Export ancestral AA sequences for tree's root node

[huddlej]

Description of proposed changes

Fixes a bug in the new augur ancestral interface for amino acid sequences where the output JSON was missing an entry for "aa_sequences" for the root node that downstream tools like augur clades relied on. The augur translate output creates this entry [1], so workflows that use the nucleotide ancestral followed by the translate command would not be affected. Workflows that use the new ancestral command would be affected in cases where augur clades looks for amino acid mutations that only exist in the root node and not on any subsequent branches (e.g., for seasonal influenza B/Victoria's NA tree).

[1]

augur/augur/translate.py

Lines 291 to 295 in b299059

	if n==tree.root:
	aa_muts[n.name]={"aa_muts":{}, "aa_sequences":{}}
	for fname, aln in translations.items():
	if n.name in aln:
	aa_muts[n.name]["aa_sequences"][fname] = "".join(aln[n.name])

Examples

Below is an example of a broken subclade annotation for a B/Vic NA tree when the MRCA doesn't date back far enough for subclade amino acid substitutions to occur on branches descending from the root.

In contrast, a recent public Vic NA tree has older sequences, so the MRCA dates back farther and subclades appear as expected.

Re-running augur ancestral and augur clades on the first Vic NA tree above from the code in this PR produces this tree with the expected subclades.

Related issue(s)

Related to #1258

Checklist

• Adds functional test for expected output
• Checks pass
• If making user-facing changes, add a message in CHANGES.md summarizing the changes in this PR

[codecov]

Codecov Report

Patch coverage is 100.00% of modified lines.

❗ Current head 34f2f47 differs from pull request most recent head 1212730. Consider uploading reports for the commit 1212730 to get more accurate results

Files Changed	Coverage
augur/ancestral.py	100.00%

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