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

###########################################################################
# 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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"""Converts :term:`NEXUS` file to :term:`PHYLOXML` file."""
import os

import colorlog
from Bio import SeqIO

from bioconvert import ConvBase
from bioconvert.core.decorators import requires

_log = colorlog.getLogger(__name__)


__all__ = ['NEXUS2PHYLOXML']


class NEXUS2PHYLOXML(ConvBase):
    """
    Converts a tree file from :term:`NEXUS` format to :term:`PHYLOXML` format. ::
    """
    _default_method = 'gotree'

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

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

    @requires("conda")
    def _method_gotree(self, *args, **kwargs):
        """uses gotree tool:

        https://github.com/fredericlemoine/gotree

        """
        self.install_tool('gotree')
        cmd = 'gotree reformat phyloxml -i {infile} -o {outfile} -f nexus'.format(
            infile=self.infile,
            outfile=self.outfile)
        self.execute(cmd)
