diff options
| -rw-r--r-- | wqflask/wqflask/correlation/correlation_gn3_api.py | 17 |
1 files changed, 10 insertions, 7 deletions
diff --git a/wqflask/wqflask/correlation/correlation_gn3_api.py b/wqflask/wqflask/correlation/correlation_gn3_api.py index c1d6132b..75bd5561 100644 --- a/wqflask/wqflask/correlation/correlation_gn3_api.py +++ b/wqflask/wqflask/correlation/correlation_gn3_api.py @@ -48,20 +48,17 @@ def create_target_this_trait(start_vars): this_trait = create_trait(dataset=this_dataset, name=start_vars['trait_id']) - sample_data = process_samples(start_vars, this_dataset.group.samplelist) + # target_dataset.get_trait_data(list(self.sample_data.keys())) - this_trait = retrieve_sample_data(this_trait, this_dataset) + # this_trait = retrieve_sample_data(this_trait, this_dataset) print(f"Starting to creat the target dataset ") dataset_start_time = time.time() + sample_data = () - target_dataset.get_trait_data(list(sample_data.keys())) + time_taken = time.time() - initial_time - print(f"the time taken to create dataset is", time.time()-dataset_start_time) - - print(f"the time taken to create dataset abnd trait is", time_taken) - return (this_dataset, this_trait, target_dataset, sample_data) @@ -89,6 +86,10 @@ def compute_correlation(start_vars, method="pearson"): # } # } + sample_data = process_samples(start_vars, this_dataset.group.samplelist) + target_dataset.get_trait_data(list(sample_data.keys())) + this_trait = retrieve_sample_data(this_trait, this_dataset) + this_trait_data = { @@ -111,8 +112,10 @@ def compute_correlation(start_vars, method="pearson"): elif corr_type == "tissue": trait_symbol_dict = this_dataset.retrieve_genes("Symbol") + time_to_retrieve = time.time() primary_tissue_data, target_tissue_data = get_tissue_correlation_input( this_trait, trait_symbol_dict) + print("Time taken to retrieve this is",time.time()-time_to_retrieve) corr_input_data = { "primary_tissue": primary_tissue_data, |