Documentation: https://uio-bmi.github.io/bionumpy/
BioNumPy is a toolkit, built on top of NumPy, for enabling array programming on biological data in Python. BioNumPy aims to make it easy to read common bioinformatics file formats efficiently into NumPy-like data structures that enable efficient operations and analysis of the data. Working in BioNumPy should feel much like working in NumPy.
- There are no existing packages in Python for getting biological data sets efficiently into NumPy-like data structures.
- Current packages for working with biological data do not use NumPy in an efficient way (e.g. individual sequences are stored as separate NumPy arrays, not together in shared arrays).
- Install with pip:
- Free software: MIT license
- Documentation: https://knutrand.github.io/bionumpy.
>>> pip install bionumpy- Check out the tutorials and getting started guide in the documentation.
The features of BioNumPy can roughly be divided into two:
- Reading biological data sets (e.g. fasta, vcf, bed) into NumPy-like objects
- Analysing, modifying, filtering these NumPy-like objects in meaningful ways
BioNumPy also supports writing most data types to file.
This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.