{"categories":[{"label":"Python Modules","url":"https://skillfed.io/packages/category/software-development-libraries-python-modules/19"},{"label":"Bio-Informatics","url":"https://skillfed.io/packages/category/scientific-engineering-bio-informatics"}],"enrichment":{"capability":"Wraps the BEDTools suite to perform genomic interval operations (subtract, intersect, closest, etc.) directly from Python, supporting all BEDTools-compatible formats and streaming results.","skillfed_tags":["bioinformatics","genomics","bedtools-wrapper"],"use_cases":["Find genes within a specific distance of intergenic variants by combining subtract and closest operations on BED/GFF files.","Filter genomic features by intersection with regulatory regions or exclusion zones using subtract and intersect.","Stream large genomic datasets through multiple operations without materializing intermediate results to disk.","Iterate over genomic features and access their attributes (name, coordinates, scores) programmatically in Python loops.","Automate repetitive genomic interval analyses that would otherwise require shell script pipelines."],"what_it_does":"pybedtools is a Python wrapper around the BEDTools suite, a widely-used toolkit for genomic interval manipulation. It lets you perform operations like subtract, intersect, and closest on genomic features directly from Python code, rather than chaining shell commands. The package supports all BEDTools-compatible file formats (BED, GFF, and others, including gzipped variants) and can stream results like Unix pipes, making it memory-efficient for large genomic datasets.\n\nThe package depends on numpy, pysam, and pandas for data handling. It's designed for bioinformaticians and computational biologists who want to avoid writing complex bash scripts for routine genomic analyses. The main trade-off is the high install friction: BEDTools itself must be available on your system as a compiled binary before pybedtools can wrap it.","worth_installing":"Yes, if you have BEDTools already installed and work regularly with genomic intervals in Python. The high install friction and aging maintenance status (516 days since release) are real drawbacks, but the package is stable, permissively licensed, and solves a genuine problem for bioinformaticians. Not worth installing if you lack BEDTools or only occasionally need interval operations."},"id":"pybedtools","links":{"html":"https://skillfed.io/packages/pybedtools","md":"https://skillfed.io/packages/pybedtools.md","pypi":"https://pypi.org/project/pybedtools/"},"maintenance":{"status":"aging"},"meta":{"latest_release":"2025-03-16","license_spdx":null,"license_treatment":"permissive","name":"pybedtools","python_support":"unspecified","summary":"Wrapper around BEDTools for bioinformatics work"},"popularity":{"monthly_downloads":109608,"position":12506,"tier":"top_15000"},"security":{"n_vulnerabilities":0},"version":"0.12.0"}