###########################################################################
# Bioconvert is a project to facilitate the interconversion #
# of life science data from one format to another. #
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# Copyright © 2018-2022 Institut Pasteur, Paris and CNRS. #
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"""Convert :term:`XMFA` to :term:`PHYLIP` format"""
import colorlog
from Bio import SeqIO
from bioconvert import ConvBase, compressor, requires
_log = colorlog.getLogger(__name__)
__all__ = ["XMFA2PHYLIP"]
[docs]class XMFA2PHYLIP(ConvBase):
"""Converts a sequence alignment from :term:`XMFA` to :term:`PHYLIP` format.
Method available 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(XMFA2PHYLIP, self).__init__(infile, outfile)
[docs] @requires(python_libraries=["biopython"])
@compressor
def _method_biopython(self, *args, **kwargs):
"""Convert :term:`XMFA` interleaved file in :term:`PHYLIP` (Mauve)format.
`Bio.SeqIO Documentation <https://biopython.org/docs/1.76/api/Bio.SeqIO.html>`_"""
sequences = list(SeqIO.parse(self.infile, "mauve"))
count = SeqIO.write(sequences, self.outfile, "phylip")
_log.info("Converted %d records to xmfa" % count)