Update functional test to reflect the ancestral aa outputs

This should fail.
nextstrain · Aug 3, 2023 · d641e95 · d641e95
1 parent ad51e1f
commit d641e95
Showing 1 changed file with 7 additions and 1 deletion.
diff --git a/tests/functional/ancestral/cram/infer-amino-acid-sequences.t b/tests/functional/ancestral/cram/infer-amino-acid-sequences.t
@@ -11,11 +11,17 @@ Infer ancestral nucleotide and amino acid sequences.
   >  --genes ENV PRO \
   >  --translations $TESTDIR/../data/aa_sequences_%GENE.fasta \
   >  --output-node-data "$CRAMTMP/$TESTFILE/ancestral_mutations.json" \
-  >  --output-sequences "$CRAMTMP/$TESTFILE/ancestral_sequences.fasta" > /dev/null
+  >  --output-sequences "$CRAMTMP/$TESTFILE/ancestral_sequences.fasta" \
+  >  --output-translations "$CRAMTMP/$TESTFILE/ancestral_aa_sequences_%GENE.fasta" > /dev/null
 
 Check that the reference length was correctly exported as the nuc annotation
 
   $ grep -E "\"(ENV|PRO|nuc)\": {" "$CRAMTMP/$TESTFILE/ancestral_mutations.json"
       "ENV": {
       "PRO": {
       "nuc": {
+
+Check that internal nodes have ancestral amino acid sequences.
+
+  $ grep "NODE" "$CRAMTMP/$TESTFILE/ancestral_aa_sequences_ENV.fasta" | wc -l
+  \s*0 .* (re)