compressio

About

Open a gzip-/bgzip-/bzip2-/lzma-/xz-compressed file or uncompressed file in binary or text mode.

The filename argument can be an actual filename (a str or bytes object), or an existing file object to read from or write to. Use "-" to open a file object to the appropriate stdin/stdout stream requested via mode. Serial readling via HTTP and FTP URL file path is supported.

The mode argument can be "r", "rb", "w", "wb", "x", "xb", "a" or "ab" for binary mode, or "rt", "wt", "xt" or "at" for text mode. The default mode is "rt". The default compresslevel for compression streams is 9.

For binary mode, the encoding, errors, and newline arguments must not be provided.

For text mode, a compressed stream object is created, then wrapped in an io.TextIOWrapper instance with the specified encoding, error handling behavior, and line ending(s).

To read from/write to compressed streams from stdin/stdout or existing file-like objects, the appropriate compression algorithm name must must passed via the compression argument (e.g., compression=gzip). When writing compresslevel must be set to a value between 1 and 9, inclusive (default is 9).

This module relies on the io, gzip, lzma, bz2, (optionally) bz2file, pysam and zstd modules internally, but others can be supplied via the compression argument, which must return an object with a callable open() method. The bz2file module is only required for Python versions earlier than 3.3. The zstd module is availble via the backports module prior to Python 3.14 and the compression module thereafter.

See Also: help(io.open)

Examples

from compressio import open

# open a file for reading on the local file system
# (algorithm 'gzip' is automatically detected):
infile = open("input.fastq.gz", mode='r')

# open a file for reading on a remote server via HTTP protocol
infile = open("http://path/to/remote/input.fastq.gz")

# open a file for reading (writing) to STDIN (STDOUT) stream. To read
# compressed files, must specify the `compression` attribute explicitly.
# Call one of the supported compression algorithms by name:
from compressio.constants import STDIO
infile = open(STDIO, mode='r', compression='gzip')

# or pass the module object directly:
import gzip
infile = open(STDIO, mode='r', compression=gzip)

outfile = open(STDIO, mode='w', compression=gzip)

Limitations

The bgzip compression interface cannot read from (or write to) existing file streams, and in such cases gzip is used. If this behavior is not desired, please open the file stream directly via compressio.open() using the file name.

Writing to files on remote servers has not been tested.

Other dependencies

• io
• locale
• os
• pysam (required for bgzip compression)
• sys
• urllib
• zstd