Merge pull request #1317 from nextstrain/export-root-aa-sequences-fro…

…m-ancestral

Export ancestral AA sequences for tree's root node

CHANGES.md

@@ -5,15 +5,20 @@
 ### Features
 
 * Support treetime 0.11.* [#1310][] (@corneliusroemer)
-* Allow minimal export using only a (newick) tree in `augur export v2`. [#1299][] (@jameshadfield)
+* export: Allow minimal export using only a (newick) tree in `augur export v2`. [#1299][] (@jameshadfield)
 * A number of schema updates and improvements [#1299][] (@jameshadfield)
     * We now require all nodes to have `node_attrs` on them with one of `div` or `num_date` present
     * Some never-used properties are removed from the schemas, including a pattern for defining nucleotide INDELs which was never used by augur or auspice.
     * Tip label defaults are now settable within the auspice-config JSON
     * Empty colorings definitions are allowed (the tree will be grey in Auspice)
 
-[#1310]: https://github.com/nextstrain/augur/pull/1310
+### Bug fixes
+
+* ancestral: Export amino acid sequences inferred for the root node of the tree in the node data JSON output for compatibility with `augur translate` output. [#1317][] (@huddlej)
+
 [#1299]: https://github.com/nextstrain/augur/pull/1299
+[#1310]: https://github.com/nextstrain/augur/pull/1310
+[#1317]: https://github.com/nextstrain/augur/pull/1317
 
 ## 23.0.0 (5 September 2023)
 

augur/ancestral.py

@@ -323,6 +323,14 @@ def run(args):
             for key, node in anc_seqs['nodes'].items():
                 if 'aa_muts' not in node: node['aa_muts'] = {}
                 node['aa_muts'][gene] = aa_result['mutations']['nodes'][key]['muts']
+
+                # Add amino acid sequences to the root node of the tree.
+                if key == T.root.name:
+                    if "aa_sequences" not in node:
+                        node["aa_sequences"] = {}
+
+                    node["aa_sequences"][gene] = aa_result['tt'].sequence(T.root, as_string=True, reconstructed=True)
+
             anc_seqs['reference'][gene] = aa_result['root_seq']
             # FIXME: Note that this is calculating the end of the CDS as 3*length of translation
             # this is equivalent to the annotation for single segment CDS, but not for cds

tests/functional/ancestral/cram/infer-amino-acid-sequences.t

@@ -21,6 +21,13 @@ Check that the reference length was correctly exported as the nuc annotation
       "PRO": {
       "nuc": {
 
+Check that amino acid sequences exist for the root node of the tree.
+
+  $ grep -A 2 "aa_sequences" "$CRAMTMP/$TESTFILE/ancestral_mutations.json"
+        "aa_sequences": {
+          "ENV": .* (re)
+          "PRO": .* (re)
+
 Check that internal nodes have ancestral amino acid sequences.
 
   $ grep "NODE" "$CRAMTMP/$TESTFILE/ancestral_aa_sequences_ENV.fasta" | wc -l