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Deprecate plink functions #1324

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Merged
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Jun 24, 2025
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Deprecate plink functions #1324

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fda3400
Deprecate plink functions
tomwhite Jun 23, 2025
72a8444
Update changlog
tomwhite Jun 24, 2025
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4 changes: 4 additions & 0 deletions docs/api.rst
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Expand Up @@ -23,6 +23,10 @@ BGEN
PLINK
-----

.. deprecated:: 0.11.0
Functions for reading and writing plink are deprecated, please use the `bio2zarr <https://github.com/sgkit-dev/bio2zarr>`_
and `vcztools <https://github.com/sgkit-dev/vcztools>`_ packages.

.. currentmodule:: sgkit.io.plink
.. autosummary::
:toctree: generated/
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8 changes: 6 additions & 2 deletions docs/changelog.rst
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Expand Up @@ -14,8 +14,12 @@ Changelog
.. Breaking changes
.. ~~~~~~~~~~~~~~~~

.. Deprecations
.. ~~~~~~~~~~~~
Deprecations
~~~~~~~~~~~~

- Functions for reading and writing plink are deprecated, please use the `bio2zarr <https://github.com/sgkit-dev/bio2zarr>`_
and `vcztools <https://github.com/sgkit-dev/vcztools>`_ packages.
(:user:`tomwhite`, :pr:`1324`, :issue:`1318`)

.. Improvements
.. ~~~~~~~~~~~~
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8 changes: 8 additions & 0 deletions sgkit/io/plink/__init__.py
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@@ -1,3 +1,11 @@
import warnings

warnings.warn(
"Functions for reading and writing plink are deprecated, please use the bio2zarr and vcztools packages.",
DeprecationWarning,
stacklevel=2,
)

try:
from .plink_reader import plink_to_zarr, read_plink
from .plink_writer import write_plink, zarr_to_plink
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8 changes: 8 additions & 0 deletions sgkit/io/plink/plink_reader.py
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Expand Up @@ -147,6 +147,10 @@ def read_plink(
Loads a single PLINK dataset as dask arrays within a Dataset
from bed, bim, and fam files.

.. deprecated:: 0.11.0
Functions for reading and writing plink are deprecated, please use the `bio2zarr <https://github.com/sgkit-dev/bio2zarr>`_
and `vcztools <https://github.com/sgkit-dev/vcztools>`_ packages.

Parameters
----------
path
Expand Down Expand Up @@ -328,6 +332,10 @@ def plink_to_zarr(

Refer to :func:`read_plink` for details and limitations.

.. deprecated:: 0.11.0
Functions for reading and writing plink are deprecated, please use the `bio2zarr <https://github.com/sgkit-dev/bio2zarr>`_
and `vcztools <https://github.com/sgkit-dev/vcztools>`_ packages.

Parameters
----------
path
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8 changes: 8 additions & 0 deletions sgkit/io/plink/plink_writer.py
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Expand Up @@ -49,6 +49,10 @@ def write_plink(
- ``sample_phenotype``: Phenotype code equal to 1 for control, 2 for case,
and -1 for missing

.. deprecated:: 0.11.0
Functions for reading and writing plink are deprecated, please use the `bio2zarr <https://github.com/sgkit-dev/bio2zarr>`_
and `vcztools <https://github.com/sgkit-dev/vcztools>`_ packages.

Parameters
----------
ds
Expand Down Expand Up @@ -146,6 +150,10 @@ def zarr_to_plink(

Refer to :func:`write_plink` for details and limitations.

.. deprecated:: 0.11.0
Functions for reading and writing plink are deprecated, please use the `bio2zarr <https://github.com/sgkit-dev/bio2zarr>`_
and `vcztools <https://github.com/sgkit-dev/vcztools>`_ packages.

Parameters
----------
input
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