Forward-time simulation of the msprime data structure (for development)
An earlier version of this code was mentioned during the Evolution 2017 talk:
Ashander, McCartney-Melstad, Ralph, Shaffer (2017) "Using Genomic Data to Inform Population Viability in a Long-Lived Endangered Vertebrate".
Note the code is pre-production but if you're building on the ideas here please cite this repository using the DOI:
The current version of this package (on HEAD
) works with msprime version 0.6.1 (current as of Oct 17 2018).
For the earlier version, used in the paper, get tag 0.0.6.
The purpose of this package is to provide python code to easily store ancestry information from a forwards-time, individual-based simulation, using msprime's "tree sequence" data format, so that after the simulation, we can
We also provide a class to facilitate doing this with simuPOP.
ftprime/argrecorder.py: Provides ARGrecorder
, which records haploid parentage and crossing over events.
ftprime/recomb_collector.py: Provides RecombCollector
, which does the bookkeeping to use ARGrecorder
with a diploid simulation with discrete loci, whose function collect_recombs
can be used as output for simuPOP's Recombinator
operator.
Tests:
ARGrecorder
.RecombCollector
.Test status and code coverage:
Clone:
git clone https://github.com/ashander/ftprime.git
cd ftprime
For best results, use miniconda,
which provides the command line dependency manager conda
.
Once you have it installed, make a new environment to do development:
conda config --add channels conda-forge
conda env create -f environment.yml -n ftprime python=3.5
source activate ftprime # Enter the development environment
Install tortoisim
in locally editable (-e
) mode and run the tests.
After the pip
command you should see a bunch of messages about requirements
already satisfied (because you've installed them with conda
, above):
pip install -e .[dev] # Don't need the [dev] if you used conda above
pytest
Legacy interface:
MeiosisTagger
, which can be used as an IdTagger in simuPOPARGrecorder
.Documentation of the problem and the methods:
Since there are many different ways to store an ARG as a set of coalescence records, a good deal of this is devoted to describing and verifying msprime's requirements for such a set, and thinking about different ways to do it.