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Pathoplexus sequence store and Translation helper

Static sequence and dataset assets served through GitHub Pages for Pathoplexus.

Config

To use translate different Nextclade datasets, pass config options using the snakemake command.

Install micromamba and activate environment using:

 micromamba create -f environment.yaml
 micromamba activate

Example:

snakemake --config dataset_name=nextstrain/ebola/zaire dataset_server="https://raw.githubusercontent.com/nextstrain/nextclade_data/ebola/data_output" output_dir="ebola-zaire"

Note: the dataset_server argument is optional and only needs to be provided when the nextclade dataset is not on the master branch of the nextclade_data repo

If you want to download multiple segments you will have to move the contents of each download as they will otherwise be overwritten by default. An example of how this could be accomplished for influenza is shown below:

mkdir artefacts/influenza/h1n1pdm
mkdir artefacts/influenza/h1n1pdm/segments
mkdir artefacts/influenza/h1n1pdm/genes
segment_names=("pb2" "pb1" "pa" "ha/CY121680" "np" "na/MW626056" "mp" "ns")
for i in {1..8}; do
    segment="${segment_names[i]}"
    echo $segment
    snakemake -F --config dataset_name=nextstrain/flu/h1n1pdm/$segment dataset_server="https://raw.githubusercontent.com/nextstrain/nextclade_data/master/data_output" output_dir="influenza/h1n1pdm/output"
    cp -rn artefacts/influenza/h1n1pdm/output/* artefacts/influenza/h1n1pdm/genes/
    mv artefacts/influenza/h1n1pdm/genes/reference.fasta artefacts/influenza/h1n1pdm/segments/seg$i.fasta
done