genebe 0.0.13

GeneBe Client: A user-friendly system for annotating genetic variants

GeneBe Utils

Welcome to GeneBe Utils, a Python package that complements the innovative GeneBe platform. GeneBe is a cutting-edge genetics platform designed to empower individuals with insights into their health and well-being.

Using this client, you can easily annotate your DNA variants with the GeneBe API. Annotations include:

• Gene, transcript, and effect
• ClinVar phenotype
• GnomAD frequency
• ACMG score
• ... if you need more, please let me know

Usage

Command line usage

Check current options using --help switch

genebe --help

Or just call

genebe input.vcf.gz output.vcf.gz

For annotating your VCF file with acmg_score field.

To use VCF annoation you have to have cyvcf2 package installed. Take a look at the Installation section below.

Python usage

GeneBe makes annotating DNA variants in pandas dataframe easy.

import genebe as gnb

input_variants = ['7-69599651-A-G']

# output as a list, with all transcripts
list = gnb.annotate_variants_list(input_variants,flatten_consequences = False)

# output as a pandas dataframe, flat
df = gnb.annotate_variants_list_to_dataframe(input_variants, flatten_consequences=True)

# parse HGVS
input_hgvs = ['NM_000277.2:c.1A>G']
parsed_variants = gnb.parse_hgvs(input_hgvs)

If you want to annotate thousands of variants, please log in to https://genebe.net, generate an API Key, and provide it using username and api_key.

Installation

You can install GeneBe Utils using pip:

pip install genebe

If you wish to install faster mmh3 implementation or use the option of annotating vcf files install using:

pip install genebe[cpp]

or install modules

pip install cyvcf2
pip install mmh3

in the environment.

This step will require build tools installed on your computer.

For more information about GeneBe, visit GeneBe website, https://genebe.net .