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https://github.com/border-lab/xftsim

eXtensible Forward Time SIMulator for complex phenogenetic architectures
https://github.com/border-lab/xftsim

simulation statistical-genetics

Last synced: about 2 months ago
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eXtensible Forward Time SIMulator for complex phenogenetic architectures

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README 

          
 



[![Documentation Status](https://readthedocs.org/projects/xftsim/badge/?version=latest)](https://xftsim.readthedocs.io/en/latest/?badge=latest) [![PyPI version](https://badge.fury.io/py/xftsim.svg)](https://badge.fury.io/py/xftsim)



# eXtensible Forward Time SIMulator

`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



## Installation



`xftsim` is on PyPI. It can be installed in a couple minutes using pip and conda:



```bash

conda create --name xftsim python=3.9.6

conda activate xftsim

pip install xftsim

```



Alternatively, you can install the latest development version from github:



```bash

git clone https://github/rborder/xftsim

cd xftsim

git checkout dev

pip -e . install

```



To enable full functionality (i.e., automatic generation of causal diagrams), you must install [pygraphviz](https://pygraphviz.github.io).



`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

```



## Getting started



To get started, [check out the documentation](https://xftsim.readthedocs.io)!



For a minimal test simulation you can run one of the built in demos (runtime < 1min):

```python3

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)

```



## Notice



`xftsim` is under active development. Please let us know if there are features missing or bugs!