diff options
| -rw-r--r-- | gn3/computations/partial_correlations.py | 27 | ||||
| -rw-r--r-- | gn3/db/correlations.py | 20 |
2 files changed, 27 insertions, 20 deletions
diff --git a/gn3/computations/partial_correlations.py b/gn3/computations/partial_correlations.py index e73edfd..4ba2ba4 100644 --- a/gn3/computations/partial_correlations.py +++ b/gn3/computations/partial_correlations.py @@ -157,3 +157,30 @@ def batch_computed_tissue_correlation( `web.webqtl.correlation.correlationFunction.batchCalTissueCorr`""" raise Exception("Not implemented!") return ({}, {}) + +def correlations_of_all_tissue_traits( + primary_trait_symbol_value_dict: dict, symbol_value_dict: dict, + method: str) -> Tuple[dict, dict]: + """ + Computes and returns the correlation of all tissue traits. + + This is a migration of the + `web.webqtl.correlation.correlationFunction.calculateCorrOfAllTissueTrait` + function in GeneNetwork1. + """ + # The section below existed in the original function, but with the migration + # and the proposed rework (in the near future), the values from the database + # should be passed into this function, rather than have the function fetch + # the data for itself. + # --------------------------------------------------- + # primary_trait_symbol_value_dict = fetch_gene_symbol_tissue_value_dict_for_trait( + # (trait_symbol,), probeset_freeze_id, conn) + # primary_trait_values = primary_trait_symbol_value_dict.vlaues()[0] + # symbol_value_dict = fetch_gene_symbol_tissue_value_dict_for_trait( + # tuple(), probeset_freeze_id, conn) + # --------------------------------------------------- + # We might end up actually getting rid of this function all together as the + # rework is done. + primary_trait_values = primary_trait_symbol_value_dict.values()[0] + return batch_computed_tissue_correlation( + primary_trait_values, symbol_value_dict, method) diff --git a/gn3/db/correlations.py b/gn3/db/correlations.py index f43b8a5..39ed499 100644 --- a/gn3/db/correlations.py +++ b/gn3/db/correlations.py @@ -281,26 +281,6 @@ 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.correlationFunction.calculateCorrOfAllTissueTrait` - function in GeneNetwork1. - """ - 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, return_number: int, conn: Any) -> str: |