Package: genebe
GeneBe UtilsPyGeneBe: A Python client seamlessly integrating with the GeneBe platform, offering efficient annotation of genetic variants through its API, while supporting pandas, VCF file formats, and HGVS parsingUsing this client, you can easily annotate your DNA variants with the GeneBe API. Annotations include:Gene, transcript, and effectClinVar phenotypeGnomAD frequencyACMG score... if you need more, please let me knowUsageFor more information about the usage, go to thehttps://pygenebe.readthedocs.io/en/latest/documentation.Command line usageCheck current options using--helpswitchgenebe --help
genebe annotate --helpAnnotating VCF usingannotatecommandGeneBe client allows you to annotate your VCF file with ease. Use the following command:genebe annotate --input input.vcf.gz --output output.vcf.gzRemember 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 havecyvcf2package 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_keyFor more information callgenebe annotate --helpUsingaccountcommandThe account command displays information about your request history statistics and limits. To check your limits without specifying a username and API key, run:genebe accountAlternatively, if you have a GeneBe account with an API key, use the following command:genebe account --username your_username --api-key your_api_keyReplace "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 --helpPython usageGeneBe makes annotating DNA variants in pandas dataframe easy.importgenebeasgnbinput_variants=['7-69599651-A-G']# output as a list, with all transcriptslist=gnb.annotate_variants_list(input_variants,flatten_consequences=False)# output as a pandas dataframe, flatdf=gnb.annotate_variants_list_to_dataframe(input_variants,flatten_consequences=True)# parse HGVSinput_hgvs=['NM_000277.2:c.1A>G']parsed_variants=gnb.parse_hgvs(input_hgvs)# annotate existing dataframe with chr, pos, ref, alt columnsdf=pd.DataFrame({'chr':['6','22'],'pos':[160585140,28695868],'ref':['T','AG'],'alt':['G','A']})annotated_df=gnb.annotate_dataframe_variants(df,genome='hg38',use_ensembl=False,use_refseq=True,genome='hg38',flatten_consequences=True)# lift over variants from hg19 to hg38input_variants=['chr6-161006172-T-G']from_genome="hg19"dest_genome="hg38"lifted_variants=gnb.lift_over_variants(input_variants,from_genome,dest_genome)If you want to annotate thousands of variants, please log in tohttps://genebe.net, generate an API Key, and provide it usingusernameandapi_key.Find out more usage examples in theexamplesdirectory.InstallationYou can install GeneBe Utils using pip:pip install genebeIf you wish to install fastermmh3implementation or use the option of annotating vcf files install using:pip install genebe[cpp]or install modulespip install cyvcf2
pip install mmh3in the environment.This step will require build tools installed on your computer.DockerThere is a dockerized version of this package, available athttps://hub.docker.com/r/genebe/pygenebe.Usage example, reading from fileinput.vcfand writing output tostdout:docker run -v input.vcf:/tmp/input.vcf --rm genebe/pygenebe:0.0.14 genebe annotate --input /tmp/input.vcf --output /dev/stdoutLimitsIf you wish to annotate thousands of variants, please log in tohttps://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 thousands). If you require a higher daily request limit, please reach out to us via thehttps://genebe.net.Troubleshooting and issuesExperiencing issues? Follow these steps:Check Existing Issues:If you encounter problems, explore existing issues on GitHubhttps://github.com/pstawinski/pygenebefor possible solutions.Report New Issues:Unable to find a resolution? You can report the problem by creating a new issue with a clear description and details onhttps://github.com/pstawinski/pygenebe.Your feedback is crucial for improving GeneBe client. Thank you for contributing to the community!OtherFor more information about GeneBe, visit GeneBe website,https://genebe.net.