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Add failing test for ancestral --genes file #1319 #1320

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Add failing test for ancestral --genes file #1319 #1320

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22 changes: 22 additions & 0 deletions tests/functional/ancestral/cram/infer-amino-acid-sequences-genes-file.t
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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 $TESTDIR/../data/aa_sequences_%GENE.fasta \
> --output-node-data "$CRAMTMP/$TESTFILE/ancestral_mutations.json" \
> --output-sequences "$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": {
2 changes: 2 additions & 0 deletions tests/functional/ancestral/data/genes.txt
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ENV
PRO
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