###########################################################################
# Bioconvert is a project to facilitate the interconversion #
# of life science data from one format to another. #
# #
# Copyright © 2018-2022 Institut Pasteur, Paris and CNRS. #
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# bioconvert is free software: you can redistribute it and/or modify #
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"""Convert :term:`GZ` file to :term:`BZ2` format"""
import bz2
import gzip
from bioconvert import ConvBase
from bioconvert.core.base import ConvArg
from bioconvert.core.decorators import requires, requires_nothing
__all__ = ["GZ2BZ2"]
[docs]class GZ2BZ2(ConvBase):
"""Convert :term:`GZ` file to :term:`BZ2` file
Unzip input file using pigz or gunzip and compress using pbzip2. Default
is pigz/pbzip2.
"""
_threading = True
#: Default value
_default_method = "pigz_pbzip2"
def __init__(self, infile, outfile, *args, **kargs):
""".. rubric:: constructor
:param str infile: input GZ file
:param str outfile: output BZ2 filename
"""
super(GZ2BZ2, self).__init__(infile, outfile, *args, **kargs)
[docs] @requires(
external_binaries=[
"pigz",
"pbzip2",
]
)
def _method_pigz_pbzip2(self, *args, **kwargs):
"""Method that uses pigz pbzip2.
`pigz documentation <https://linux.die.net/man/1/pigz>`_
`pbzip2 documentation <https://linux.die.net/man/1/pbzip2>`_"""
# conversion
cmd = "pigz -d -c -p {threads} {input} | pbzip2 -p{threads} > {output}"
self.execute(cmd.format(threads=self.threads, input=self.infile, output=self.outfile))
[docs] @requires(
external_binaries=[
"gunzip",
"bzip2",
]
)
def _method_gunzip_bzip2(self, *args, **kwargs):
"""Single theaded conversion. Method that uses gunzip bzip2.
`gunzip documentation <https://linux.die.net/man/1/gunzip>`_
`bzip2 documentation <http://www.delafond.org/traducmanfr/man/man1/bzip2.1.html>`_"""
cmd = "gunzip --to-stdout {input} | bzip2 > {output}"
self.execute(cmd.format(input=self.infile, output=self.outfile))
[docs] @requires_nothing
def _method_python(self, *args, **kwargs):
"""Internal method"""
with gzip.open(self.infile, "rb") as f, bz2.open(self.outfile, "wb") as g:
g.write(f.read())