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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