Read PLINK files into Pandas data frames
Project description
pandas-plink
============
|Travis| |AppVeyor| |Documentation| |Gitter|
| Pandas-plink is a Python package for reading `PLINK binary file
format <https://www.cog-genomics.org/plink2/formats>`__.
| The file reading is taken place via `lazy
loading <https://en.wikipedia.org/wiki/Lazy_loading>`__, meaning that it
saves up memory by actually reading only the genotypes that are actually
accessed by the user.
Install
-------
We recommend installing it via
`conda <http://conda.pydata.org/docs/index.html>`__:
.. code:: bash
conda install -c conda-forge pandas-plink
The above method is preferable because it does not require building
tools, which makes the installation less prone to errors.
Alternatively, pandas-plink can also be installed using
`pip <https://pypi.python.org/pypi/pip>`__:
.. code:: bash
pip install pandas-plink
| The above method will perform some compilation and the installation is
very likely to be successful, as we test every release under Windows,
Linux, and macOS platforms.
| If by any change it fails, please, consider submitting a `new
issue <https://github.com/limix/pandas-plink/issues/new>`__.
Usage
-----
It is as simple as
.. code:: python
from pandas_plink import read_plink
(bim, fam, G) = read_plink('/path/to/files_prefix')
| for which ``files_prefix.bed``, ``files_prefix.bim``, and
``files_prefix.fam`` contain the data.
| Portions of the genotype will be read as the user access them. Please,
refer to the `documentation <https://pandas-plink.readthedocs.io/>`__
for more information.
Authors
-------
- `Danilo Horta <https://github.com/horta>`__
License
-------
This project is licensed under the `MIT
License <https://raw.githubusercontent.com/limix/pandas-plink/master/LICENSE.md>`__.
.. |Travis| image:: https://img.shields.io/travis/limix/pandas-plink.svg?style=flat-square&label=linux%20%2F%20macos%20build
:target: https://travis-ci.org/limix/pandas-plink
.. |AppVeyor| image:: https://img.shields.io/appveyor/ci/Horta/pandas-plink.svg?style=flat-square&label=windows%20build
:target: https://ci.appveyor.com/project/Horta/pandas-plink
.. |Documentation| image:: https://img.shields.io/readthedocs/pandas-plink.svg?style=flat-square&version=stable
:target: https://pandas-plink.readthedocs.io/
.. |Gitter| image:: https://img.shields.io/gitter/room/limix/pandas-plink.js.svg?style=flat-square
:target: https://gitter.im/pandas-plink/Lobby
============
|Travis| |AppVeyor| |Documentation| |Gitter|
| Pandas-plink is a Python package for reading `PLINK binary file
format <https://www.cog-genomics.org/plink2/formats>`__.
| The file reading is taken place via `lazy
loading <https://en.wikipedia.org/wiki/Lazy_loading>`__, meaning that it
saves up memory by actually reading only the genotypes that are actually
accessed by the user.
Install
-------
We recommend installing it via
`conda <http://conda.pydata.org/docs/index.html>`__:
.. code:: bash
conda install -c conda-forge pandas-plink
The above method is preferable because it does not require building
tools, which makes the installation less prone to errors.
Alternatively, pandas-plink can also be installed using
`pip <https://pypi.python.org/pypi/pip>`__:
.. code:: bash
pip install pandas-plink
| The above method will perform some compilation and the installation is
very likely to be successful, as we test every release under Windows,
Linux, and macOS platforms.
| If by any change it fails, please, consider submitting a `new
issue <https://github.com/limix/pandas-plink/issues/new>`__.
Usage
-----
It is as simple as
.. code:: python
from pandas_plink import read_plink
(bim, fam, G) = read_plink('/path/to/files_prefix')
| for which ``files_prefix.bed``, ``files_prefix.bim``, and
``files_prefix.fam`` contain the data.
| Portions of the genotype will be read as the user access them. Please,
refer to the `documentation <https://pandas-plink.readthedocs.io/>`__
for more information.
Authors
-------
- `Danilo Horta <https://github.com/horta>`__
License
-------
This project is licensed under the `MIT
License <https://raw.githubusercontent.com/limix/pandas-plink/master/LICENSE.md>`__.
.. |Travis| image:: https://img.shields.io/travis/limix/pandas-plink.svg?style=flat-square&label=linux%20%2F%20macos%20build
:target: https://travis-ci.org/limix/pandas-plink
.. |AppVeyor| image:: https://img.shields.io/appveyor/ci/Horta/pandas-plink.svg?style=flat-square&label=windows%20build
:target: https://ci.appveyor.com/project/Horta/pandas-plink
.. |Documentation| image:: https://img.shields.io/readthedocs/pandas-plink.svg?style=flat-square&version=stable
:target: https://pandas-plink.readthedocs.io/
.. |Gitter| image:: https://img.shields.io/gitter/room/limix/pandas-plink.js.svg?style=flat-square
:target: https://gitter.im/pandas-plink/Lobby
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