Open compressed files transparently
This small Python module provides a xopen function that works like the built-in 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. For example, simply using gzip.open is very slow in older Pythons, and it is a lot faster to use a gzip subprocess. For writing to gzip files, xopen uses pigz when available.
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 2.6, 2.7, 3.3, 3.4, 3.5 and 3.6.
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 for writing:
from xopen import xopen with xopen('file.txt.gz', mode='w') as f: f.write('Hello')
The name xopen was taken from the C function of the same name in the utils.h file which is part of BWA.
Kyle Beauchamp <https://github.com/kyleabeauchamp/> has contributed support for appending to files.
Some ideas were taken from the canopener project. If you also want to open S3 files, you may want to use that module instead.
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|
|xopen-0.3.0-py2.py3-none-any.whl (6.5 kB) Copy SHA256 hash SHA256||Wheel||py2.py3||Nov 15, 2017|
|xopen-0.3.0.tar.gz (4.5 kB) Copy SHA256 hash SHA256||Source||None||Nov 15, 2017|