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Source code for galaxy.util.compression_utils

import gzip
import io
import sys
import zipfile

from .checkers import (

if sys.version_info < (3, 3):
    import bz2file as bz2
    gzip.GzipFile.read1 = gzip.GzipFile.read  # workaround for https://bugs.python.org/issue12591
    import bz2

[docs]def get_fileobj(filename, mode="r", compressed_formats=None): """ Returns a fileobj. If the file is compressed, return an appropriate file reader. In text mode, always use 'utf-8' encoding. :param filename: path to file that should be opened :param mode: mode to pass to opener :param compressed_formats: list of allowed compressed file formats among 'bz2', 'gzip' and 'zip'. If left to None, all 3 formats are allowed """ if compressed_formats is None: compressed_formats = ['bz2', 'gzip', 'zip'] # Remove 't' from mode, which may cause an error for compressed files mode = mode.replace('t', '') # the various compression readers don't support 'U' mode, # so we open in 'r'. if mode == 'U': cmode = 'r' else: cmode = mode if 'gzip' in compressed_formats and is_gzip(filename): fh = gzip.GzipFile(filename, cmode) elif 'bz2' in compressed_formats and is_bz2(filename): fh = bz2.BZ2File(filename, cmode) elif 'zip' in compressed_formats and zipfile.is_zipfile(filename): # Return fileobj for the first file in a zip file. with zipfile.ZipFile(filename, cmode) as zh: fh = zh.open(zh.namelist()[0], cmode) elif 'b' in mode: return open(filename, mode) else: return io.open(filename, mode, encoding='utf-8') if 'b' not in mode: return io.TextIOWrapper(fh, encoding='utf-8') else: return fh