Fixing tutorial

monarch-initiative · Oct 10, 2023 · 945cebc · 945cebc
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diff --git a/docs/tutorial.rst b/docs/tutorial.rst
@@ -51,7 +51,7 @@ We can then view the data using the list commands.
   [('NP_09876.5', 26)]
   >>> tx_dict = cohort.list_data_by_tx('NM_1234.5')
   >>> sorted(tx_dict['NM_1234.5'].items())
-  [(VariantEffect.FRAMESHIFT_VARIANT, 1), (VariantEffect.MISSENSE_VARIANT, 1)]
+  [('frameshift_variant', 1), ('missense_variant', 1)]
 
 Using the counts, we can choose and run what analyses we want.
 For instance, we can partition the patients into two groups based on presence/absence of a *frameshift* variant:

diff --git a/src/genophenocorr/model/_cohort.py b/src/genophenocorr/model/_cohort.py
@@ -252,7 +252,7 @@ def list_data_by_tx(self, transcript=None):
         for var in self.all_variants:
             for trans in var.tx_annotations:
                 if trans.transcript_id in var_type_dict:
-                    var_type_dict.get(trans.transcript_id).update(trans.variant_effects)
+                    var_type_dict.get(trans.transcript_id).update([var_eff.name for var_eff in trans.variant_effects])
         too_small = []
         for tx_id, var_effect_counter in var_type_dict.items():
             if len(var_effect_counter) <= 1: