###########################################################################
# Bioconvert is a project to facilitate the interconversion #
# of life science data from one format to another. #
# #
# Copyright © 2018-2022 Institut Pasteur, Paris and CNRS. #
# #
# bioconvert is free software: you can redistribute it and/or modify #
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# bioconvert is distributed in the hope that it will be useful, #
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# Repository: https://github.com/bioconvert/bioconvert #
# Documentation: http://bioconvert.readthedocs.io #
###########################################################################
"""Converts :term:`PHYLOXML` file to :term:`NEXUS` format."""
import colorlog
from bioconvert import ConvBase
from bioconvert.core.decorators import compressor, requires
_log = colorlog.getLogger(__name__)
__all__ = ["PHYLOXML2NEXUS"]
[docs]class PHYLOXML2NEXUS(ConvBase):
"""
Converts a tree file from :term:`PHYLOXML` 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:`PHYLOXML` 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:`PHYLOXML` 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 phyloxml"
cmd = cmd.format(infile=self.infile, outfile=self.outfile)
self.execute(cmd)