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viruspop

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  • VIRUS POP

    Virus Pop is a tool for building fake realistic viral protein sequences belonging to a taxonomic group given as input.

    Installing

    This pipeline needs snakemake (eg. via pip pip3 install snakemake) and Apptainer to be installed.

    Let $MV_DIR be the directory in which Virus Pop is located.

    Clone the repository

    git clone git@gitlab.pasteur.fr:ldp/mock-viruses.git

    Then the singularity container has to be build (as root or with sudo, only needed for building, not for usage):

    cd $MV_DIR/Virus_Pop
    sudo singularity build singularity/virus_pop.sif singularity/virus_pop.def

    Examples

    cd $MV_DIR/Virus_Pop
    
    # fetch as much as much as 15 genomes per species, work on clusters of at least 20 sequences
    python3 ./run_virus_pop.py group_name Orthopneumovirus Orthopneumovirus_simu -t 15 -s 20
    # load the real protein trees in iTOL (usefull to choose none where you want to branch simulations)
    python3 ./load_in_ITOL.py Orthopneumovirus_simu --ITOL_info ${your_itol_batch_number} ${existing_itol_project_name}
    
    # fetch as much as much 15 genomes per species and generate simulations on all ancestral nodes
    python3 ./run_virus_pop.py group_name Pestivirus Pestivirus_simu -t 15 --all_ancestral_nodes
    
    # use the provided homologous dataset, generate 2 ancestral sequences at each internal node and simulate the specified distances and infer tree with the simulations
    python3 ./run_virus_pop.py homologous_protein_file DATA_example/sarbecovirus.spike.fa Sarbecovirus_spike_simu --all_ancestral_nodes -n 2 --evolution_distance '0.1 0.5 1 2 3 4 5'