###########################################################################
# Bioconvert is a project to facilitate the interconversion               #
# of life science data from one format to another.                        #
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# Authors: see CONTRIBUTORS.rst                                           #
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"""Convert :term:`FASTA` to :term:`NEXUS` format"""
import colorlog
from bioconvert.core.decorators import compressor
from bioconvert import ConvBase
from bioconvert.core.decorators import requires

_log = colorlog.getLogger(__name__)


__all__ = ["FASTA2NEXUS"]


class FASTA2NEXUS(ConvBase):
    """Converts a sequence alignment in :term:`FASTA` format to :term:`NEXUS` format

    Methods available are based on squizz [GOALIGN]_.

    """

    #: Default value
    _default_method = "goalign"

    def __init__(self, infile, outfile=None, alphabet=None, *args, **kwargs):
        """.. rubric:: constructor

        :param str infile: input :term:`FASTA` file.
        :param str outfile: (optional) output :term:`NEXUS` file
        """
        super(FASTA2NEXUS, self).__init__(infile, outfile)

    @requires("go")
    @compressor
    def _method_goalign(self, *args, **kwargs):
        """Convert fasta file in Nexus format using goalign tool.

        `goalign documentation <https://github.com/fredericlemoine/goalign>`_

        The fasta file must be an alignemnt file, yhis mean all the sequences must
        have the same length (with the gap) otherwise an error will be raised.
        """
        self.install_tool("goalign")
        cmd = "goalign reformat nexus -i {infile} -o {outfile}".format(
            infile=self.infile, outfile=self.outfile
        )
        self.execute(cmd)
