Python module to read binary Plink files.
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Build Status Coverage Status PyPI version

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 (2.7 and 3.3 or higher are supported) with the following modules:

  1. numpy version 1.8.2 or latest
  2. pandas version 0.17.1 or latest
  3. six version 1.9.0 or latest

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 (for both Python 2 and 3) of the PyPlink module.