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| author | zsloan | 2020-12-04 15:18:18 -0600 |
|---|---|---|
| committer | zsloan | 2020-12-04 15:18:18 -0600 |
| commit | 75ef9f817f8b80f6d4bd732bfede2ad575a50fab (patch) | |
| tree | 0cc7df07c398625a8ba3c71642fcafc7690232cf | |
| parent | 48969878b1321e80b55e06ec9367ba428bb2fc36 (diff) | |
| download | genenetwork2-75ef9f817f8b80f6d4bd732bfede2ad575a50fab.tar.gz | |
Fixed issue where chromosome names weren't being fetched correctly, causing an error in GEMMA
| -rw-r--r-- | wqflask/wqflask/marker_regression/gemma_mapping.py | 3 |
1 files changed, 2 insertions, 1 deletions
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index 02f91a32..16e639dc 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -31,7 +31,8 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf gwa_output_filename = this_dataset.group.name + "_GWA_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) this_chromosomes = this_dataset.species.chromosomes.chromosomes - this_chromosomes_name=[chromosome.name for chromosome in this_chromosomes] + this_chromosomes_name=[this_chromosomes[chromosome].name for chromosome in this_chromosomes] + chr_list_string=",".join(this_chromosomes_name) if covariates != "": |