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

Danilo Horta

License

This project is licensed under the MIT License.

Metadata

Release files for pandas-plink 2.3.2

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Release files / pandas_plink-2.3.2-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl

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Publishing platform: GitHub Actions
Publishing repository: github.com/limix/pandas-plink
Publishing commit: github.com/limix/pandas-plink/tree/865f5a52719602e55dae034444ec7a22fe01e653

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Artifact

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Release files / pandas_plink-2.3.2-cp312-cp312-macosx_14_0_arm64.whl

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Publishing repository: github.com/limix/pandas-plink
Publishing commit: github.com/limix/pandas-plink/tree/865f5a52719602e55dae034444ec7a22fe01e653

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Identity

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Publishing repository: github.com/limix/pandas-plink
Publishing commit: github.com/limix/pandas-plink/tree/865f5a52719602e55dae034444ec7a22fe01e653

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Release files / pandas_plink-2.3.2-cp311-cp311-win_amd64.whl

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Identity

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Publishing repository: github.com/limix/pandas-plink
Publishing commit: github.com/limix/pandas-plink/tree/865f5a52719602e55dae034444ec7a22fe01e653

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Release files / pandas_plink-2.3.2-cp311-cp311-musllinux_1_2_x86_64.whl

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Provenance

Identity

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Publishing repository: github.com/limix/pandas-plink
Publishing commit: github.com/limix/pandas-plink/tree/865f5a52719602e55dae034444ec7a22fe01e653

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Identity

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Publishing repository: github.com/limix/pandas-plink
Publishing commit: github.com/limix/pandas-plink/tree/865f5a52719602e55dae034444ec7a22fe01e653

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Provenance

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/limix/pandas-plink
Publishing commit: github.com/limix/pandas-plink/tree/865f5a52719602e55dae034444ec7a22fe01e653

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Release files / pandas_plink-2.3.2-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl

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Provenance

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/limix/pandas-plink
Publishing commit: github.com/limix/pandas-plink/tree/865f5a52719602e55dae034444ec7a22fe01e653

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Release files / pandas_plink-2.3.2-cp311-cp311-macosx_14_0_arm64.whl

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Uploaded via	`twine/6.1.0 CPython/3.12.9`

Provenance

Identity

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Publishing repository: github.com/limix/pandas-plink
Publishing commit: github.com/limix/pandas-plink/tree/865f5a52719602e55dae034444ec7a22fe01e653

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Release files / pandas_plink-2.3.2-cp311-cp311-macosx_13_0_x86_64.whl

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Provenance

Identity

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Publishing repository: github.com/limix/pandas-plink
Publishing commit: github.com/limix/pandas-plink/tree/865f5a52719602e55dae034444ec7a22fe01e653

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Release files / pandas_plink-2.3.2-cp310-cp310-win_amd64.whl

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Provenance

Identity

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Publishing repository: github.com/limix/pandas-plink
Publishing commit: github.com/limix/pandas-plink/tree/865f5a52719602e55dae034444ec7a22fe01e653

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Release files / pandas_plink-2.3.2-cp310-cp310-musllinux_1_2_x86_64.whl

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Uploaded via	`twine/6.1.0 CPython/3.12.9`

Provenance

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/limix/pandas-plink
Publishing commit: github.com/limix/pandas-plink/tree/865f5a52719602e55dae034444ec7a22fe01e653

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Release files / pandas_plink-2.3.2-cp310-cp310-musllinux_1_2_aarch64.whl

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Uploaded using Trusted Publishing? What is trusted publishing?	Yes
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Provenance

Identity

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Publishing repository: github.com/limix/pandas-plink
Publishing commit: github.com/limix/pandas-plink/tree/865f5a52719602e55dae034444ec7a22fe01e653

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Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/6.1.0 CPython/3.12.9`

Provenance

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/limix/pandas-plink
Publishing commit: github.com/limix/pandas-plink/tree/865f5a52719602e55dae034444ec7a22fe01e653

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Release files / pandas_plink-2.3.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl

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Upload date	May 12, 2025
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/6.1.0 CPython/3.12.9`

Provenance

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/limix/pandas-plink
Publishing commit: github.com/limix/pandas-plink/tree/865f5a52719602e55dae034444ec7a22fe01e653

