Fws

Installation

Supported Python versions are 3.10 and 3.11:

python3.11 -m pip install git+https://github.com/bjeight/fws

Fws will run much faster if you have numba installed:

python3.11 -m pip install numba

Use

> Python
Python 3.11.6 (main, Nov 30 2023, 12:53:53) [Clang 15.0.0 (clang-1500.0.40.1)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from fws import fws
>>> help(fws)
Help on function fws in module fws:

fws(a: typing.Annotated[numpy.ndarray[typing.Any, numpy.dtype[~DType]], typing.Literal['N', 2]], input: str = 'AD') -> <built-in function array>
    Calculate Fws for each sample in a population, from an array of biallelic allele depth or genotype information

    Parameters
    ----------
    a : ArrayNxNx2
        numpy.array with shape: (n_sites x n_samples x 2) containing allele depth (AD)
        or genotype (GT) information at biallelic sites for each sample.
    input: str = "AD" [| "GT"]
        specifies what the contents of `a` are - either the allele depth for each allele
        for each sample at each site (the default), or diploid genotype calls.

    Returns
    -------
    np.array[float]
        An array of fws values, in the same order as the samples in the input

You can try the functionality using the numpy arrays in this respository: testdata/AD.npy and testdata/GT.npy:

>>> import numpy as np
>>> from fws import fws
>>>
>>> AD = np.load("path/to/AD.npy")
>>> fws(AD)
array([0.99514152, 0.99817753, 0.99540397, 0.99217399, 0.99927452,
       0.99928477, 0.99831041, 0.99925686, 0.99913666, 0.99934953,
       ...
>>> GT = np.load("path/to/GT.npy")
>>> fws(GT, "GT")
array([0.99937286, 0.99928378, 0.99932071, 0.99837554, 0.99939141,
       0.99950813, 0.99884664, 0.99925243, 0.99962376, 0.99944396,
       ...    

Tests

Require pytest to be installed:

python3.11 -m pip install pytest

then:

> git clone https://github.com/bjeight/fws.git
> cd fws
> pytest