From 6e8afe5a6871a680778bfaed6b79c934b33d0307 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 28 Apr 2021 19:40:58 +0000
Subject: Account for temp traits when adding covariates with GEMMA mapping

---
 wqflask/wqflask/marker_regression/gemma_mapping.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

(limited to 'wqflask')

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)
-- 
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