From 49d1af523c520a80f48f2e8d021877f6fb0f12a3 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 19 Mar 2020 11:46:49 -0500
Subject: Made a minor change just to help qtlreaper deal with genotype files
 with positions in bases instead of megabases

---
 wqflask/wqflask/marker_regression/qtlreaper_mapping.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
index 41764c1c..0c560582 100644
--- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
+++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
@@ -97,7 +97,10 @@ def parse_reaper_output(gwa_filename, permu_filename, bootstrap_filename):
                 except:
                     marker['chr'] = line.split("\t")[2]
                 marker['cM'] = float(line.split("\t")[3])
-                marker['Mb'] = float(line.split("\t")[4])
+                if float(line.split("\t")[4]) > 1000:
+                    marker['Mb'] = float(line.split("\t")[4])/1000000
+                else:
+                    marker['Mb'] = float(line.split("\t")[4])
                 if float(line.split("\t")[7]) != 1:
                     marker['p_value'] = float(line.split("\t")[7])
                 marker['lrs_value'] = float(line.split("\t")[5])
-- 
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