###########################################################################
# 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 #
# it under the terms of the GNU General Public License as published by #
# the Free Software Foundation, either version 3 of the License, or #
# (at your option) any later version. #
# #
# bioconvert is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details. #
# #
# You should have received a copy of the GNU General Public License #
# along with this program (COPYING file). #
# If not, see <http://www.gnu.org/licenses/>. #
# #
# Repository: https://github.com/bioconvert/bioconvert #
# Documentation: http://bioconvert.readthedocs.io #
###########################################################################
"""Converts :term:`STOCKHOLM` to :term:`PHYLIP` format."""
import colorlog
from Bio import SeqIO
from bioconvert import ConvBase
from bioconvert.core.decorators import compressor, requires
_log = colorlog.getLogger(__name__)
__all__ = ["STOCKHOLM2PHYLIP"]
[docs]class STOCKHOLM2PHYLIP(ConvBase):
"""
Converts a sequence alignment from :term:`STOCKHOLM` format to :term:`PHYLIP` interleaved format
Methods available are based on squizz [SQUIZZ]_, and
biopython [BIOPYTHON]_.
"""
#: Default value
_default_method = "biopython"
def __init__(self, infile, outfile=None, *args, **kwargs):
""".. rubric:: constructor
:param str infile: input :term:`STOCKHOLM` file.
:param str outfile: (optional) output :term:`FASTA` file
"""
super(STOCKHOLM2PHYLIP, self).__init__(infile, outfile)
[docs] @requires(python_library="biopython")
@compressor
def _method_biopython(self, *args, **kwargs):
"""Convert :term:`STOCKHOLM` interleaved file in :term:`PHYLIP` format using biopython.
`Bio.SeqIO Documentation <https://biopython.org/docs/1.76/api/Bio.SeqIO.html>`_"""
sequences = list(SeqIO.parse(self.infile, "stockholm"))
count = SeqIO.write(sequences, self.outfile, "phylip")
_log.info("Converted %d records to phylip" % count)
[docs] @requires("squizz")
@compressor
def _method_squizz(self, *args, **kwargs):
"""Convert :term:`STOCKHOLM` interleaved file in :term:`PHYLIP` interleaved format using squizz tool."""
cmd = "squizz -c PHYLIPI {infile} > {outfile}".format(infile=self.infile, outfile=self.outfile)
self.execute(cmd)