###########################################################################
# Bioconvert is a project to facilitate the interconversion #
# of life science data from one format to another. #
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""" Convert a compressed :term:`FASTQ` from :term:`DSRC` to :term:`FASTQ` format"""
import colorlog
from bioconvert import ConvBase
from bioconvert.core.decorators import requires
logger = colorlog.getLogger(__name__)
__all__ = ["DSRC2GZ"]
[docs]class DSRC2GZ(ConvBase):
"""Convert a compressed :term:`FASTQ` from :term:`DSRC` to :term:`GZ` format
Methods available are based on dsrc [DSRC]_ and pigz [PIGZ]_.
"""
#: Default value
_default_method = "dsrcpigz"
_threading = True
def __init__(self, infile, outfile, *args, **kargs):
""".. rubric:: constructor
:param str infile: input DSRC filename
:param str outfile: output GZ filename
"""
super(DSRC2GZ, self).__init__(infile, outfile, *args, **kargs)
[docs] @requires("dsrc")
def _method_dsrcpigz(self, *args, **kwargs):
"""Do the conversion dsrc -> :term:`GZ`.
Method that uses pigz and dsrc.
`pigz documentation <https://linux.die.net/man/1/pigz>`_
`dsrc documentation <https://github.com/refresh-bio/DSRC>`_
option threadig does not work with the dsrc version from conda so we
do not add the -t threads option
"""
cmd = "dsrc d -s {input} | pigz -c -p {threads} > {output}"
self.execute(cmd.format(threads=self.threads, input=self.infile, output=self.outfile))