diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/correlation/correlation_gn3_api.py | 39 |
1 files changed, 28 insertions, 11 deletions
diff --git a/wqflask/wqflask/correlation/correlation_gn3_api.py b/wqflask/wqflask/correlation/correlation_gn3_api.py index 4949bbe2..d68bb604 100644 --- a/wqflask/wqflask/correlation/correlation_gn3_api.py +++ b/wqflask/wqflask/correlation/correlation_gn3_api.py @@ -83,6 +83,23 @@ def tissue_for_trait_lists(corr_results, this_dataset, this_trait): return corr_results +def lit_for_trait_list(corr_results, this_dataset, this_trait): + (this_trait_geneid, geneid_dict, species) = do_lit_correlation( + this_trait, this_dataset) + + trait_lists = {list(corr_results)[0]: 1 for corr_result in corr_results} + + geneid_dict = {trait_name: geneid for (trait_name, geneid) in geneid_dict if + trait_lists.get(trait_name)} + + conn, _cursor_object = database_connector() + correlation_results = compute_all_lit_correlation( + conn=conn, trait_lists=list(geneid_dict.items()), + species=species, gene_id=this_trait_geneid) + + return correlation_results[0:corr_return_results] + + def compute_correlation(start_vars, method="pearson"): """compute correlation for to call gn3 api""" # pylint: disable-msg=too-many-locals @@ -136,30 +153,30 @@ def compute_correlation(start_vars, method="pearson"): conn, _cursor_object = database_connector() with conn: correlation_results = compute_all_lit_correlation( - conn=conn, trait_lists=list(geneid_dict.items()), - species=species, gene_id=this_trait_geneid) + conn = conn, trait_lists = list(geneid_dict.items()), + species = species, gene_id = this_trait_geneid) return correlation_results[0:corr_return_results] def do_lit_correlation(this_trait, this_dataset): """function for fetching lit inputs""" - geneid_dict = this_dataset.retrieve_genes("GeneId") - species = this_dataset.group.species.lower() - trait_geneid = this_trait.geneid + geneid_dict=this_dataset.retrieve_genes("GeneId") + species=this_dataset.group.species.lower() + trait_geneid=this_trait.geneid return (trait_geneid, geneid_dict, species) def get_tissue_correlation_input(this_trait, trait_symbol_dict): """Gets tissue expression values for the primary trait and target tissues values""" - primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values( - symbol_list=[this_trait.symbol]) + primary_trait_tissue_vals_dict=correlation_functions.get_trait_symbol_and_tissue_values( + symbol_list = [this_trait.symbol]) if this_trait.symbol.lower() in primary_trait_tissue_vals_dict: - primary_trait_tissue_values = primary_trait_tissue_vals_dict[this_trait.symbol.lower( + primary_trait_tissue_values=primary_trait_tissue_vals_dict[this_trait.symbol.lower( )] - corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values( - symbol_list=list(trait_symbol_dict.values())) - primary_tissue_data = { + corr_result_tissue_vals_dict=correlation_functions.get_trait_symbol_and_tissue_values( + symbol_list = list(trait_symbol_dict.values())) + primary_tissue_data={ "this_id": this_trait.name, "tissue_values": primary_trait_tissue_values |