pybedtools
Wrapper around BEDTools for bioinformatics work
Decision gist · record as of 2026-08-14
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.AI-flagged interpretation of the facts on this page — verify before relying
Before you install
- BEDTools must be installed and available on the system as a compiled binary before pybedtools can wrap it.
- High install friction: requires BEDTools as a compiled system dependency.
- Package is aging (516 days since last release) but repo is not archived with recent activity on 2025-03-16.
License · maintenance · safety
MIT (permissive) — MIT license is permissive; you can use, modify, and distribute pybedtools with minimal restrictions, suitable for academic and commercial projects.
last release 2025-03-16 (516 days) · last repo commit 2025-03-16 · 330 stars
0 known vulnerabilities (OSV.dev, 2026-08-14) · 109,608 downloads/mo, #12,506 on PyPI
Alternatives
Verify before relying
from pybedtools import BedTool
snps = BedTool('snps.bed.gz')
genes = BedTool('hg19.gff')
intergenic_snps = snps.subtract(genes)
nearby = genes.closest(intergenic_snps, d=True, stream=True)
for gene in nearby:
if int(gene[-1]) < 5000:
print(gene.name)- Whether BEDTools must be pre-installed on the system or if pybedtools handles installation automatically
- Compatibility with Python versions beyond 3.8 (classifiers list 3.6, 3.7, 3.8 but requires_python is unspecified)
What it is and 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.
The 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.
Use it for
- 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.
Worth the install?
AI-flagged interpretation of the facts on this page. Verify before relying on it.
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.
Install
pybedtools on PyPI
Before you install
High install friction: requires BEDTools as a compiled system dependency. Package is aging (516 days since last release) but repo is not archived with recent activity on 2025-03-16.
BEDTools must be installed and available on the system as a compiled binary before pybedtools can wrap it.
License in practice
MIT license is permissive; you can use, modify, and distribute pybedtools with minimal restrictions, suitable for academic and commercial projects.
Quickstart
from pybedtools import BedTool
snps = BedTool('snps.bed.gz')
genes = BedTool('hg19.gff')
intergenic_snps = snps.subtract(genes)
nearby = genes.closest(intergenic_snps, d=True, stream=True)
for gene in nearby:
if int(gene[-1]) < 5000:
print(gene.name)Verify before relying
- Whether BEDTools must be pre-installed on the system or if pybedtools handles installation automatically
- Compatibility with Python versions beyond 3.8 (classifiers list 3.6, 3.7, 3.8 but requires_python is unspecified)
Package facts
| License | MIT permissive |
| Python support | Not specified |
| Install friction | High. Source build required |
| Runtime dependencies | 3 packagesnumpypysampandas |
| Maintenance | Aging 516 days since the last release |
| Last repo commit | |
| First released | |
| Downloads | 109,608 / month, #12,506 on PyPI 30-day window, as of 2026-08-14 |
| Known vulnerabilities | None known OSV.dev, checked 2026-08-14 |
| Classifiers | Development Status :: 5 - Production/StableIntended Audience :: Science/ResearchLicense :: OSI Approved :: MIT LicenseProgramming Language :: PythonProgramming Language :: Python :: 3Programming Language :: Python :: 3.6Programming Language :: Python :: 3.7Programming Language :: Python :: 3.8Topic :: Scientific/Engineering :: Bio-InformaticsTopic :: Software Development :: Libraries :: Python Modules |
Evidence: pybedtools-0.12.0.tar.gz
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