From 6bd9983ea67d6f2bbd027dc177fe674ea5a94685 Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Wed, 25 Sep 2024 16:47:06 -0700
Subject: [PATCH] Allow FileNotFoundError to be handled at the top level

The removed error handling is flawed: it assumes that FileNotFoundError
can only come from a missing input file (--sequences). The reality is
that FileNotFoundError can also come from a missing output directory
(--output). The top-level exception handler parses the filepath from the
error directly, which is accurate.
---
 augur/index.py | 14 +++++---------
 1 file changed, 5 insertions(+), 9 deletions(-)

diff --git a/augur/index.py b/augur/index.py
index 883cefd37..4f77432bc 100644
--- a/augur/index.py
+++ b/augur/index.py
@@ -209,15 +209,11 @@ def run(args):
     ("?" and "-"), and other invalid characters in a set of sequences and write
     the composition as a data frame to the given sequence index path.
     '''
-    try:
-        if is_vcf(args.sequences):
-            num_of_seqs = index_vcf(args.sequences, args.output)
-            tot_length = None
-        else:
-            num_of_seqs, tot_length = index_sequences(args.sequences, args.output)
-    except FileNotFoundError:
-        print(f"ERROR: Could not open sequences file '{args.sequences}'.", file=sys.stderr)
-        return 1
+    if is_vcf(args.sequences):
+        num_of_seqs = index_vcf(args.sequences, args.output)
+        tot_length = None
+    else:
+        num_of_seqs, tot_length = index_sequences(args.sequences, args.output)
 
     if args.verbose:
         if tot_length: