pybigtools

library0.2.5pypypi✓ verified 89d ago

Python bindings to the Bigtools Rust library for high-performance BigWig and BigBed I/O. Version 0.2.5 (latest) focuses on reading and writing genomic interval files with performance comparable to the Rust implementation. Release cadence is irregular; the library is actively maintained.

data serialization

pip install pybigtools

github ↗package ↗docs ↗

INSTALL

IMPORT

SIG · PYBIGTOOLS

pybigtools

datapythonv0.2.5

harness data pending

Install & Compatibility

Where this runs

No compatibility data collected yet for this library.

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

open

✓ from pybigtools import open

✗ import pybigtools

Direct import of the 'open' function is required; the module itself is not callable.

BigWig

✓ from pybigtools import BigWig

✗ from pybigtools import bigwig

Class name is BigWig, not lowercase bigwig.

BigBed

✓ from pybigtools import BigBed

✗ from pybigtools import bigbed

Class name is BigBed, not lowercase bigbed.

Open a BigWig file, list chromosomes, and fetch values over a region.

from pybigtools import open with open('example.bw') as bw: print(bw.chroms) vals = bw.fetch('chr1', 1000000, 1000100) print(vals)

Debug

Known issues

breakingIn pybigtools v0.1.x, the main function was named 'read_bigwig' instead of 'open'. Code written for v0.1.x must be updated.

fix

Replace 'read_bigwig' with 'open' from pybigtools.

affects: <0.2.0

gotchaThe 'open' function does not auto-detect file type; you must use the correct class (BigWig or BigBed) or rely on the context manager which returns a generic object with common methods. Manually constructing BigWig or BigBed objects is preferred for type safety.

fix

Use 'from pybigtools import BigWig, BigBed' and instantiate directly: 'bw = BigWig('file.bw')' to get BigWig-specific methods.

affects: all

gotchaFile handles must be closed explicitly or used with 'with' statement; resources are not freed on garbage collection alone.

fix

Always use 'with open(...) as f:' or call '.close()' on the object.

affects: all

Errors

Common errors & fixes

AttributeError: module 'pybigtools' has no attribute 'read_bigwig'

API changed from read_bigwig to open in v0.2.0.

fix

Use 'from pybigtools import open' and call 'open(filename)'.

TypeError: 'Bytes' object cannot be interpreted as an integer

Fetch returns values as bytes; expecting int list.

fix

Use '.tolist()' or specify dtype; ensure the region coordinates are correct.

Upgrade

Version history

0.2.5latest on PyPI · released Feb 13, 2026

Audit

Dependencies

No dependency data recorded yet.

Agent activity

8 hits · last 30 days

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Resources

githubhttps://github.com/jackh726/bigtools ↗

packagehttps://pypi.org/project/pybigtools/ ↗

docshttps://bigtools.readthedocs.io ↗