https://github.com/lemieuxl/pybgen
Python module to process BGEN files as dosage data
https://github.com/lemieuxl/pybgen
bioinformatics genetics genomics
Last synced: 4 months ago
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Python module to process BGEN files as dosage data
- Host: GitHub
- URL: https://github.com/lemieuxl/pybgen
- Owner: lemieuxl
- License: mit
- Created: 2017-07-05T18:40:40.000Z (almost 9 years ago)
- Default Branch: master
- Last Pushed: 2024-02-14T14:42:08.000Z (about 2 years ago)
- Last Synced: 2025-08-20T03:22:24.697Z (9 months ago)
- Topics: bioinformatics, genetics, genomics
- Language: Python
- Homepage:
- Size: 7.01 MB
- Stars: 5
- Watchers: 1
- Forks: 4
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE.txt
Awesome Lists containing this project
README
# pybgen - Module to process BGEN files
[](https://github.com/lemieuxl/pybgen/actions)
[](https://pypi.org/project/pybgen/)
`PyBGEN` is a Python module to read and write BGEN binary files and extract
dosage data.
A short documentation is available at
[https://lemieuxl.github.io/pybgen/](https://lemieuxl.github.io/pybgen/).
## Dependencies
The tool requires a standard [Python](http://python.org/) installation (2.7 and
3.6 or higher are supported) with the following modules:
1. [numpy](http://www.numpy.org/) version 1.12.0 or latest
2. [six](https://pythonhosted.org/six/) version 1.10.0 or latest
The tool has been tested on *Linux*, but should work on *MacOS* and *Windows*
operating systems as well.
## Installation
Using `pip`:
```bash
pip install pybgen
```
Using `conda`:
```bash
conda install pybgen -c http://statgen.org/wp-content/uploads/Softwares/pybgen
```
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/pybgen
```
### Updating
To update the module using `pip`:
```bash
pip install -U pybgen
```
To update the module using `conda`:
```bash
# If the channel has been configured (see above)
conda update pybgen
# Otherwise
conda update pybgen -c http://statgen.org/wp-content/uploads/Softwares/pybgen
```
## Testing
To test the module, just perform the following command:
```console
$ python -m pybgen.tests
......................................................................
......................................................................
......................................................................
......................................................................
......................................................................
......................................................................
......................................................................
......................................
----------------------------------------------------------------------
Ran 528 tests in 13.171s
OK
```