aboutsummaryrefslogtreecommitdiff
path: root/wqflask
diff options
context:
space:
mode:
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/wqflask/correlation/correlation_gn3_api.py39
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