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pandas-plink

Pandas-plink is a Python package for reading PLINK binary file format and realized relationship matrices (PLINK or GCTA). The file reading is taken place via lazy loading, meaning that it saves up memory by actually reading only the genotypes that are actually accessed by the user.

Notable changes can be found at the CHANGELOG.md.

Install

It can be installed using pip:

pip install pandas-plink

Alternatively it can be intalled via conda:

conda install -c conda-forge pandas-plink

Usage

It is as simple as

>>> from pandas_plink import read_plink1_bin
>>> G = read_plink1_bin("chr11.bed", "chr11.bim", "chr11.fam", verbose=False)
>>> print(G)
<xarray.DataArray 'genotype' (sample: 14, variant: 779)>
dask.array<shape=(14, 779), dtype=float64, chunksize=(14, 779)>
Coordinates:
  * sample   (sample) object 'B001' 'B002' 'B003' ... 'B012' 'B013' 'B014'
  * variant  (variant) object '11_316849996' '11_316874359' ... '11_345698259'
    father   (sample) <U1 '0' '0' '0' '0' '0' '0' ... '0' '0' '0' '0' '0' '0'
    fid      (sample) <U4 'B001' 'B002' 'B003' 'B004' ... 'B012' 'B013' 'B014'
    gender   (sample) <U1 '0' '0' '0' '0' '0' '0' ... '0' '0' '0' '0' '0' '0'
    i        (sample) int64 0 1 2 3 4 5 6 7 8 9 10 11 12 13
    iid      (sample) <U4 'B001' 'B002' 'B003' 'B004' ... 'B012' 'B013' 'B014'
    mother   (sample) <U1 '0' '0' '0' '0' '0' '0' ... '0' '0' '0' '0' '0' '0'
    trait    (sample) <U2 '-9' '-9' '-9' '-9' '-9' ... '-9' '-9' '-9' '-9' '-9'
    a0       (variant) <U1 'C' 'G' 'G' 'C' 'C' 'T' ... 'T' 'A' 'C' 'A' 'A' 'T'
    a1       (variant) <U1 'T' 'C' 'C' 'T' 'T' 'A' ... 'C' 'G' 'T' 'G' 'C' 'C'
    chrom    (variant) <U2 '11' '11' '11' '11' '11' ... '11' '11' '11' '11' '11'
    cm       (variant) float64 0.0 0.0 0.0 0.0 0.0 0.0 ... 0.0 0.0 0.0 0.0 0.0
    pos      (variant) int64 157439 181802 248969 ... 28937375 28961091 29005702
    snp      (variant) <U9 '316849996' '316874359' ... '345653648' '345698259'
>>> print(G.sel(sample="B003", variant="11_316874359").values)
0.0
>>> print(G.a0.sel(variant="11_316874359").values)
G
>>> print(G.sel(sample="B003", variant="11_316941526").values)
2.0
>>> print(G.a1.sel(variant="11_316941526").values)
C

Portions of the genotype will be read as the user access them.

Covariance matrices can also be read very easily. Example:

