https://github.com/lemieuxl/pyplink
Python module to read binary Plink files.
https://github.com/lemieuxl/pyplink
bioinformatics genetics genomics
Last synced: 3 months ago
JSON representation
Python module to read binary Plink files.
- Host: GitHub
- URL: https://github.com/lemieuxl/pyplink
- Owner: lemieuxl
- License: mit
- Created: 2014-12-02T14:34:17.000Z (over 11 years ago)
- Default Branch: master
- Last Pushed: 2024-06-18T13:19:40.000Z (almost 2 years ago)
- Last Synced: 2025-12-07T11:42:50.328Z (5 months ago)
- Topics: bioinformatics, genetics, genomics
- Language: Python
- Size: 429 KB
- Stars: 17
- Watchers: 2
- Forks: 4
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE.txt
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# 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/](https://lemieuxl.github.io/pyplink/).
## Dependencies
The tool requires a standard [Python](http://python.org/) installation (3.7 or
higher are supported) with the following modules:
1. [numpy](http://www.numpy.org/)
2. [pandas](http://pandas.pydata.org/)
The tool has been tested on *Linux* only, but should work on *MacOS* and
*Windows* operating systems as well.
## Installation
Using `pip`:
```bash
pip install pyplink
```
Using `conda`:
```bash
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:
```bash
conda config --add channels http://statgen.org/wp-content/uploads/Softwares/pyplink
```
### Updating
To update the module using `pip`:
```bash
pip install -U pyplink
```
To update the module using `conda`:
```bash
# 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:
```console
$ python -m pyplink.tests
.............................................
----------------------------------------------------------------------
Ran 45 tests in 0.334s
OK
```
## Example
The following
[notebook](http://nbviewer.ipython.org/github/lemieuxl/pyplink/blob/master/demo/PyPlink%20Demo.ipynb)
contains a demonstration of the `PyPlink` module.