{"categories":[{"label":"Bio-Informatics","url":"https://skillfed.io/packages/category/scientific-engineering-bio-informatics"}],"enrichment":{"capability":"Provides fast random access to subsequences in FASTA files using a samtools-compatible index, with a pure Python implementation for indexing, retrieval, and in-place modification.","skillfed_tags":["bioinformatics","genomics","fasta-indexing"],"use_cases":["Extract specific genomic regions from reference genomes for variant analysis or annotation pipelines.","Build sequence databases for rapid lookup of genes or transcripts by identifier without full file loads.","Perform reverse-complement operations on DNA sequences for primer design or alignment validation.","Slice and manipulate FASTA sequences programmatically in Python-based bioinformatics workflows.","Use the faidx command-line tool to extract or modify FASTA records without writing custom scripts."],"what_it_does":"pyfaidx is a pure Python implementation of samtools' faidx functionality, enabling efficient random access to any subsequence in a FASTA file without loading the entire file into memory. It creates a small flat index file (.fai) that allows seeking directly to the sequence you need. The package provides both a Python API (with dictionary-like and method-based access) and a command-line tool for FASTA manipulation without programming.\n\nThe library supports slicing, reverse complements, spliced sequences, and coordinate transformations (1-based and 0-based). It works with sequences indexed by name or position, handles custom key functions for flexible naming schemes, and can filter sequences during indexing. The API is compatible with pygr's seqdb module, making it a drop-in replacement for existing bioinformatics workflows.","worth_installing":"Yes. pyfaidx is production-stable, actively maintained, has no known vulnerabilities, and solves a real problem in bioinformatics workflows. Low install friction and permissive licensing make it a straightforward choice for anyone working with FASTA files in Python."},"id":"pyfaidx","links":{"html":"https://skillfed.io/packages/pyfaidx","md":"https://skillfed.io/packages/pyfaidx.md","pypi":"https://pypi.org/project/pyfaidx/"},"maintenance":{"status":"active"},"meta":{"latest_release":"2026-03-19","license_spdx":null,"license_treatment":"permissive","name":"pyfaidx","python_support":"supports_current","summary":"pyfaidx: efficient pythonic random access to fasta subsequences"},"popularity":{"monthly_downloads":529907,"position":6159,"tier":"top_15000"},"security":{"n_vulnerabilities":0},"version":"0.9.0.4"}