From aae0640f7b25d19520d52dd8e1a39b8ea8dab694 Mon Sep 17 00:00:00 2001
From: Cornelius Roemer <cornelius.roemer@gmail.com>
Date: Tue, 26 Sep 2023 04:56:56 +0200
Subject: [PATCH] Add test for ancestral --genes file

---
 .../infer-amino-acid-sequences-genes-file.t   | 22 +++++++++++++++++++
 tests/functional/ancestral/data/genes.txt     |  2 ++
 2 files changed, 24 insertions(+)
 create mode 100644 tests/functional/ancestral/cram/infer-amino-acid-sequences-genes-file.t
 create mode 100644 tests/functional/ancestral/data/genes.txt

diff --git a/tests/functional/ancestral/cram/infer-amino-acid-sequences-genes-file.t b/tests/functional/ancestral/cram/infer-amino-acid-sequences-genes-file.t
new file mode 100644
index 000000000..09ed75bb4
--- /dev/null
+++ b/tests/functional/ancestral/cram/infer-amino-acid-sequences-genes-file.t
@@ -0,0 +1,22 @@
+Setup
+
+  $ source "$TESTDIR"/_setup.sh
+
+Infer ancestral nucleotide and amino acid sequences, using a genes file.
+
+  $ ${AUGUR} ancestral \
+  >  --tree $TESTDIR/../data/tree.nwk \
+  >  --alignment $TESTDIR/../data/aligned.fasta \
+  >  --annotation $TESTDIR/../data/zika_outgroup.gb \
+  >  --genes $TESTDIR/../data/genes.txt \
+  >  --translations $TESTDIR/../data/aa_sequences_%GENE.fasta \
+  >  --output-node-data ancestral_mutations.json \
+  >  --output-sequences ancestral_sequences.fasta \
+  >  --output-translations ancestral_aa_sequences_%GENE.fasta > /dev/null
+
+Check that the reference length was correctly exported as the nuc annotation
+
+  $ grep -E "\"(ENV|PRO|nuc)\": {" ancestral_mutations.json
+      "ENV": {
+      "PRO": {
+      "nuc": {
diff --git a/tests/functional/ancestral/data/genes.txt b/tests/functional/ancestral/data/genes.txt
new file mode 100644
index 000000000..7451d03eb
--- /dev/null
+++ b/tests/functional/ancestral/data/genes.txt
@@ -0,0 +1,2 @@
+ENV
+PRO