Installation
You can install GeneBe Utils using pip:
pip install genebe
If you wish to install a faster mmh3 implementation or use the option of annotating VCF files, install using:
pip install genebe[cpp]
or install modules separately:
pip install cyvcf2
pip install mmh3
This step will require build tools installed on your computer.
Docker
There is a dockerized version of this package, available at https://hub.docker.com/r/genebe/pygenebe.
Usage example, reading from file input.vcf and writing output to stdout:
docker run -v input.vcf:/tmp/input.vcf --rm genebe/pygenebe:0.0.14 genebe annotate --input /tmp/input.vcf --output /dev/stdout
Limits
If you wish to annotate thousands of variants, please log in to https://genebe.net, generate an API Key, and provide it using –username and –api-key.
The number of daily requests from a single IP is restricted to prevent abuse and excessive resource consumption on our server. Account holders with an API Key enjoy significantly higher limits (in the tens of thou