From 233ed8a88c3f5681ed984a965080be2388e4ebbf Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 24 Sep 2019 12:17:08 -0500
Subject: Fixed issue that caused GEMMA to not work with genotype files without
 cM, though this issue still needs to be dealt with to get the new qtlreaper
 working

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

(limited to 'wqflask')

diff --git a/wqflask/utility/gen_geno_ob.py b/wqflask/utility/gen_geno_ob.py
index 5172369f..e8780879 100644
--- a/wqflask/utility/gen_geno_ob.py
+++ b/wqflask/utility/gen_geno_ob.py
@@ -115,7 +115,10 @@ class Locus(object):
     def __init__(self, marker_row, geno_ob):
         self.chr = marker_row[0]
         self.name = marker_row[1]
-        self.cM = float(marker_row[geno_ob.cm_column])
+        try:
+            self.cM = float(marker_row[geno_ob.cm_column])
+        except:
+            self.cM = float(marker_row[geno_ob.mb_column]) if geno_ob.mb_exists else 0
         self.Mb = float(marker_row[geno_ob.mb_column]) if geno_ob.mb_exists else None
 
         geno_table = {
-- 
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