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| author | zsloan | 2017-02-08 18:27:13 +0000 |
|---|---|---|
| committer | zsloan | 2017-02-08 18:27:13 +0000 |
| commit | d015b37f863c69932072d4ecf9fa1c1cd7fd3ee0 (patch) | |
| tree | cc515905822ac8e8118c614c9a34b07a5f02ddda /wqflask | |
| parent | 160503c3c04ca19c9262d5c3b6100b7ac2242e0e (diff) | |
| download | genenetwork2-d015b37f863c69932072d4ecf9fa1c1cd7fd3ee0.tar.gz | |
Changed the way .fam files are written/read, which fixes the issue with GEMMA mapping accuracy.
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/maintenance/get_group_samplelists.py | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/gemma_mapping.py | 2 |
2 files changed, 2 insertions, 2 deletions
diff --git a/wqflask/maintenance/get_group_samplelists.py b/wqflask/maintenance/get_group_samplelists.py index 2d48ce78..04e94886 100644 --- a/wqflask/maintenance/get_group_samplelists.py +++ b/wqflask/maintenance/get_group_samplelists.py @@ -51,6 +51,6 @@ def get_samplelist_from_plink(genofilename): samplelist = [] for line in genofile: line = line.split(" ") - samplelist.append(line[0]) + samplelist.append(line[1]) return samplelist diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index 66bed5a2..3bde61cd 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -41,7 +41,7 @@ def gen_pheno_txt_file(this_dataset, samples, vals): this_val = -9 else: this_val = vals[i] - outfile.write(line[0] + " " + line[1] + " " + line[2] + " " + line[3] + " " + line[4] + " " + str(this_val) + "\n") + outfile.write("0" + " " + line[1] + " " + line[2] + " " + line[3] + " " + line[4] + " " + str(this_val) + "\n") def parse_gemma_output(this_dataset): included_markers = [] |