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Utilities for working with files.

Project description

xphyle: extraordinarily simple file handling

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xphyle is a small python library that makes it easy to open compressed files. Most importantly, xphyle will use the appropriate program (e.g. 'gzip') to compress/decompress a file if it is available on your system; this is almost always faster than using the corresponding python library. xphyle also provides methods that simplify common file I/O operations.

Recent version of xphyle (4.0.0+) require python 3.6. Older versions of xphyle support python 3.4+.

Please note that xphyle may work on Windows, but it is not tested.

Installation

pip install xphyle

Building from source

Clone this repository and run

make

Example usages:

from xphyle import *
from xphyle.paths import STDIN, STDOUT

# Open a compressed file...
myfile = xopen('infile.gz')

# ...or a compressed stream
# e.g. gzip -c afile | python my_program.py
stdin = xopen(STDIN)

# Easily write to the stdin of a subprocess
with open_('|cat', 'wt') as process:
    process.write('foo')

# We have to tell xopen what kind of compression
# to use when writing to stdout
stdout = xopen(STDOUT, compression='gz')

# The `open_` method ensures that the file is usable with the `with` keyword.
# Print all lines in a compressed file...
with open_('infile.gz') as myfile:
    for line in myfile:
        print(line)

# ... or a compressed URL
with open_('http://foo.com/myfile.gz') as myfile:
    for line in myfile:
        print(line)

# Transparently handle paths and file objects
def dostuff(path_or_file):
    with open_(path_or_file) as myfile:
        for line in myfile:
            print(line)

# Read all lines in a compressed file into a list
from xphyle.utils import read_lines
lines = list(read_lines('infile.gz'))

# Sum the rows in a compressed file where each line is an integer value
total = sum(read_lines('infile.gz', convert=int))

See the Documentation for full usage information.

Supported compression formats

  • gzip (uses igzip or pigz if available)
  • bgzip
  • bzip2 (uses pbzip2 if available)
  • lzma
  • zstd

Issues

Please report bugs and request enhancements using the issue tracker.

Roadmap

Future releases are mapped out using GitHub Projects.

Citing xphyle

Didion, JP (2017) xphyle: Extraordinarily simple file handling. Journal of Open Source Software; doi:10.21105/joss.00255

Acknowledgements

Project details


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