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-rw-r--r--gn3/computations/partial_correlations.py34
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",