This small Python module provides an
xopen function that works like the
open function, but can also deal with compressed files.
Supported compression formats are gzip, bzip2 and xz. They are automatically
recognized by their file extensions .gz, .bz2 or .xz.
The focus is on being as efficient as possible on all supported Python versions.
pigz, which is a parallel version of
.gz files, which is faster than using the built-in
pigz can use multiple threads when compressing, but is also faster
.gz files, so it is used both for reading and writing if it is
This module has originally been developed as part of the Cutadapt tool that is used in bioinformatics to manipulate sequencing data. It has been in successful use within that software for a few years.
xopen is compatible with Python versions 3.5 to 3.8.
Open a file for reading:
from xopen import xopen with xopen('file.txt.xz') as f: content = f.read()
Or without context manager:
from xopen import xopen f = xopen('file.txt.xz') content = f.read() f.close()
Open a file in binary mode for writing:
from xopen import xopen with xopen('file.txt.gz', mode='wb') as f: f.write(b'Hello')
xopen was taken from the C function of the same name in the
utils.h file which is part of
Kyle Beauchamp <https://github.com/kyleabeauchamp/> has contributed support for appending to files.
Ruben Vorderman <https://github.com/rhpvorderman/> contributed improvements to make reading gzipped files faster.
Benjamin Vaisvil <https://github.com/bvaisvil> contributed support for format detection from content.
Some ideas were taken from the canopener project. If you also want to open S3 files, you may want to use that module instead.
- When the file name extension of a file to be opened for reading is not available, the content is inspected (if possible) and used to determine which compression format applies.
- This release drops Python 2.7 and 3.4 support. Python 3.5 or later is now required.
- When reading gzipped files, force
pigzto use only a single process.
pigzcannot use multiple cores anyway when decompressing. By default, it would use extra I/O processes, which slightly reduces wall-clock time, but increases CPU time. Single-core decompression with
pigzis still about twice as fast as regular
threads=0for specifying that no external
gzipprocess should be used (then regular
gzip.open()is used instead).
- When reading gzipped files, let
pigzuse at most four threads by default. This limit previously only applied when writing to a file.
- Support Python 3.8
- Speed improvements when iterating over gzipped files.
- For reading from gzipped files, xopen will now use a
pigzsubprocess. This is faster than using
- Python 2 support will be dropped in one of the next releases.
- By default, pigz is now only allowed to use at most four threads. This hopefully reduces problems some users had with too many threads when opening many files at the same time.
- xopen now accepts pathlib.Path objects.