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

###########################################################################
# Bioconvert is a project to facilitate the interconversion               #
# of life science data from one format to another.                        #
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"""Converts :term:`STOCKHOLM` file to :term:`CLUSTAL` file."""
import colorlog
from Bio import SeqIO

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

_log = colorlog.getLogger(__name__)


__all__ = ["STOCKHOLM2CLUSTAL"]


class STOCKHOLM2CLUSTAL(ConvBase):
    """
    Converts a sequence alignment from :term:`STOCKHOLM` format to :term:`CLUSTAL` format

    Methods available are based on squizz [SQUIZZ]_ and biopython [BIOPYTHON]_.

    """
    _default_method = 'biopython'

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

        :param str infile: input :term:`STOCKHOLM` file.
        :param str outfile: (optional) output :term:`CLUSTAL` file
        """
        super(STOCKHOLM2CLUSTAL, self).__init__(infile, outfile)

    @requires(python_library="biopython")
    @compressor
    def _method_biopython(self, *args, **kwargs):
        """
        Convert :term:`STOCKHOLM` interleaved file in :term:`CLUSTAL` format using biopython.

        """
        sequences = list(SeqIO.parse(self.infile, "stockholm"))
        count = SeqIO.write(sequences, self.outfile, "clustal")
        _log.debug("Converted %d records to clustal" % count)

    @requires("squizz")
    @compressor
    def _method_squizz(self, *args, **kwargs):
        """
        Convert :term:`STOCKHOLM` file in :term:`CLUSTAL` format using squizz tool.

        """
        cmd = 'squizz -c CLUSTAL {infile} > {outfile}'.format(
            infile=self.infile,
            outfile=self.outfile)
        self.execute(cmd)
