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authorzsloan2020-03-19 11:46:49 -0500
committerGN22020-03-19 11:48:10 -0500
commit49d1af523c520a80f48f2e8d021877f6fb0f12a3 (patch)
tree2d7c81ebc922585cea0fd25c664da23d4d9b6560 /wqflask
parentdbaea134b1cee2a9cdc4968dac50e50e44c162bb (diff)
downloadgenenetwork2-49d1af523c520a80f48f2e8d021877f6fb0f12a3.tar.gz
Made a minor change just to help qtlreaper deal with genotype files with positions in bases instead of megabases
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/wqflask/marker_regression/qtlreaper_mapping.py5
1 files changed, 4 insertions, 1 deletions
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])