Metadata-Version: 2.1
Name: xopen
Version: 0.8.4
Summary: Open compressed files transparently
Home-page: https://github.com/marcelm/xopen/
Author: Marcel Martin
Author-email: mail@marcelm.net
License: MIT
Description: .. image:: https://travis-ci.org/marcelm/xopen.svg?branch=master
          :target: https://travis-ci.org/marcelm/xopen
          :alt: 
          
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          :target: https://pypi.python.org/pypi/xopen
        
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        =====
        xopen
        =====
        
        This small Python module provides an ``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, ``xopen`` uses ``pigz``, which is a parallel version of ``gzip``,
        to open ``.gz`` files, which is faster than using the built-in ``gzip.open``
        function. ``pigz`` can use multiple threads when compressing, but is also faster
        when reading ``.gz`` files, so it is used both for reading and writing if it is
        available.
        
        This module has originally been developed as part of the `cutadapt
        tool <https://cutadapt.readthedocs.io/>`_ 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 2.7 and 3.4 to 3.8.
        
        
        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 in binary mode for writing::
        
            from xopen import xopen
        
            with xopen('file.txt.gz', mode='wb') as f:
                f.write(b'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 <https://github.com/lh3/bwa/blob/83662032a2192d5712996f36069ab02db82acf67/utils.h>`_.
        
        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.
        
        Some ideas were taken from the `canopener project <https://github.com/selassid/canopener>`_.
        If you also want to open S3 files, you may want to use that module instead.
        
        
        Changes
        -------
        
        v0.8.4
        ~~~~~~
        * When reading gzipped files, force ``pigz`` to use only a single process.
          ``pigz`` cannot 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 ``pigz`` is still
          about twice as fast as regular ``gzip``.
        * Allow ``threads=0`` for specifying that no external ``pigz``/``gzip``
          process should be used (then regular ``gzip.open()`` is used instead).
        
        v0.8.3
        ~~~~~~
        * When reading gzipped files, let ``pigz`` use at most four threads by default.
          This limit previously only applied when writing to a file.
        * Support Python 3.8
        
        v0.8.0
        ~~~~~~
        * Speed improvements when iterating over gzipped files.
        
        v0.6.0
        ~~~~~~
        * For reading from gzipped files, xopen will now use a ``pigz`` subprocess.
          This is faster than using ``gzip.open``.
        * Python 2 support will be dropped in one of the next releases.
        
        v0.5.0
        ~~~~~~
        * 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.
        
        
        Author
        ------
        
        Marcel Martin <mail@marcelm.net> (`@marcelm_ on Twitter <https://twitter.com/marcelm_>`_)
        
        Links
        -----
        
        * `Source code <https://github.com/marcelm/xopen/>`_
        * `Report an issue <https://github.com/marcelm/xopen/issues>`_
        * `Project page on PyPI (Python package index) <https://pypi.python.org/pypi/xopen/>`_
        
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Requires-Python: >=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, <4
Provides-Extra: dev