Exclude name from an export

sorgerlab · Jun 11, 2023 · 7f6fc91 · 7f6fc91
1 parent 8c846ba
commit 7f6fc91
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Showing 2 changed files with 7 additions and 3 deletions.
diff --git a/export/famplex_groundings.tsv b/export/famplex_groundings.tsv
@@ -2447,7 +2447,6 @@ TIF-IB	TIF_IB	fplx	Family
 TIM22 complex	TIM22_complex	fplx	Family
 TIM22-complex	TIM22_complex	fplx	Family
 TK	TK	fplx	Family
-TLE	TLE	fplx	Family
 TLE family	TLE	fplx	Family
 TLR	TLR	fplx	Family
 TLR2	O60603	uniprot	Gene_or_gene_product

diff --git a/export/reach_bioresources.py b/export/reach_bioresources.py
@@ -9,6 +9,8 @@
 entities_file = os.path.join(path_this, os.pardir, 'entities.csv')
 
 
+name_exclude = {'TLE'}
+
 def get_groundings():
     groundings = []
     text_appearances = []
@@ -70,10 +72,13 @@ def get_groundings():
             entity_txt = entity.replace('_', '-')
             # If it isn't already a synonym
             if entity_txt not in cnt:
+                if entity in name_exclude:
+                    continue
                 # If the name of the family happens to be a gene symbol
                 # we don't add it
-                if not hgnc_client.get_hgnc_id(entity):
-                    groundings.append((entity_txt, entity, 'fplx', 'Family'))
+                if hgnc_client.get_hgnc_id(entity):
+                    continue
+                groundings.append((entity_txt, entity, 'fplx', 'Family'))
 
     ambiguous_txts = {t for t, c in cnt.items() if c >= 2}
     groundings = [g for g in sorted(groundings) if g[0] not in ambiguous_txts]