fix file handler issue when running as cli (#4)

papaemmelab · May 23, 2024 · 0e55d09 · 0e55d09
1 parent 48ba24d
commit 0e55d09
Showing 1 changed file with 3 additions and 2 deletions.
diff --git a/mergesvvcf/mergedfile.py b/mergesvvcf/mergedfile.py
@@ -270,8 +270,9 @@ def passed_variant(record):
         "String",
         "Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)",
     )
-
-    outfile = open(outfile,'w')
+    # outfile should be a file handler. if it's a file name open it
+    if isinstance(outfile, str):
+        outfile = open(outfile,'w')
     print(outvcf.header, end="", file=outfile)
 
     for variant in sorted(calldict, key=operator.itemgetter(0)):