This repository aims at gathering various SLiM scripts to help people simulate bacterial populations.
SLiM implements two simulations frameworks, under the Wright-Fisher model or not. Depending on the framework, the simulation are handled differently.
It contains the main scripts to run the simulations under a given SLiM model.
Just create a conda environment by using the following command once you're in this directory:
conda env create
It will install the following dependencies for you:
Clone this repo if you want to share your model, or just download it to reuse an existing one. Chose a model among the one available under Models/. A model defines what we are going to simulate (e.g. a constant population size). Define the parameters for your model, including whether you want to simulate under WF, nonWF or both, and the number of replicates. Examples can be found under params/.
Then, just run:
$ ./scripts/bacterial_slimulation.py params/ConstantSize.json
It will create a folder in your current directory named ConstantSize (after the model's parameter in the .json's file) with the following architecture :
ConstantSize
├── nonWF
│ ├── ConstantSize-100_myScenario
│ │ ├── ConstantSize-100_myScenario_1.npz
│ │ ├── ConstantSize-100_myScenario_1.out
│ │ ├── ConstantSize-100_myScenario_1.time
│ │ ├── ConstantSize-100_myScenario_1_final.trees
│ │ ├── ...
│ └── sumstats
│ ├── ConstantSize-100_myScenario.ld
│ ├── ConstantSize-100_myScenario.sfs
└── WF
├── ConstantSize-100_myScenario
│ ├── ConstantSize-100_myScenario_1.npz
│ ├── ConstantSize-100_myScenario_1.out
│ ├── ConstantSize-100_myScenario_1.time
│ ├── ...
└── sumstats
├── ConstantSize-100_myScenario.ld
├── ConstantSize-100_myScenario.sfs
With a subfolder for WF and nonWF types of simulation.
Within each of these folders, there will be one folder per scenario (as per the scenario: line in the parameter's file.)
It is thus possible to simulate different scenario within the same model, and they will be stored in the same model's scenario.
Replicates are available within each scenario's folder and contains different types of file:
.out: the output of SLiM.npz: the snp matrix an position vector in numpy compressed file format.time: the timing of the burnin and forward part_final.trees: The tree sequence after recapitation, in the nonWF version.
In the folder Other_models, the script are self-contained, and can be executed without the rest of this repo.
It contains the following models:
- Bacteria growing on a Petri dish, half of which contains antibiotics. Resistance mutation may occur, but at a cost in absence of antibiotic. The simulation is spatially constrained.