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# tstrait | ||
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**tstrait** is a Quantitative trait simulator of [tskit](https://tskit.readthedocs.io/) tree sequences. It supports simulation from various trait models, and the details of the package are indicated in the [documentation]. | ||
**tstrait** is a quantitative trait simulator of [tskit](https://tskit.readthedocs.io/) tree sequences. | ||
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- Documentation: | ||
- Source code: https://github.com/tskit-dev/tstrait | ||
- Tree sequence documentation: https://tskit.dev/learn/ | ||
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It provides: | ||
- Simulation of quantitative traits | ||
- Simulation of genetic effect sizes from various distributions | ||
- Simulation of pleiotropic phenotypes | ||
- Simulation of environmental noise | ||
- Computation of individual genetic values given the effect sizes of causal mutations |
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msprime | ||
numba | ||
numpy | ||
packaging | ||
pandas | ||
pre-commit | ||
pytest | ||
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[metadata] | ||
name = tstrait | ||
version = 0.0.1 | ||
license = MIT | ||
author = Daiki Tagami | ||
author_email = [email protected] | ||
description = Quantitative trait simulation | ||
#long_description_content_type = text/markdown | ||
#long_description = file: README.md | ||
#url = https://github.com/daikitag/tstrait | ||
maintainer = Tskit Developers | ||
maintainer_email = [email protected] | ||
description = Quantitative trait simulation of tree sequence data | ||
long_description = file: README.md | ||
long_description_content_type = text/markdown | ||
url = https://tskit.dev/tstrait/ | ||
auuthor = Daiki Tagami et al. | ||
download_url = https://pypi.python.org/pypi/tstrait | ||
project_urls = | ||
Github = https://github.com/daikitag/tstrait | ||
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classifiers = | ||
Programming Language :: Python :: 3 | ||
Bug Tracker = https://github.com/tskit-dev/tstrait/issues | ||
Documentation = https://tskit.dev/tstrait/docs/ | ||
Source Code = https://github.com/tskit-dev/tstrait | ||
license = MIT | ||
classifiers = | ||
Development Status :: 5 - Production/Stable | ||
Intended Audience :: Science/Research | ||
Intended Audience :: Developers | ||
License :: OSI Approved :: MIT License | ||
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Programming Language :: Python | ||
Programming Language :: Python :: 3 | ||
Programming Language :: Python :: 3.8 | ||
Programming Language :: Python :: 3.9 | ||
Programming Language :: Python :: 3.10 | ||
Programming Language :: Python :: 3.11 | ||
Programming Language :: Python :: 3 :: Only | ||
Topic :: Scientific/Engineering | ||
Topic :: Scientific/Engineering :: Bio-Informatics | ||
Operating System :: Microsoft :: Windows | ||
Operating System :: POSIX | ||
Operating System :: MacOS | ||
platforms = | ||
POSIX | ||
Windows | ||
MacOS X | ||
keywords = | ||
gwas | ||
population genetics | ||
quantitative trait | ||
simulation | ||
statistical genetics | ||
tree sequence | ||
tskit | ||
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[options] | ||
packages = tstrait | ||
python_requires = >=3.7 | ||
python_requires = >=3.8 | ||
install_requires = | ||
numpy | ||
numba>=0.57.0 | ||
pandas | ||
tskit>=0.5.5 | ||
setup_requires = | ||
setuptools_scm | ||
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[options.extras_require] | ||
tests = | ||
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import setuptools | ||
from setuptools import setup | ||
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if __name__ == "__main__": | ||
setuptools.setup() | ||
setup( | ||
use_scm_version={"write_to": "tstrait/_version.py"}, | ||
) |
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import tstrait | ||
from tstrait.provenance import __version__ | ||
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class TestVersion: | ||
def test_version(self): | ||
assert tstrait.__version__ == __version__ |
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from tstrait.simulate_effect_size import sim_trait | ||
from tstrait.simulate_effect_size import TraitSimulator | ||
from tstrait.simulate_phenotype import GenotypeResult | ||
from tstrait.simulate_phenotype import PhenotypeResult | ||
from tstrait.simulate_phenotype import PhenotypeSimulator | ||
from tstrait.simulate_phenotype import Result | ||
from tstrait.simulate_phenotype import sim_phenotype | ||
from tstrait.trait_model import trait_model | ||
from tstrait.trait_model import TraitModel | ||
from tstrait.trait_model import TraitModelExponential | ||
from tstrait.trait_model import TraitModelFixed | ||
from tstrait.trait_model import TraitModelGamma | ||
from tstrait.trait_model import TraitModelMultivariateNormal | ||
from tstrait.trait_model import TraitModelNormal | ||
from tstrait.trait_model import TraitModelT | ||
""" | ||
tstrait | ||
======= | ||
tstrait is a quantitative trait simulator of a tree sequence data. | ||
See https://tskit.dev/ for complete documentation. | ||
""" | ||
from .provenance import __version__ # NOQA | ||
from .simulate_effect_size import sim_trait | ||
from .simulate_effect_size import TraitSimulator | ||
from .simulate_phenotype import GenotypeResult | ||
from .simulate_phenotype import PhenotypeResult | ||
from .simulate_phenotype import PhenotypeSimulator | ||
from .simulate_phenotype import Result | ||
from .simulate_phenotype import sim_phenotype | ||
from .trait_model import trait_model | ||
from .trait_model import TraitModel | ||
from .trait_model import TraitModelExponential | ||
from .trait_model import TraitModelFixed | ||
from .trait_model import TraitModelGamma | ||
from .trait_model import TraitModelMultivariateNormal | ||
from .trait_model import TraitModelNormal | ||
from .trait_model import TraitModelT | ||
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__all__ = [ | ||
"TraitSimulator", | ||
"__version__", | ||
"sim_trait", | ||
"sim_phenotype", | ||
"PhenotypeSimulator", | ||
"Result", | ||
"TraitSimulator", | ||
"GenotypeResult", | ||
"PhenotypeResult", | ||
"PhenotypeSimulator", | ||
"Result", | ||
"sim_phenotype", | ||
"trait_model", | ||
"TraitModel", | ||
"TraitModelExponential", | ||
"TraitModelFixed", | ||
"TraitModelGamma", | ||
"TraitModelMultivariateNormal", | ||
"TraitModelNormal", | ||
"TraitModelT", | ||
"TraitModelMultivariateNormal", | ||
] |
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__version__ = "undefined" | ||
try: | ||
from . import _version | ||
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__version__ = _version.version | ||
except ImportError: # pragma: nocover | ||
pass |