Feat/parse nextclade annotation #1263
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augur ancestral so far only dealt with nucleotide sequences, while translation were done codon by codon from the nucleotide sequences in later steps. If translations for tips are available, the ancestral amino acid sequences can be determined analogously via ancestral reconstruction. This is implemented in this commit. For each node, the node data structure will contain a `muts` and a `aa_muts` field. The latter is a dict with gene/cds names as keys and `<ancestral><pos><derived>` mutations (same as in augur translate). In addition, an annotation and reference sequences are derived stored in the node-data-json.
…notation and translation
1 task
Reorganize functional tests for augur ancestral to follow the standard pattern with "cram" and "data" subdirectories and separate cram files for individual functional tests. Paves the way for adding another functional test for amino acid sequence reconstruction.
Adds amino acid sequences for the corresponding nucleotide alignment in the ancestral data directory (created from augur translate but mimicking output from Nextalign) and adds a functional test for the new interface that allows reconstruction of amino acid sequences for internal nodes from the given tip sequences per gene.
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Description of proposed changes
parse output of genome annotation form nextclade (v3) genemap format
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