From 99fd5070a84f37f91993f329f9cc8dd82a4b9339 Mon Sep 17 00:00:00 2001
From: Alexander_Kabui
Date: Wed, 19 Feb 2025 16:10:16 +0300
Subject: fix: Read and parse correct permutation file from R/qtl2.

---
 gn3/computations/rqtl2.py | 10 +++-------
 1 file changed, 3 insertions(+), 7 deletions(-)

(limited to 'gn3/computations/rqtl2.py')

diff --git a/gn3/computations/rqtl2.py b/gn3/computations/rqtl2.py
index ae1e475..ec0636b 100644
--- a/gn3/computations/rqtl2.py
+++ b/gn3/computations/rqtl2.py
@@ -133,16 +133,12 @@ def process_permutation(data):
     """
 
     perm_file = data.get("permutation_file")
-    perm_results = {}
     with open(perm_file, "r", encoding="utf-8") as file_handler:
         reader = csv.reader(file_handler)
         phenotypes = next(reader)[1:]
-        for line in reader:
-            permutation_id, *permutation_values = line
-            perm_results[permutation_id] = permutation_values
-
-    _, significance = fetch_significance_results(data.get("significance_file"))
-    return {
+        perm_results = {_id:float(val) for (_id,val)  in reader}
+        _, significance = fetch_significance_results(data.get("significance_file"))
+        return {
         "phenotypes": phenotypes,
         "perm_results": perm_results,
         "significance": significance,
-- 
cgit 1.4.1