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# Bioconvert is a project to facilitate the interconversion #
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"""Convert :term:`BZ2` to :term:`GZ` format"""
import bz2
import gzip
import colorlog
from bioconvert import ConvBase
from bioconvert.core.decorators import requires, requires_nothing
logger = colorlog.getLogger(__name__)
__all__ = ["BZ22GZ"]
[docs]class BZ22GZ(ConvBase):
"""Convert :term:`BZ2` file to :term:`GZ` file
Methods based on bunzip2 or zlib/bz2 Python libraries.
"""
#: Default value
_default_method = "bz2_gz"
_threading = True
def __init__(self, infile, outfile, *args, **kargs):
""".. rubric:: constructor
:param str infile: input BZ2 file
:param str outfile: output GZ filename
"""
super(BZ22GZ, self).__init__(infile, outfile, *args, **kargs)
[docs] @requires("bunzip2")
def _method_bz2_gz(self, *args, **kwargs):
"""Method that uses bunzip2 gzip.
`bunzip2 documentation <https://docs.oracle.com/cd/E86824_01/html/E54763/bunzip2-1.html>`_
`gzip documentation <https://www.gnu.org/software/gzip/manual/gzip.html>`_"""
# conversion
cmd = "bunzip2 -c {input} | gzip > {output}".format(input=self.infile, output=self.outfile)
self.execute(cmd)
[docs] @requires_nothing
def _method_python(self, *args, **kargs):
"""Internal method"""
with bz2.open(self.infile, "rb") as f, gzip.open(self.outfile, "wb") as g:
g.write(f.read())