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authorAlexander Kabui2021-05-10 08:33:22 +0300
committerAlexander Kabui2021-05-10 08:33:22 +0300
commit93baf59aca12fb85e668315e67d36137c854f12d (patch)
tree2f736008e83031e97d0d5e75305b173e2f1d0c45
parentbc29c9dd907c8c1b024231fa713040b3c4092f3a (diff)
downloadgenenetwork2-93baf59aca12fb85e668315e67d36137c854f12d.tar.gz
minor changes to interface
-rw-r--r--wqflask/wqflask/correlation/correlation_gn3_api.py60
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