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# Bioconvert is a project to facilitate the interconversion #
# of life science data from one format to another. #
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"""Convert :term:`PLINK` to :term:`BPLINK`"""
import colorlog
from bioconvert import ConvBase
from bioconvert.core.decorators import requires
from bioconvert.core.utils import generate_outfile_name
_log = colorlog.getLogger(__name__)
[docs]class PLINK2BPLINK(ConvBase):
"""Converts a genotype dataset ped+map in :term:`PLINK` format to
bed+bim+fam :term:`BPLINK` format
Conversion is based on plink executable
"""
#: Default value
_default_method = "plink"
def __init__(self, infile, outfile=None, *args, **kwargs):
""".. rubric:: constructor
:param str infile: input :term:`PLINK` file.
:param str outfile: (optional) output :term:`BPLINK` file
"""
if not outfile:
outfile = infile
super().__init__(infile, outfile)
[docs] @requires("plink")
def _method_plink(self, *args, **kwargs):
"""Convert plink file in text using plink executable.
`plink documentation <http://hpc.ilri.cgiar.org/beca/training/data_mgt_2017/BackgroundMaterial/PlinkTutorial.pdf>`_"""
cmd = "plink --file {infile} --make-bed --out {outfile}".format(infile=self.infile, outfile=self.outfile)
self.execute(cmd)