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authorzsloan2021-04-28 19:40:58 +0000
committerzsloan2021-04-28 19:40:58 +0000
commit6e8afe5a6871a680778bfaed6b79c934b33d0307 (patch)
tree59f2fe617f66832da1b951804fe4d5101a3e43d3 /wqflask
parent68ee0a995fceaf6aefdd3c8f780e46a83b51a0e8 (diff)
downloadgenenetwork2-6e8afe5a6871a680778bfaed6b79c934b33d0307.tar.gz
Account for temp traits when adding covariates with GEMMA mapping
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/wqflask/marker_regression/gemma_mapping.py7
1 files changed, 6 insertions, 1 deletions
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 83ebcdf9..06c9300a 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -146,7 +146,12 @@ def gen_covariates_file(this_dataset, covariates, samples):
for covariate in covariate_list:
this_covariate_data = []
trait_name = covariate.split(":")[0]
- dataset_ob = create_dataset(covariate.split(":")[1])
+ dataset_name = covariate.split(":")[1]
+ if dataset_name == "Temp":
+ temp_group = trait_name.split("_")[2]
+ dataset_ob = create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = temp_group)
+ else:
+ dataset_ob = create_dataset(covariate.split(":")[1])
trait_ob = create_trait(dataset=dataset_ob,
name=trait_name,
cellid=None)