From 905626a2a27332f2fab74195bbcf615bf5c5b6bf Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 9 Nov 2021 16:41:48 +0300
Subject: replace list with generators

---
 gn3/computations/correlations.py | 31 ++++++++++++++-----------------
 1 file changed, 14 insertions(+), 17 deletions(-)

(limited to 'gn3')

diff --git a/gn3/computations/correlations.py b/gn3/computations/correlations.py
index c930df0..8eaa523 100644
--- a/gn3/computations/correlations.py
+++ b/gn3/computations/correlations.py
@@ -49,13 +49,9 @@ def normalize_values(a_values: List,
     ([2.3, 4.1, 5], [3.4, 6.2, 4.1], 3)
 
     """
-    a_new = []
-    b_new = []
     for a_val, b_val in zip(a_values, b_values):
         if (a_val and b_val is not None):
-            a_new.append(a_val)
-            b_new.append(b_val)
-    return a_new, b_new, len(a_new)
+            yield a_val, b_val
 
 
 def compute_corr_coeff_p_value(primary_values: List, target_values: List,
@@ -81,8 +77,10 @@ def compute_sample_r_correlation(trait_name, corr_method, trait_vals,
     correlation coeff and p value
 
     """
-    (sanitized_traits_vals, sanitized_target_vals,
-     num_overlap) = normalize_values(trait_vals, target_samples_vals)
+
+    sanitized_traits_vals, sanitized_target_vals = list(
+        zip(*list(normalize_values(trait_vals, target_samples_vals))))
+    num_overlap = len(sanitized_traits_vals)
 
     if num_overlap > 5:
 
@@ -114,13 +112,9 @@ def filter_shared_sample_keys(this_samplelist,
     filter the values using the shared keys
 
     """
-    this_vals = []
-    target_vals = []
     for key, value in target_samplelist.items():
         if key in this_samplelist:
-            target_vals.append(value)
-            this_vals.append(this_samplelist[key])
-    return (this_vals, target_vals)
+            yield value, this_samplelist[key]
 
 
 def fast_compute_all_sample_correlation(this_trait,
@@ -139,9 +133,10 @@ def fast_compute_all_sample_correlation(this_trait,
     for target_trait in target_dataset:
         trait_name = target_trait.get("trait_id")
         target_trait_data = target_trait["trait_sample_data"]
-        processed_values.append((trait_name, corr_method, *filter_shared_sample_keys(
-            this_trait_samples, target_trait_data)))
-    with multiprocessing.Pool(4) as pool:
+        processed_values.append((trait_name, corr_method, *list(zip(*list(filter_shared_sample_keys(
+            this_trait_samples, target_trait_data))))
+        ))
+    with multiprocessing.Pool() as pool:
         results = pool.starmap(compute_sample_r_correlation, processed_values)
 
         for sample_correlation in results:
@@ -172,8 +167,10 @@ def compute_all_sample_correlation(this_trait,
     for target_trait in target_dataset:
         trait_name = target_trait.get("trait_id")
         target_trait_data = target_trait["trait_sample_data"]
-        this_vals, target_vals = filter_shared_sample_keys(
-            this_trait_samples, target_trait_data)
+        this_vals, target_vals = list(zip(*list(filter_shared_sample_keys(
+            this_trait_samples, target_trait_data))))
+        # this_vals, target_vals = filter_shared_sample_keys(
+        #     this_trait_samples, target_trait_data)
 
         sample_correlation = compute_sample_r_correlation(
             trait_name=trait_name,
-- 
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