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Artifact

Subject: pandas_plink-2.3.2-cp310-cp310-manylinux2014_aarch64.manylinux_2_17_aarch64.whl
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Download URL	pandas_plink-2.3.2-cp310-cp310-macosx_14_0_arm64.whl
Size	29.2 kB
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This release

File	Interpreter	ABI	Platform	Actions Reset
pandas_plink-2.3.2-pp310-pypy310_pp73-win_amd64.whl 55.8 kB May 12, 2025 With provenance	PyPy 3.10	PyPy 3.10 7.3	Windows x86-64	Details for pandas_plink-2.3.2-pp310-pypy310_pp73-win_amd64.whl
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 83.3 kB May 12, 2025 With provenance	PyPy 3.10	PyPy 3.10 7.3	Linux glibc 2.5+ x86-64, Linux glibc 2.17+ x86-64	Details for 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
pandas_plink-2.3.2-pp310-pypy310_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 46.4 kB May 12, 2025 With provenance	PyPy 3.10	PyPy 3.10 7.3	Linux glibc 2.17+ ARM64	Details for pandas_plink-2.3.2-pp310-pypy310_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
pandas_plink-2.3.2-pp310-pypy310_pp73-macosx_14_0_arm64.whl 43.0 kB May 12, 2025 With provenance	PyPy 3.10	PyPy 3.10 7.3	macOS 14.0+ ARM64	Details for pandas_plink-2.3.2-pp310-pypy310_pp73-macosx_14_0_arm64.whl
pandas_plink-2.3.2-pp310-pypy310_pp73-macosx_13_0_x86_64.whl 42.1 kB May 12, 2025 With provenance	PyPy 3.10	PyPy 3.10 7.3	macOS 13.0+ x86-64	Details for pandas_plink-2.3.2-pp310-pypy310_pp73-macosx_13_0_x86_64.whl
pandas_plink-2.3.2-cp312-cp312-win_amd64.whl 49.2 kB May 12, 2025 With provenance	CPython 3.12	CPython 3.12	Windows x86-64	Details for pandas_plink-2.3.2-cp312-cp312-win_amd64.whl
pandas_plink-2.3.2-cp312-cp312-musllinux_1_2_x86_64.whl 77.4 kB May 12, 2025 With provenance	CPython 3.12	CPython 3.12	Linux musl 1.2+ x86-64	Details for pandas_plink-2.3.2-cp312-cp312-musllinux_1_2_x86_64.whl
pandas_plink-2.3.2-cp312-cp312-musllinux_1_2_aarch64.whl 42.1 kB May 12, 2025 With provenance	CPython 3.12	CPython 3.12	Linux musl 1.2+ ARM64	Details for pandas_plink-2.3.2-cp312-cp312-musllinux_1_2_aarch64.whl
pandas_plink-2.3.2-cp312-cp312-manylinux_2_17_x86_64.manylinux_2_5_x86_64.manylinux1_x86_64.manylinux2014_x86_64.whl 79.4 kB May 12, 2025 With provenance	CPython 3.12	CPython 3.12	Linux glibc 2.17+ x86-64, Linux glibc 2.5+ x86-64	Details for pandas_plink-2.3.2-cp312-cp312-manylinux_2_17_x86_64.manylinux_2_5_x86_64.manylinux1_x86_64.manylinux2014_x86_64.whl
pandas_plink-2.3.2-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 42.4 kB May 12, 2025 With provenance	CPython 3.12	CPython 3.12	Linux glibc 2.17+ ARM64	Details for pandas_plink-2.3.2-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
pandas_plink-2.3.2-cp312-cp312-macosx_14_0_arm64.whl 40.1 kB May 12, 2025 With provenance	CPython 3.12	CPython 3.12	macOS 14.0+ ARM64	Details for pandas_plink-2.3.2-cp312-cp312-macosx_14_0_arm64.whl
pandas_plink-2.3.2-cp312-cp312-macosx_13_0_x86_64.whl 39.4 kB May 12, 2025 With provenance	CPython 3.12	CPython 3.12	macOS 13.0+ x86-64	Details for pandas_plink-2.3.2-cp312-cp312-macosx_13_0_x86_64.whl
