diff options
| -rw-r--r-- | wqflask/wqflask/correlation/correlation_gn3_api.py | 60 |
1 files changed, 38 insertions, 22 deletions
diff --git a/wqflask/wqflask/correlation/correlation_gn3_api.py b/wqflask/wqflask/correlation/correlation_gn3_api.py index d68bb604..98d52591 100644 --- a/wqflask/wqflask/correlation/correlation_gn3_api.py +++ b/wqflask/wqflask/correlation/correlation_gn3_api.py @@ -68,9 +68,9 @@ def sample_for_trait_lists(corr_results, target_dataset, def tissue_for_trait_lists(corr_results, this_dataset, this_trait): """interface function for doing tissue corr_results on trait_list""" - # trait_lists = dict([(list(corr_result)[0], True) - # for corr_result in corr_results]) - trait_lists = {list(corr_results)[0]: 1 for corr_result in corr_results} + trait_lists = dict([(list(corr_result)[0], True) + for corr_result in corr_results]) + # trait_lists = {list(corr_results)[0]: 1 for corr_result in corr_results} traits_symbol_dict = this_dataset.retrieve_genes("Symbol") traits_symbol_dict = dict({trait_name: symbol for ( trait_name, symbol) in traits_symbol_dict.items() if trait_lists.get(trait_name)}) @@ -85,19 +85,24 @@ def tissue_for_trait_lists(corr_results, this_dataset, this_trait): def lit_for_trait_list(corr_results, this_dataset, this_trait): (this_trait_geneid, geneid_dict, species) = do_lit_correlation( - this_trait, this_dataset) + this_trait, this_dataset) - trait_lists = {list(corr_results)[0]: 1 for corr_result in corr_results} + # trait_lists = {list(corr_results)[0]: 1 for corr_result in corr_results} + trait_lists = dict([(list(corr_result)[0], True) + for corr_result in corr_results]) - geneid_dict = {trait_name: geneid for (trait_name, geneid) in geneid_dict if - trait_lists.get(trait_name)} + geneid_dict = {trait_name: geneid for (trait_name, geneid) in geneid_dict.items() 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] + with conn: + + correlation_results = compute_all_lit_correlation( + conn=conn, trait_lists=list(geneid_dict.items()), + species=species, gene_id=this_trait_geneid) + + return correlation_results def compute_correlation(start_vars, method="pearson"): @@ -129,6 +134,17 @@ def compute_correlation(start_vars, method="pearson"): this_trait=this_trait_data, target_dataset=results) + # do tissue correaltion + + # code to be use later + + # tissue_result = tissue_for_trait_lists( + # correlation_results, this_dataset, this_trait) + # # lit spoils the party so slow + # lit_result = lit_for_trait_list( + # correlation_results, this_dataset, this_trait) + + elif corr_type == "tissue": trait_symbol_dict = this_dataset.retrieve_genes("Symbol") primary_tissue_data, target_tissue_data = get_tissue_correlation_input( @@ -153,30 +169,30 @@ 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 |