Bigtools

Bigtools is a modern, high-performance library and associated tools for reading and writing BigWig and BigBed files. Bigtools is written in Rust and bindings for Python are available.

CLI binaries

Drop-in replacements for the UCSC binaries. Install with cargo or via bioconda (conda, mamba, pixi, etc.).

cargo install bigtools

conda install -c bioconda bigtools

Python package

Python bindings to the bigtools Rust library is provided by the pybigtools package. Install with pip, uv or via bioconda (conda, mamba, pixi, etc.).

pip install pybigtools

conda install -c bioconda pybigtools

To open a file for reading, open() auto-detects whether the file is a BigWig or BigBed and returns a BBIReader:

import pybigtools

b = pybigtools.open("path/to/file.bigWig")  # also accepts an http(s) URL
print(b.chroms())          # {'chr1': 248956422, ...}
print(b.info())            # version, summary stats, zoom levels, ...

To rasterize values over a region as a NumPy array:

values = b.values("chr1", 0, 1000)        # one value per base
binned = b.values("chr1", 0, 1_000_000, bins=1000, summary="mean")

To iterate over raw records (intervals for BigWig, BED entries for BigBed):

for start, end, value in b.records("chr1"):
    ...

Files can be used as context managers, and file-like objects are accepted in place of a path:

with pybigtools.open(open("path/to/file.bigBed", "rb")) as b:
    schema = b.sql(parse=True)

For writing:

import pybigtools

w = pybigtools.open("out.bigWig", "w")
w.write(
    {"chr1": 248956422},
    [("chr1", 0, 100, 1.5), ("chr1", 100, 200, 2.0)],
)
# the file is closed automatically once write() completes

See the API reference for the full set of methods and options.

Rust crate

To use bigtools in your Rust project, add bigtools to your Cargo.toml or run:

cargo add bigtools

See the Rust documentation here.