fixup! merge: Support sequences

augur/merge.py

@@ -617,6 +617,10 @@ def merge_sequences(
                 print_info(f"Reading sequences from {s.path!r}…")
                 subprocess.Popen(cat(s.path), stdout=f)
 
+                # Add an newline character to support FASTA files that are missing one at the end.
+                # Extraneous newline characters are stripped by seqkit.
+                print(file=f)
+
         print_info(f"Merging sequences and writing to {output_sequences!r}…")
         process = seqkit('rmdup', temp_file.name, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
 

tests/functional/merge/cram/merge-sequences.t

@@ -58,3 +58,28 @@ Duplicates are not allowed within individual sequence inputs.
     'three'
 
   [2]
+
+FASTA files without trailing newlines are supported.
+
+  $ cat >y.fasta <<~~
+  > >two
+  > ATCG
+  > >three
+  > GCTA
+  > ~~
+
+  $ truncate -s -1 x.fasta
+  $ truncate -s -1 y.fasta
+
+  $ ${AUGUR} merge \
+  >   --sequences x.fasta y.fasta \
+  >   --output-sequences - > merged.fasta \
+  >   --quiet
+
+  $ cat merged.fasta
+  >two
+  ATCG
+  >three
+  GCTA
+  >one
+  ATCG