>>> from pandas_plink import read_rel
>>> K = read_rel("plink2.rel.bin")
>>> print(K)
<xarray.DataArray (sample_0: 10, sample_1: 10)>
array([[ 0.885782,  0.233846, -0.186339, -0.009789, -0.138897,  0.287779,
         0.269977, -0.231279, -0.095472, -0.213979],
       [ 0.233846,  1.077493, -0.452858,  0.192877, -0.186027,  0.171027,
         0.406056, -0.013149, -0.131477, -0.134314],
       [-0.186339, -0.452858,  1.183312, -0.040948, -0.146034, -0.204510,
        -0.314808, -0.042503,  0.296828, -0.011661],
       [-0.009789,  0.192877, -0.040948,  0.895360, -0.068605,  0.012023,
         0.057827, -0.192152, -0.089094,  0.174269],
       [-0.138897, -0.186027, -0.146034, -0.068605,  1.183237,  0.085104,
        -0.032974,  0.103608,  0.215769,  0.166648],
       [ 0.287779,  0.171027, -0.204510,  0.012023,  0.085104,  0.956921,
         0.065427, -0.043752, -0.091492, -0.227673],
       [ 0.269977,  0.406056, -0.314808,  0.057827, -0.032974,  0.065427,
         0.714746, -0.101254, -0.088171, -0.063964],
       [-0.231279, -0.013149, -0.042503, -0.192152,  0.103608, -0.043752,
        -0.101254,  1.423033, -0.298255, -0.074334],
       [-0.095472, -0.131477,  0.296828, -0.089094,  0.215769, -0.091492,
        -0.088171, -0.298255,  0.910274, -0.024663],
       [-0.213979, -0.134314, -0.011661,  0.174269,  0.166648, -0.227673,
        -0.063964, -0.074334, -0.024663,  0.914586]])
Coordinates:
  * sample_0  (sample_0) object 'HG00419' 'HG00650' ... 'NA20508' 'NA20753'
  * sample_1  (sample_1) object 'HG00419' 'HG00650' ... 'NA20508' 'NA20753'
    fid       (sample_1) object 'HG00419' 'HG00650' ... 'NA20508' 'NA20753'
    iid       (sample_1) object 'HG00419' 'HG00650' ... 'NA20508' 'NA20753'
>>> print(K.values)
[[ 0.89  0.23 -0.19 -0.01 -0.14  0.29  0.27 -0.23 -0.10 -0.21]
 [ 0.23  1.08 -0.45  0.19 -0.19  0.17  0.41 -0.01 -0.13 -0.13]
 [-0.19 -0.45  1.18 -0.04 -0.15 -0.20 -0.31 -0.04  0.30 -0.01]
 [-0.01  0.19 -0.04  0.90 -0.07  0.01  0.06 -0.19 -0.09  0.17]
 [-0.14 -0.19 -0.15 -0.07  1.18  0.09 -0.03  0.10  0.22  0.17]
 [ 0.29  0.17 -0.20  0.01  0.09  0.96  0.07 -0.04 -0.09 -0.23]
 [ 0.27  0.41 -0.31  0.06 -0.03  0.07  0.71 -0.10 -0.09 -0.06]
 [-0.23 -0.01 -0.04 -0.19  0.10 -0.04 -0.10  1.42 -0.30 -0.07]
 [-0.10 -0.13  0.30 -0.09  0.22 -0.09 -0.09 -0.30  0.91 -0.02]
 [-0.21 -0.13 -0.01  0.17  0.17 -0.23 -0.06 -0.07 -0.02  0.91]]

Please, refer to the pandas-plink documentation for more information.

Authors

License

This project is licensed under the MIT License.

Metadata

Release files for pandas-plink 2.3.2

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for pandas-plink 2.3.2
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pandas_plink-2.3.2.tar.gz 18.4 kB Details

Built distributions (wheels)

