# -*- coding: utf-8 -*-

###########################################################################
# Bioconvert is a project to facilitate the interconversion               #
# of life science data from one format to another.                        #
#                                                                         #
# Authors: see CONTRIBUTORS.rst                                           #
# Copyright © 2018  Institut Pasteur, Paris and CNRS.                     #
# See the COPYRIGHT file for details                                      #
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# bioconvert is free software: you can redistribute it and/or modify      #
# it under the terms of the GNU General Public License as published by    #
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# bioconvert is distributed in the hope that it will be useful,           #
# but WITHOUT ANY WARRANTY; without even the implied warranty of          #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the           #
# GNU General Public License for more details.                            #
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# along with this program (COPYING file).                                 #
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"""Convert :term:`VCF` format to :term:`WIGGLE` formats"""
from bioconvert import ConvBase
import colorlog

from bioconvert.core.decorators import requires

_log = colorlog.getLogger(__name__)

__all__ = ["VCF2WIGGLE"]


class VCF2WIGGLE(ConvBase):
    """Convert sorted :term:`VCF` file into :term:`WIGGLE` file 

    """
    _default_method = "wiggletools"

    def __init__(self, infile, outfile):
        """
        :param str infile: The path to the input VCF file. **It must be sorted**.
        :param str outfile: The path to the output file
        """
        super().__init__(infile, outfile)

    @requires("wiggletools")
    def _method_wiggletools(self, *args, **kwargs):
        """

        """
        cmd = "wiggletools {} > {}".format(self.infile, self.outfile)
        self.execute(cmd)

