Open jbloom opened 2 years ago
Right now, we're using SouthAfrica/NHLS-UCT-LA-Z957/2022 as basal BA.2. This manifests in multiple locations:
Data files:
data/ba2_outgroup_metadata.tsv
data/ba2_outgroup_sequences/fasta
refine:
root: "SouthAfrica/NHLS-UCT-LA-Z957/2022"
in escape_profiles/escape/builds.yaml
reference
is set in escape_profiles/escape/sequence_to_escape.py
. I grabbed this from the workflow artifact results/escape/translations/aligned.gene.S.fasta
I'm actually not very worried about having to have multiple places where this shows up. However, it would be good to make sure that this is a properly basal BA.2 virus.
Sounds good. Is there a recommended way to determine what is a good basal BA.2 virus?
Right now the spike for the reference is hardcoded into the script Trevor generated (https://github.com/blab/ncov-escape/commit/81e43a2b50b85b55d0b29f3e60380e3eaf54ce7e#diff-54f0382e7ad5485edc0f8936ebc650ad9a30d03bd39bcd4e0b1080800bf757afR15-R17), which doesn't seem ideal. How do we make this better and read from data?