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# Bioconvert is a project to facilitate the interconversion #
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"""Converts :term:`NEWICK` file to :term:`NEXUS` format."""
import colorlog
from bioconvert import ConvBase
from bioconvert.core.decorators import compressor, requires
_log = colorlog.getLogger(__name__)
__all__ = ["NEWICK2NEXUS"]
[docs]class NEWICK2NEXUS(ConvBase):
"""
Converts a tree file from :term:`NEWICK` format to :term:`NEXUS` format.
Methods available are based on gotree [GOTREE]_.
"""
#: Default value
_default_method = "gotree"
def __init__(self, infile, outfile=None, *args, **kwargs):
""".. rubric:: constructor
:param str infile: input :term:`NEWICK` file.
:param str outfile: (optional) output :term:`NEXUS` file
"""
super().__init__(infile, outfile)
[docs] @requires("gotree")
@compressor
def _method_gotree(self, *args, **kwargs):
"""Convert :term:`NEWICK` file in :term:`NEXUS` format using gotree tool.
`gotree documentation <https://github.com/fredericlemoine/gotree>`_"""
self.install_tool("gotree")
cmd = "gotree reformat nexus -i {infile} -o {outfile} -f newick"
cmd = cmd.format(infile=self.infile, outfile=self.outfile)
self.execute(cmd)