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