{"categories":[{"label":"Bio-Informatics","url":"https://skillfed.io/packages/category/scientific-engineering-bio-informatics"}],"enrichment":{"capability":"PyEnsembl provides a Python interface to query Ensembl reference genome metadata\u2014genes, transcripts, exons, and their genomic coordinates\u2014by downloading GTF and FASTA files and indexing them locally or loading custom genome data.","skillfed_tags":["bioinformatics","genomics","reference-data"],"use_cases":["Annotate genomic variants (SNPs, indels) by looking up overlapping genes and transcripts at their genomic coordinates.","Retrieve transcript structures and exon boundaries for a given gene name to design primers or analyze splicing.","Build a local reference database for a specific Ensembl release and species to support reproducible bioinformatics pipelines.","Query the nearest gene to a genomic position when no gene directly overlaps, useful for intergenic variant classification.","Load and index custom genome annotations (non-Ensembl GTF/FASTA) for organisms or assemblies not in the Ensembl repository."],"what_it_does":"PyEnsembl is a Python library that wraps Ensembl reference genome data\u2014exons, transcripts, genes, and their chromosomal locations\u2014making it queryable through a Python API. It downloads GTF (gene transfer format) and FASTA sequence files from the Ensembl FTP server, indexes them into a local database, and exposes methods to look up genes by name or ID, find transcripts, retrieve exon coordinates, and query genomic features at specific loci. It also supports custom genomes loaded from user-supplied GTF and FASTA files or remote URLs.\n\nThe package is designed for bioinformatics workflows where you need to resolve gene names to genomic coordinates, retrieve transcript structures, or annotate genomic variants against a reference. It handles the download and caching automatically and stores data in a platform-specific cache directory (configurable via environment variable). The API provides many query methods\u2014by gene ID, gene name, transcript ID, exon ID, chromosomal position, and strand\u2014returning Gene, Transcript, and Exon objects with associated metadata.","worth_installing":"Yes. PyEnsembl is actively maintained, has low install friction, carries no known vulnerabilities, and is the standard tool for programmatic access to Ensembl genome metadata in Python. Install it if you need to query genes, transcripts, or exons by name or genomic position in a bioinformatics workflow. The main gotcha is the separate data-download step required before first use."},"id":"pyensembl","links":{"html":"https://skillfed.io/packages/pyensembl","md":"https://skillfed.io/packages/pyensembl.md","pypi":"https://pypi.org/project/pyensembl/"},"maintenance":{"status":"active"},"meta":{"latest_release":"2026-07-08","license_spdx":"Apache-2.0","license_treatment":"permissive","name":"pyensembl","python_support":"supports_current","summary":"Python interface to Ensembl reference genome metadata"},"popularity":{"monthly_downloads":104221,"position":12761,"tier":"top_15000"},"security":{"n_vulnerabilities":0},"version":"2.10.4"}