###########################################################################
# Bioconvert is a project to facilitate the interconversion #
# of life science data from one format to another. #
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"""Converts :term:`PHYLIP` file to :term:`XMFA` format."""
import colorlog
from Bio import AlignIO
from bioconvert import ConvBase
from bioconvert.core.decorators import compressor, requires
_log = colorlog.getLogger(__name__)
__all__ = ["PHYLIP2XMFA"]
[docs]class PHYLIP2XMFA(ConvBase):
"""
Converts a sequence alignment from :term:`PHYLIP` format to :term:`XMFA`
Methods available are based on biopython [BIOPYTHON]_.
"""
#: Default value
_default_method = "biopython"
def __init__(self, infile, outfile=None, *args, **kwargs):
""".. rubric:: constructor
:param str infile: input :term:`PHYLIP` file.
:param str outfile: (optional) output :term:`NEXUS` file
"""
super().__init__(infile, outfile)
[docs] @requires(python_libraries=["biopython"])
@compressor
def _method_biopython(self, *args, **kwargs):
"""Convert :term:`PHYLIP` interleaved file in :term:`XMFA` (Mauve)format.
`Bio.AlignIO <https://biopython.org/docs/1.76/api/Bio.AlignIO.html>`_"""
sequences = list(AlignIO.parse(self.infile, "phylip"))
count = AlignIO.write(sequences, self.outfile, "mauve")
_log.info("Converted %d records to phylip" % count)