WISE mutation frequency data uploader

This script helps upload metadata to https://wise-loculus.genspectrum.org/ for use in https://genspectrum.org/swiss-wastewater/rsv and https://genspectrum.org/swiss-wastewater/influenza.

It assumes metadata is a tsv format, with the columns:

• submissionId: string
• reference: string
• primerProtocol: string
• date: string, format YYYY-MM-DD
• location: string
• nucleotideMutationFrequency: string, json object with format "{""A10052G"": null, ""T9956C"": 0.0}"
• aminoAcidMutationFrequency: string, json object with format "{""A10052G"": null, ""T9956C"": 0.0}"
• lineageFrequencyEstimates: string, json object with format "{""lineage"": null, ""lineage"": ""xx""}"

SubmissionId should be unique for each sample (reference, date, location pair).

Installation

Run this script by first installing and activating micromamba:

micromamba create -f environment.yaml
micromamba activate uploader

You then need to add your password and username to the config.yaml to submit sequences - by default this script submits to group 1 (WISE) but this can be altered in the config.

python scripts/upload_data.py --data-folder {PATH} --config-file config.yaml --organism {ORGANISM}

All metadata from the same organism should be kept in the same data-folder, organism, can take values influenza or rsv.

WARNING!! This script assumes that (date, location, reference) pairs are unique, even if they are split up among files - but it doesn't verify this! Please check that this is true before running this script.

For example, for RSV submissionIds were duplicated across files. Each RSV-B and RSV-A sample was in both files, but each file only had mutations to one reference, i.e. only mutations from RSV-B or RSV-A. Thus, the empty duplications, i.e. RSV-B sequences in the RSV-A results file had to be removed before running the script. I did this using the commands:

tsv-filter   --header --str-eq  2:RSV-A data/WISE-rsv/timeline_mutation_multiple_batches_EPI_ISL_412866.tsv > timeline_mutation_multiple_batches_EPI_ISL_412866_filtered.tsv

tsv-filter  --header --str-eq  2:RSV-B data/WISE-rsv/timeline_mutation_multiple_batches_EPI_ISL_1653999.tsv > timeline_mutation_multiple_batches_EPI_ISL_1653999_filtered.tsv