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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:`BPLINK` to :term:`PLINK` format"""
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 BPLINK2PLINK(ConvBase):
"""Converts a genotype dataset bed+bim+fam in :term:`BPLINK` format to
ped+map :term:`PLINK` format.
Conversion is based on plink [PLINK]_ executable.
.. warning:: **plink** takes several inputs and outputs and does not need
extensions. What is required is a prefix. Bioconvert usage is therefore::
bioconvert bplink2plink plink_toy
Since there is no extension, you must be explicit by providing the
conversion name (bplink2plink). This command will search for 3 input
files plink_toy.bed, plink_toy.bim and plink_toy.fam. It will then
create two output files named plink_toy.ped and plink_toy.map
"""
#: Default value
_default_method = "plink"
def __init__(self, infile, outfile=None, *args, **kwargs):
""".. rubric:: constructor
:param str infile: input :term:`BPLINK` files.
:param str outfile: (optional) output :term:`PLINK` files.
"""
if not outfile:
outfile = infile
super(BPLINK2PLINK, self).__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 --bfile {infile} --recode --out {outfile}".format(infile=self.infile, outfile=self.outfile)
self.execute(cmd)