pyplink - Module to process Plink's binary files

PyPlink is a Python module to read and write Plink's binary files. Short documentation available at https://lemieuxl.github.io/pyplink/.

Dependencies

The tool requires a standard Python installation (3.7 or higher are supported) with the following modules:

1. numpy
2. pandas

The tool has been tested on Linux only, but should work on MacOS and Windows operating systems as well.

Installation

Using pip:

pip install pyplink

Using conda:

conda install pyplink -c http://statgen.org/wp-content/uploads/Softwares/pyplink

It is possible to add the channel to conda's configuration, so that the -c http://statgen.org/... can be omitted to update or install the package. To add the channel, perform the following command:

conda config --add channels http://statgen.org/wp-content/uploads/Softwares/pyplink

Updating

To update the module using pip:

pip install -U pyplink

To update the module using conda:

# If the channel has been configured (see above)
conda update pyplink

# Otherwise
conda update pyplink -c http://statgen.org/wp-content/uploads/Softwares/pyplink

Testing

To test the module, just perform the following command:

$ python -m pyplink.tests
.............................................
----------------------------------------------------------------------
Ran 45 tests in 0.334s

OK

Example

The following notebook contains a demonstration of the PyPlink module.