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Open compressed files transparently

Project Description

xopen

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 slow in older Pythons, and it is a lot faster to use a gzip subprocess.

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.

Usage

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')

Credits

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.

Author

Marcel Martin <mail@marcelm.net> (@marcelm_ on Twitter)

Release History

Release History

This version
History Node

0.2.1

History Node

0.1.1

History Node

0.1.0

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File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
xopen-0.2.1-py2.py3-none-any.whl (6.3 kB) Copy SHA256 Checksum SHA256 py2.py3 Wheel May 31, 2017
xopen-0.2.1.tar.gz (4.4 kB) Copy SHA256 Checksum SHA256 Source May 31, 2017

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