From 2852a935d67f1fe319ee925f412d40f7d8e88582 Mon Sep 17 00:00:00 2001
From: Alexander_Kabui
Date: Wed, 19 Feb 2025 15:54:51 +0300
Subject: fix: Read and parse correct permutation file from R/qtl1

---
 gn3/computations/rqtl.py | 17 +++++++----------
 1 file changed, 7 insertions(+), 10 deletions(-)

(limited to 'gn3/computations')

diff --git a/gn3/computations/rqtl.py b/gn3/computations/rqtl.py
index c8a828d..941a19b 100644
--- a/gn3/computations/rqtl.py
+++ b/gn3/computations/rqtl.py
@@ -1,5 +1,6 @@
 """Procedures related to R/qtl computations"""
 import os
+import csv
 from bisect import bisect
 from typing import Dict, List, Tuple, Union
 
@@ -317,14 +318,10 @@ def process_perm_output(file_name: str) -> Tuple[List, float, float]:
     outdir = os.path.join(get_tmpdir(), "gn3")
 
     with open(os.path.join(outdir, file_name),
-              "r", encoding="utf-8") as the_file:
-
-        for i, line in enumerate(the_file):
-            if i == 0:
-                # Skip header line
-                continue
-            _snp, _chromosome, _position, lod_score = line.split(",")
-            perm_results.append(float(lod_score))
-    suggestive = np.percentile(np.array(perm_results), 67)
-    significant = np.percentile(np.array(perm_results), 95)
+              "r", encoding="utf-8") as file_handler:
+        reader = csv.reader(file_handler)
+        next(reader)
+        perm_results = [float(row[1]) for row in reader]  # Extract LOD values
+        suggestive = np.percentile(np.array(perm_results), 67)
+        significant = np.percentile(np.array(perm_results), 95)
     return perm_results, suggestive, significant
-- 
cgit 1.4.1