue_value_dict_for_trait( + tuple(), probeset_freeze_id, conn) + if method == "1": + return batch_computed_tissue_correlation( + primaryTraitValue,SymbolValueDict,method='spearman') + return batch_computed_tissue_correlation(primaryTraitValue,SymbolValueDict) def build_temporary_tissue_correlations_table( trait_symbol: str, probeset_freeze_id: int, method: str, @@ -298,6 +310,8 @@ def build_temporary_tissue_correlations_table( This is a migration of the `web.webqtl.correlation.CorrelationPage.getTempTissueCorrTable` function in GeneNetwork1.""" + symbol_corr_dict, symbol_p_value_dict = correlations_of_all_tissue_traits( + trait_symbol, probeset_freeze_id, method, conn) raise Exception("Unimplemented!!!") return "" |