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| author | zsloan | 2020-03-19 11:46:49 -0500 |
|---|---|---|
| committer | GN2 | 2020-03-19 11:48:10 -0500 |
| commit | 49d1af523c520a80f48f2e8d021877f6fb0f12a3 (patch) | |
| tree | 2d7c81ebc922585cea0fd25c664da23d4d9b6560 /wqflask | |
| parent | dbaea134b1cee2a9cdc4968dac50e50e44c162bb (diff) | |
| download | genenetwork2-49d1af523c520a80f48f2e8d021877f6fb0f12a3.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.py | 5 |
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]) |