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authorzsloan2021-05-25 20:49:48 +0000
committerzsloan2021-05-25 20:49:48 +0000
commit666494b49bef48a46145cf415262d532530aba46 (patch)
tree4f8dde2b5d72ace719cf7698ab1e9ac9b16b52ec
parent4d15c32e7d86885cffce1720db0df394bd6a02ff (diff)
downloadgenenetwork2-666494b49bef48a46145cf415262d532530aba46.tar.gz
Fixed/shortened get_categorical_variables function and correctly pass them to show_trait template
-rw-r--r--wqflask/wqflask/show_trait/show_trait.py18
1 files changed, 5 insertions, 13 deletions
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 837c7a54..a02da872 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -279,6 +279,8 @@ class ShowTrait:
hddn['suggestive'] = 0
hddn['num_perm'] = 0
hddn['categorical_vars'] = ""
+ if categorical_var_list:
+ hddn['categorical_vars'] = ",".join(categorical_var_list)
hddn['manhattan_plot'] = ""
hddn['control_marker'] = ""
if not self.temp_trait:
@@ -684,23 +686,13 @@ def get_ncbi_summary(this_trait):
return None
-def get_categorical_variables(this_trait, sample_list):
+def get_categorical_variables(this_trait, sample_list) -> list:
categorical_var_list = []
if len(sample_list.attributes) > 0:
for attribute in sample_list.attributes:
- attribute_vals = []
- for sample_name in list(this_trait.data.keys()):
- if sample_list.attributes[attribute].name in this_trait.data[sample_name].extra_attributes:
- attribute_vals.append(
- this_trait.data[sample_name].extra_attributes[sample_list.attributes[attribute].name])
- else:
- attribute_vals.append("N/A")
- num_distinct = len(set(attribute_vals))
-
- if num_distinct < 10:
- categorical_var_list.append(
- sample_list.attributes[attribute].name)
+ if len(sample_list.attributes[attribute].distinct_values) < 10:
+ categorical_var_list.append(sample_list.attributes[attribute].name)
return categorical_var_list