pandas_plink-2.3.2-cp311-cp311-win_amd64.whl 40.9 kB May 12, 2025 With provenance	CPython 3.11	CPython 3.11	Windows x86-64	Details for pandas_plink-2.3.2-cp311-cp311-win_amd64.whl
pandas_plink-2.3.2-cp311-cp311-musllinux_1_2_x86_64.whl 59.4 kB May 12, 2025 With provenance	CPython 3.11	CPython 3.11	Linux musl 1.2+ x86-64	Details for pandas_plink-2.3.2-cp311-cp311-musllinux_1_2_x86_64.whl
pandas_plink-2.3.2-cp311-cp311-musllinux_1_2_aarch64.whl 42.0 kB May 12, 2025 With provenance	CPython 3.11	CPython 3.11	Linux musl 1.2+ ARM64	Details for pandas_plink-2.3.2-cp311-cp311-musllinux_1_2_aarch64.whl
pandas_plink-2.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux_2_5_x86_64.manylinux1_x86_64.manylinux2014_x86_64.whl 60.6 kB May 12, 2025 With provenance	CPython 3.11	CPython 3.11	Linux glibc 2.5+ x86-64, Linux glibc 2.17+ x86-64	Details for pandas_plink-2.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux_2_5_x86_64.manylinux1_x86_64.manylinux2014_x86_64.whl
pandas_plink-2.3.2-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 42.1 kB May 12, 2025 With provenance	CPython 3.11	CPython 3.11	Linux glibc 2.17+ ARM64	Details for pandas_plink-2.3.2-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
pandas_plink-2.3.2-cp311-cp311-macosx_14_0_arm64.whl 34.6 kB May 12, 2025 With provenance	CPython 3.11	CPython 3.11	macOS 14.0+ ARM64	Details for pandas_plink-2.3.2-cp311-cp311-macosx_14_0_arm64.whl
pandas_plink-2.3.2-cp311-cp311-macosx_13_0_x86_64.whl 34.2 kB May 12, 2025 With provenance	CPython 3.11	CPython 3.11	macOS 13.0+ x86-64	Details for pandas_plink-2.3.2-cp311-cp311-macosx_13_0_x86_64.whl
pandas_plink-2.3.2-cp310-cp310-win_amd64.whl 32.3 kB May 12, 2025 With provenance	CPython 3.10	CPython 3.10	Windows x86-64	Details for pandas_plink-2.3.2-cp310-cp310-win_amd64.whl
pandas_plink-2.3.2-cp310-cp310-musllinux_1_2_x86_64.whl 41.6 kB May 12, 2025 With provenance	CPython 3.10	CPython 3.10	Linux musl 1.2+ x86-64	Details for pandas_plink-2.3.2-cp310-cp310-musllinux_1_2_x86_64.whl
pandas_plink-2.3.2-cp310-cp310-musllinux_1_2_aarch64.whl 41.9 kB May 12, 2025 With provenance	CPython 3.10	CPython 3.10	Linux musl 1.2+ ARM64	Details for pandas_plink-2.3.2-cp310-cp310-musllinux_1_2_aarch64.whl
pandas_plink-2.3.2-cp310-cp310-manylinux_2_17_x86_64.manylinux_2_5_x86_64.manylinux1_x86_64.manylinux2014_x86_64.whl 42.2 kB May 12, 2025 With provenance	CPython 3.10	CPython 3.10	Linux glibc 2.5+ x86-64, Linux glibc 2.17+ x86-64	Details for pandas_plink-2.3.2-cp310-cp310-manylinux_2_17_x86_64.manylinux_2_5_x86_64.manylinux1_x86_64.manylinux2014_x86_64.whl
pandas_plink-2.3.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 42.1 kB May 12, 2025 With provenance	CPython 3.10	CPython 3.10	Linux glibc 2.17+ ARM64	Details for pandas_plink-2.3.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
pandas_plink-2.3.2-cp310-cp310-macosx_14_0_arm64.whl 29.2 kB May 12, 2025 With provenance	CPython 3.10	CPython 3.10	macOS 14.0+ ARM64	Details for pandas_plink-2.3.2-cp310-cp310-macosx_14_0_arm64.whl
pandas_plink-2.3.2-cp310-cp310-macosx_13_0_x86_64.whl 29.0 kB May 12, 2025 With provenance	CPython 3.10	CPython 3.10	macOS 13.0+ x86-64	Details for pandas_plink-2.3.2-cp310-cp310-macosx_13_0_x86_64.whl

pandas-plink 2.3.2

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