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Pythonanywhere platform: Compute the Cross-Reactivity between two lineages

(OBSOLETE)

Binder platform: Compute the Cross-Reactivity between two lineages

Dependencies

See VASIL repository

Run Simulations With Vaccination Timeline Included

Step 0:

First, run the main pipeline VASIL as instructed here if the following necessary files are not present in your working directory (e.g., working_directory = data/ByCountry/Germany)

• "working_directory/Daily_SpikeGroups_Freq.csv"
• "working_directory/results/Cross_react_dic_spikegroups_ALL.pck"
• "working_directory/Spikegroups_membership.pck"

Step 1: Adapt scripts/Vaccination/Process_Vaccination_Timeline.py to your problem

• Add vaccination timeline dataset in the working directory ... For example, data/ByCountry/Germany/germany_vaccinations_timeseries_v3.csv

Check if scripts/Vaccination/Process_Vaccination_Timeline.py contains elements in the vaccination timeline dataset and edit if needed. The name of the variant representing the vaccine is added to the name of each vaccine considered (from the front): The mutation profile of this variant is used to compute a neutralization probability that corresponds to the vaccine, and this variant must be listed in the file working_directory/Daily_SpikeGroups_Freq.csv dataset, otherwise there will be a code error

Step 2: Run snakemake pipeline (run twice to complete)

• Configure parameters working_directory/vacc_config.yaml ... For example, working_directory = data/ByCountry/Germany
• Run the snakemake pipeline from the terminal

  snakemake --snakefile VACC --configfile working_directory/vacc_config.yaml -j -d working_directory
  

• The results will be found in a newly created or updated directory working_directory/vaccination. The RELEVANT results are
  • Directory working_directory/vaccination/Immunological_Landscape_ALL contains the immune landscape without vaccination, and the weighted mean is working_directory/vaccination/Susceptible_weighted_mean_over_spikegroups_all_PK.csv
  • Directory working_directory/vaccination/ImL_ALL_cs_Vacc_ver2 contains the immune landscape with vaccination, and the weighted mean is working_directory/vaccination/Susceptible_weighted_mean_over_spikegroups_vs_Vacc_ver2_all_PK.csv
  • Directory working_directory/vaccination/Timeline contains vaccination timeline (total, and per vaccine)
  • Directory working_directory/vaccination/Cross_Vacc contains cross-reactivity between variants in the timeline and vaccines
  • Directory working_directory/vaccination/plots/ALL_vs_Vacc_ver2 contains plots of the results with vaccination
  • Directory working_directory/vaccination/plots/relative_groups contains plots of the relative fitness for simulations including vaccination (as requested in working_directory/vacc_config.yaml)