A collection of routines and related Python classes to handle bioinformatics data.

We recommend to install bioformats via pip:

pip install bioformats

pip automatically resolves bioformats dependencies and installs required packages.

The package tools are called via the main wrapper script bioformats. For example, one may get the genotype count table from a VCF file by calling the vcfgeno2bed tool in the following way:

bioformats vcfgeno2bed variants.vcf genotype_counts.txt

For every tool, the help message is available by using the -h option. Also one may get the list of the package tools by calling bioformats with the -h option.