###########################################################################
# 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. #
# #
# bioconvert is free software: you can redistribute it and/or modify #
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# #
# bioconvert is distributed in the hope that it will be useful, #
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# Repository: https://github.com/bioconvert/bioconvert #
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###########################################################################
"""Convert :term:`GZ` to :term:`DSRC` format"""
import colorlog
from bioconvert import ConvBase, requires
logger = colorlog.getLogger(__name__)
__all__ = ["GZ2DSRC"]
[docs]class GZ2DSRC(ConvBase):
"""Convert compressed fastq.gz file into `DSRC` compressed file
.. plot::
from bioconvert.gz2dsrc import GZ2DSRC
from bioconvert import bioconvert_data
from bioconvert import TempFile
with TempFile(suffix=".dsrc") as fh:
infile = bioconvert_data("test_SP1.fq.gz")
convert = GZ2DSRC(infile, fh.name)
convert.boxplot_benchmark()
"""
#: Default value
_default_method = "pigzdsrc"
_threading = True
def __init__(self, infile, outfile, *args, **kargs):
""".. rubric:: constructor
:param str infile: input GZ filename
:param str outfile: output DSRC filename
"""
super(GZ2DSRC, self).__init__(infile, outfile, *args, **kargs)
[docs] @requires(external_binaries=["pigz", "dsrc"])
def _method_pigzdsrc(self, *args, **kwargs):
"""do the conversion gz -> :term:`DSRC`
:return: the standard output
:rtype: :class:`io.StringIO` object.
Method that uses pigz and dsrc.
`pigz documentation <https://linux.die.net/man/1/pigz>`_
`dsrc documentation <https://github.com/refresh-bio/DSRC>`_"""
cmd = "pigz -d -c -p {threads} {input} | dsrc c -s -t{threads} {output}"
self.execute(cmd.format(threads=self.threads, input=self.infile, output=self.outfile))