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authorzsloan2020-12-04 15:18:18 -0600
committerzsloan2020-12-04 15:18:18 -0600
commit75ef9f817f8b80f6d4bd732bfede2ad575a50fab (patch)
tree0cc7df07c398625a8ba3c71642fcafc7690232cf
parent48969878b1321e80b55e06ec9367ba428bb2fc36 (diff)
downloadgenenetwork2-75ef9f817f8b80f6d4bd732bfede2ad575a50fab.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.py3
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 != "":