Table of built distributions (wheels) for pandas-plink 2.3.2
File
pandas_plink-2.3.2-pp310-pypy310_pp73-win_amd64.whl PyPy 3.10 PyPy 3.10 7.3 Windows x86-64 Details
pandas_plink-2.3.2-pp310-pypy310_pp73-manylinux_2_17_x86_64.manylinux_2_5_x86_64.manylinux1_x86_64.manylinux2014_x86_64.whl PyPy 3.10 PyPy 3.10 7.3 Linux glibc 2.5+ x86-64, Linux glibc 2.17+ x86-64 Details
pandas_plink-2.3.2-pp310-pypy310_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl PyPy 3.10 PyPy 3.10 7.3 Linux glibc 2.17+ ARM64 Details
pandas_plink-2.3.2-pp310-pypy310_pp73-macosx_14_0_arm64.whl PyPy 3.10 PyPy 3.10 7.3 macOS 14.0+ ARM64 Details
pandas_plink-2.3.2-pp310-pypy310_pp73-macosx_13_0_x86_64.whl PyPy 3.10 PyPy 3.10 7.3 macOS 13.0+ x86-64 Details
pandas_plink-2.3.2-cp312-cp312-win_amd64.whl CPython 3.12 CPython 3.12 Windows x86-64 Details
pandas_plink-2.3.2-cp312-cp312-musllinux_1_2_x86_64.whl CPython 3.12 CPython 3.12 Linux musl 1.2+ x86-64 Details
pandas_plink-2.3.2-cp312-cp312-musllinux_1_2_aarch64.whl CPython 3.12 CPython 3.12 Linux musl 1.2+ ARM64 Details
pandas_plink-2.3.2-cp312-cp312-manylinux_2_17_x86_64.manylinux_2_5_x86_64.manylinux1_x86_64.manylinux2014_x86_64.whl CPython 3.12 CPython 3.12 Linux glibc 2.17+ x86-64, Linux glibc 2.5+ x86-64 Details
pandas_plink-2.3.2-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl CPython 3.12 CPython 3.12 Linux glibc 2.17+ ARM64 Details
pandas_plink-2.3.2-cp312-cp312-macosx_14_0_arm64.whl CPython 3.12 CPython 3.12 macOS 14.0+ ARM64 Details
pandas_plink-2.3.2-cp312-cp312-macosx_13_0_x86_64.whl CPython 3.12 CPython 3.12 macOS 13.0+ x86-64 Details
pandas_plink-2.3.2-cp311-cp311-win_amd64.whl CPython 3.11 CPython 3.11 Windows x86-64 Details
pandas_plink-2.3.2-cp311-cp311-musllinux_1_2_x86_64.whl CPython 3.11 CPython 3.11 Linux musl 1.2+ x86-64 Details
pandas_plink-2.3.2-cp311-cp311-musllinux_1_2_aarch64.whl CPython 3.11 CPython 3.11 Linux musl 1.2+ ARM64 Details
pandas_plink-2.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux_2_5_x86_64.manylinux1_x86_64.manylinux2014_x86_64.whl CPython 3.11 CPython 3.11 Linux glibc 2.5+ x86-64, Linux glibc 2.17+ x86-64 Details
pandas_plink-2.3.2-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl CPython 3.11 CPython 3.11 Linux glibc 2.17+ ARM64 Details
pandas_plink-2.3.2-cp311-cp311-macosx_14_0_arm64.whl CPython 3.11 CPython 3.11 macOS 14.0+ ARM64 Details
pandas_plink-2.3.2-cp311-cp311-macosx_13_0_x86_64.whl CPython 3.11 CPython 3.11 macOS 13.0+ x86-64 Details
pandas_plink-2.3.2-cp310-cp310-win_amd64.whl CPython 3.10 CPython 3.10 Windows x86-64 Details
pandas_plink-2.3.2-cp310-cp310-musllinux_1_2_x86_64.whl CPython 3.10 CPython 3.10 Linux musl 1.2+ x86-64 Details
pandas_plink-2.3.2-cp310-cp310-musllinux_1_2_aarch64.whl CPython 3.10 CPython 3.10 Linux musl 1.2+ ARM64 Details
pandas_plink-2.3.2-cp310-cp310-manylinux_2_17_x86_64.manylinux_2_5_x86_64.manylinux1_x86_64.manylinux2014_x86_64.whl CPython 3.10 CPython 3.10 Linux glibc 2.5+ x86-64, Linux glibc 2.17+ x86-64 Details
pandas_plink-2.3.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl CPython 3.10 CPython 3.10 Linux glibc 2.17+ ARM64 Details
pandas_plink-2.3.2-cp310-cp310-macosx_14_0_arm64.whl CPython 3.10 CPython 3.10 macOS 14.0+ ARM64 Details
pandas_plink-2.3.2-cp310-cp310-macosx_13_0_x86_64.whl CPython 3.10 CPython 3.10 macOS 13.0+ x86-64 Details

Total release size: 1.2 MB

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