pybigtools

0.2.5 verified Fri May 01 auth: no python

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.

pip install pybigtools

Common errors

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

cause API changed from read_bigwig to open in v0.2.0.

fix

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

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

cause Fetch returns values as bytes; expecting int list.

fix

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

Warnings

breaking In 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.

gotcha The '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.

gotcha File 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.

Imports

open
wrong
```
import pybigtools
```
correct
```
from pybigtools import open
```
Direct import of the 'open' function is required; the module itself is not callable.

BigWig

wrong

from pybigtools import bigwig

correct

from pybigtools import BigWig

Class name is BigWig, not lowercase bigwig.

BigBed

wrong

from pybigtools import bigbed

correct

from pybigtools import BigBed

Class name is BigBed, not lowercase bigbed.

Quickstart

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)