bgzip: block gzip streams

bgzip provides streams for block gzip files.

Cython is used under the hood to bypass Python's GIL and provide fast, parallelized inflation/deflation.

with open("my_bgzipped_file.gz", "rb") as raw:
    with bgzip.BGZipReader(raw) as fh:
        data = fh.read(number_of_bytes)

with open("my_bgzipped_file.gz", "wb") as raw:
    with bgzip.BGZipWriter(raw) as fh:
        fh.write(my_data)

Installation

pip install bgzip

Requirements

bgzip requires openmp.

MacOS

On MacOS openmp can be installed with:

brew install llvm

Depending on your system, you may need to set the following environment variables to the locaion of llvm library and headers. The following values are common for homebrew installations, but my be different on your system!

export LDFLAGS="-L/opt/homebrew/opt/llvm/lib"
export CPPFLAGS="-I/opt/homebrew/opt/llvm/include"

Links

Project home page GitHub
Package distribution PyPI

Bugs

Please report bugs, issues, feature requests, etc. on GitHub.

Cloud Development Environment

launch gitpod workspace