Feat/parse nextclade annotation #1263
Open
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
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.
victorlin
force-pushed
the
feat/aa-ancestral
branch
from
0b1c44a
to
f740b14
Compare
huddlej
force-pushed
the
feat/aa-ancestral
branch
from
c4c2dec
to
7cfbd9b
Compare
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Description of proposed changes
parse output of genome annotation form nextclade (v3) genemap format
Checklist