GeneBe Client: A user-friendly system for annotating genetic variants
Project description
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
genebe annotate --help
Annotating VCF using annotate
command
GeneBe client allows you to annotate your VCF file with ease. Use the following command:
genebe annotate --input input.vcf.gz --output output.vcf.gz
Remember that your VCF file must be in a single allelic format! Utilize bcftools (https://samtools.github.io/bcftools/) to split the file. The output VCF will contain additional fields.
To use VCF annoation you have to have cyvcf2
package installed. Take a look at the Installation section below.
If your VCF file is large (over 10.000 variants), you may encounter request limits. To avoid this, create a GeneBe account with an API Key and provide your login/key using the --username and --api-key arguments. You can always check your limits with the account command. Update your annotation command as follows:
genebe annotate --input input.vcf.gz --output output.vcf.gz --username your_username --api-key your_api_key
For more information call
genebe annotate --help
Using account
command
The account command displays information about your request history statistics and limits. To check your limits without specifying a username and API key, run:
genebe account
Alternatively, if you have a GeneBe account with an API key, use the following command:
genebe account --username your_username --api-key your_api_key
Replace "your_username" and "your_api_key" with your GeneBe account credentials.
For more details and options, you can refer to the help documentation:
genebe account --help
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.
Docker
There is a dockerized version of this package, available at
For more information about GeneBe, visit GeneBe website, https://genebe.net .
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