xftsim simulates complex phenotype/genotype data with an emphasis on short timescale phenomena. xftsim is designed with two primary goals:
-
make it easy for statistical geneticists to perform reproducible and systematic sensitivity analyses to better understand limitations and assumptions
-
enable evaulation of methods for analyzing complex traits under realistically complex generative models
xftsim is on PyPI. It can be installed in a couple minutes using pip and conda:
conda create --name xftsim python=3.9.6
conda activate xftsim
pip install xftsimAlternatively, you can install the latest development version from github:
git clone https://github/rborder/xftsim
cd xftsim
git checkout dev
pip -e . installTo enable full functionality (i.e., automatic generation of causal diagrams), you must install pygraphviz.
xftsim has been tested on MacOS 13.4 and the following GNU/Linux distributions: Ubuntu 22.04, Ubuntu 24.04, PopOS 22.04, and RHEL 7 using Python version 3.9.6.
`xftsim` depends on the following packages...
asciitree==0.3.3
attrs==23.2.0
cattrs==23.2.3
certifi==2023.11.17
cffi==1.17.1
charset-normalizer==3.3.2
chembl-webresource-client==0.10.9
click==8.1.7
cloudpickle==3.1.0
contourpy==1.2.0
csrgraph==0.1.28
cycler==0.12.1
dask==2024.8.0
dask-expr==1.1.10
dask-glm==0.3.2
dask-ml==2024.4.4
Deprecated==1.2.14
distributed==2024.8.0
easydict==1.13
exceptiongroup==1.2.0
fasteners==0.19
fonttools==4.46.0
fsspec==2024.10.0
funcy==2.0
gensim==4.3.2
idna==3.6
importlib-metadata==8.5.0
importlib-resources==6.1.1
iniconfig==2.0.0
jinja2==3.1.4
joblib==1.3.2
kiwisolver==1.4.5
llvmlite==0.39.1
locket==1.0.0
MarkupSafe==3.0.2
matplotlib==3.8.2
msgpack==1.1.0
multipledispatch==1.0.0
networkx==2.8.8
node2vec==0.4.6
nodevectors==0.1.23
nptyping==2.5.0
numba==0.56.4
numcodecs==0.12.1
numpy==1.23.5
packaging==23.2
pandas==2.1.4
pandas-plink==2.2.9
partd==1.4.2
Pillow==10.1.0
platformdirs==4.2.0
pluggy==1.5.0
psutil==6.1.0
pyarrow==18.0.0
pycparser==2.22
pyparsing==3.1.1
pytest==8.3.3
python-dateutil==2.8.2
pytz==2023.3.post1
PyYAML==6.0.2
rdkit==2023.9.5
requests==2.31.0
requests-cache==1.2.0
scikit-learn==1.3.2
scipy==1.11.4
seaborn==0.13.0
sgkit==0.9.0
six==1.16.0
smart-open==7.0.1
sortedcontainers==2.4.0
sparse==0.15.4
tblib==3.0.0
threadpoolctl==3.2.0
tomli==2.0.2
toolz==1.0.0
tornado==6.4.1
tqdm==4.66.2
typing-extensions==4.10.0
tzdata==2023.3
url-normalize==1.4.3
urllib3==2.1.0
wrapt==1.16.0
xarray==2024.7.0
xftsim==0.2.0
zarr==2.18.2
zict==3.0.0
zipp==3.20.2
zstandard==0.23.0
To get started, check out the documentation!
For a minimal test simulation you can run one of the built in demos (runtime < 1min):
import warnings
warnings.simplefilter(action='ignore', category=FutureWarning)
import xftsim as xft
demo = xft.sim.DemoSimulation('BGRM')
demo.run(3)
xft.utils.print_tree(demo.results)xftsim is under active development. Please let us know if there are features missing or bugs!