(c) 2019 Eva Bons

SeqSimEvo - simulations of sequence evolution with selection

Installation

installation requires a working installation of python (v2.7 or higher)

python setup.py install

Usage

Simulations can be run in several ways:

• run a pre-existing scenario

Initialize the simulation

from SeqSimEvo import simulation

sim = simulation.Simulation(simulation_settings)

simulation settings can be set by

• providing a default (currently, 'HIV' and 'phix174' are available)

    sim = seq_sim.Simulation(simulation_settings)
  

• pointing to your own settings file (a template is available in the folder simulation_settings):

    sim = seq_sim.Simulation(simulation_settings = 'path/to/my/settings')
  

• providing the settings as keyword arguments (this is always possible, and will override settings provided in a settings file): e.g.

    sim = seq_sim.Simulation(mut_rate = 1e-10, model='lognormal', parameters = {'fl': 0.2, 'mu':0.2, 'sigma': 0.2})
    sim = seq_sim.Simulation('phix174', model='spikes')
  

see help(simulation.Simulation) for all possible settings

Run a simulation

for gen in range(nr_gen):
    sim.new_generation()

Get output

• for fasta output of any number of sequences (use nseq = sim.current_gen.n_seq for all sequences in the simulation)

    sim.current_gen.to_fasta(n_seq)
  

• to see some statistics

    sim.current_gen.stats()
  

Scenarios - simulation of specific scenarios using SeqSimEvo

The GUI

Usage

• run SeqSimEvo_gui in the terminal
• choose the organism and scenarios
• change settings if required (changes are not saved to the original file!)
• run a simulation
• view results (fasta, highlighter or neighbor-joining tree)

Adding new scenarios

Write a python function for the new scenario, make sure it can take a library with scenario_settings and organism_settings as arguments and returns a string formatted as a fasta-file

new_scenario(scenario_settings, organism_settings)

Add an entry to the run funtion in scenarios.py

if scenario == 'NewScenario':
  fasta = new_scenario(scenario_settings, organism_settings)

Add a settings file (or template) to settings_files. the File type must be of the format NewScenario[_something]

Making new settings files

• Everything before the underscore must match what is checked in the if-statement in the run-function in scenarios.py for this scenarios
• The file must be in the 'yaml' format (http://www.yaml.org/spec/1.2/spec.html)
• Due to issues with scientific notation parsing, it is important to always use a decimal point when using scientific notation of numbers (1.0e5 rather than 1e5)

Simple simulation

simply run a simulation for a certain number of generations.

run SeqSimEvo_simpleSim [options] in the terminal.

see SeqSimEvo_simpleSim -h

recreate dataset

run a simulation of sequence diversification until the number of unique mutations matches that in a given dataset

run SeqSimEvo_recreateDataset [options] in the terminal.

see SeqSimEvo_recreateDataset -h for all options.

multiple multiple_compartments

run a simulations with multiple compartments, with migration between the compartments

run SeqSimEvo_multipleCompartments [options] in the terminal.

see SeqSimEvo_multipleCompartments -h