Skip to main content

Python bindings to UCSC Big Binary (bigWig/bigBed) file library

Project description


Python interface to Jim Kent's big binary file (bbi) [1] library from the UCSC Genome Browser source tree using Cython.

This provides read-level access to local and remote bigWig and bigBed files but no write capabilitites. The main feature is fast retrieval of range queries into numpy arrays.



These accept a local file path or URL.

  • bbi.is_bbi(path) --> bool
  • bbi.is_bigwig(path) --> bool
  • bbi.is_bigbed(path) --> bool
  • bbi.chromsizes(path) --> OrderedDict
  • bbi.zooms(path) --> list
  • --> dict

Array output

These accept either a bigWig or bigBed file path / URL. The signal of a bigBed file is the genomic coverage of its intervals.

For a single range query:

  • bbi.fetch(path, chrom, start, end, [bins [, missing [, oob, [, summary]]]]) --> 1D numpy array

For a list of equal-length segments (i.e. to produce a stacked heatmap):

  • bbi.stackup(path, chroms, starts, ends, [bins [, missing [, oob, [, summary]]]]) --> 2D numpy array

Summary querying is supported by specifying the number of bins for coarsegraining. The summary statistic can be one of: 'mean', 'min', 'max', 'cov', or 'std'. (default = 'mean').

Missing data can be filled with a custom fill value, missing (default = 0).

Out-of-bounds ranges (i.e. start less than zero or end greater than the chromosome length) are permitted because of their utility e.g., for generating vertical heatmap stacks centered at specific genomic features. A separate custom fill value, oob can be provided for out-of-bounds positions (default = NaN).

Interval output

Accepts either a bigWig or bigBed file path / URL.

  • bbi.fetch_intervals(path, chrom, start, end) --> iterator

See the docstrings for complete documentation.



  • Linux/MacOS
  • C compiler, zlib, pthreads, libpng, openssl, make
  • Python 2.7/3.3+
  • numpy and cython

On fresh Ubuntu instance, you'll need build-essential, make, libssl-dev, libpng16-dev. It seems to work on the Windows Subsystem for Linux too.

pybbi is now on PyPI as a source distribution. It ships with (slightly modified) kent utils source, which it will compile before building the extension module.

$ pip install pybbi

For development, clone the repo and install in editable mode:

$ git clone
$ cd pybbi
$ pip install -e .

Related projects

  • libBigWig: Alternative C library for bigWig and bigBed files by Devon Ryan
  • pyBigWig: Python bindings for libBigWig by the same author
  • bw-python: Alternative Python wrapper to libBigWig by Brent Pederson
  • bx-python: Python bioinformatics library from James Taylor's group that includes tools for bbi files.

This library provides bindings to the reference UCSC bbi library code. Check out @dpryan79's libBigWig for an alternative and dedicated C library for big binary files. pyBigWig also provides numpy-based retrieval and bigBed support.




On OSX, you may get errors about missing header files (e.g., png.h, openssl/sha.h), which even if installed may not be located in standard include locations. Either create the required symlinks or update the C_INCLUDE_PATH environment variable accordingly before installing pybbi.

export C_INCLUDE_PATH="/usr/local/include/libpng:/usr/local/opt/openssl/include:$C_INCLUDE_PATH"


Unfortunately, Kent's C source is not well-behaved library code, as it is littered with error calls that call exit(). pybbi will catch and pre-empt common input errors, but if somehow an internal error does get raised, it will terminate your interpreter instance.

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Filename, size & hash SHA256 hash help File type Python version Upload date
pybbi-0.2.0.tar.gz (21.4 MB) Copy SHA256 hash SHA256 Source None

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN SignalFx SignalFx Supporter DigiCert DigiCert EV certificate StatusPage StatusPage Status page