fixed bug when looking for symbols matches with * alleles

jeremymcrae · Aug 18, 2017 · 12ccb48 · 12ccb48
1 parent 73b3ce3
commit 12ccb48
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Showing 2 changed files with 7 additions and 2 deletions.
diff --git a/clinicalfilter/reporting.py b/clinicalfilter/reporting.py
@@ -144,7 +144,12 @@ def _get_output_line(candidate, family):
 
     prefs = ['HGNC', 'SYMBOL']
 
-    genes = [ var.child.info.symbols[0].get(x, prefs) for x in candidate[3] ]
+    for x in var.child.info.symbols:
+        try:
+            genes = [ x.get(y, prefs) for y in candidate[3] ]
+            break
+        except KeyError:
+            continue
     genes = [ x for x in genes if x is not None ]
     genes = ','.join(sorted(set(genes)))
     result = ','.join(sorted(candidate[1]))

diff --git a/setup.py b/setup.py
@@ -20,7 +20,7 @@
 
 setup(
     name = "clinical-filter",
-    version = "0.5.2",
+    version = "0.5.3",
     author = "Jeremy McRae",
     author_email = "jeremy.mcrae@sanger.ac.uk",
     description="Clinical filtering for trios.",