diff options
| -rw-r--r-- | gn3/computations/partial_correlations.py | 34 |
1 files changed, 12 insertions, 22 deletions
diff --git a/gn3/computations/partial_correlations.py b/gn3/computations/partial_correlations.py index 5017796..2921852 100644 --- a/gn3/computations/partial_correlations.py +++ b/gn3/computations/partial_correlations.py @@ -223,21 +223,16 @@ def partial_correlations_fast(# pylint: disable=[R0913, R0914] trait_name = trait_line[0] trait_data = trait_line[1:] if trait_name in fetched_correlations.keys(): - return ( - acc[0] + (trait_name,), - acc[1] + tuple( - trait_data[i] if i in good_dataset_samples else None - for i in range(len(trait_data)))) - return acc - - processed_trait_names_values: tuple = reduce( - __process_trait_names_and_values__, dataset[1:], (tuple(), tuple())) - all_target_trait_names: Tuple[str, ...] = processed_trait_names_values[0] - all_target_trait_values: Tuple[float, ...] = processed_trait_names_values[1] + yield acc + ((trait_name,) + tuple( + trait_data[i] if i in good_dataset_samples else None + for i in range(len(trait_data)))) + yield acc + + processed_target_traits: tuple = reduce( + __process_trait_names_and_values__, dataset[1:], tuple()) all_correlations = compute_partial( - primary_vals, control_vals, all_target_trait_names, - all_target_trait_values, method) + primary_vals, control_vals, processed_target_traits, 1, method) ## Line 772 to 779 in GN1 are the cause of the weird complexity in the ## return below. Once the surrounding code is successfully migrated and ## reworked, this complexity might go away, by getting rid of the @@ -309,7 +304,7 @@ def compute_trait_info(primary_vals, control_vals, target, method): zero_order_corr["r"][0], zero_order_corr["p-val"][0]) def compute_partial( - primary_vals, control_vals, target_vals, target_names, + primary_vals, control_vals, targets, data_start_pos, method: str) -> Tuple[ Union[ Tuple[str, int, float, float, float, float], None], @@ -327,8 +322,8 @@ def compute_partial( return tuple( result for result in ( compute_trait_info( - primary_vals, control_vals, (tvals, tname), method) - for tvals, tname in zip(target_vals, target_names)) + primary_vals, control_vals, (target[data_start_pos:], target[0]), method) + for target in targets) if result is not None) def partial_correlations_normal(# pylint: disable=R0913 @@ -358,13 +353,8 @@ def partial_correlations_normal(# pylint: disable=R0913 return tuple(item) + (trait_database[1], trait_database[2]) return item - target_trait_names, target_trait_vals = reduce(# type: ignore[var-annotated] - lambda acc, item: (acc[0]+(item[0],), acc[1]+(item[data_start_pos:],)), - trait_database, (tuple(), tuple())) - all_correlations = compute_partial( - primary_vals, control_vals, target_trait_vals, target_trait_names, - method) + primary_vals, control_vals, trait_database, data_start_pos, method) if (input_trait_gene_id and db_type == "ProbeSet" and method.lower() in ( "sgo literature correlation", "tissue correlation, pearson's r", |