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# Bioconvert is a project to facilitate the interconversion #
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"""Converts :term:`STOCKHOLM` file to :term:`CLUSTAL` file."""
import colorlog
from Bio import SeqIO
from bioconvert import ConvBase
from bioconvert.core.decorators import compressor, requires
_log = colorlog.getLogger(__name__)
__all__ = ["STOCKHOLM2CLUSTAL"]
[docs]class STOCKHOLM2CLUSTAL(ConvBase):
"""
Converts a sequence alignment from :term:`STOCKHOLM` format to :term:`CLUSTAL` format
Methods available are based on squizz [SQUIZZ]_ and biopython [BIOPYTHON]_.
"""
#: Default value
_default_method = "biopython"
def __init__(self, infile, outfile=None, alphabet=None, *args, **kwargs):
""".. rubric:: constructor
:param str infile: input :term:`STOCKHOLM` file.
:param str outfile: (optional) output :term:`CLUSTAL` file
"""
super(STOCKHOLM2CLUSTAL, self).__init__(infile, outfile)
[docs] @requires(python_library="biopython")
@compressor
def _method_biopython(self, *args, **kwargs):
"""Convert :term:`STOCKHOLM` interleaved file in :term:`CLUSTAL` 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, "clustal")
_log.debug("Converted %d records to clustal" % count)
[docs] @requires("squizz")
@compressor
def _method_squizz(self, *args, **kwargs):
"""Convert :term:`STOCKHOLM` file in :term:`CLUSTAL` format using squizz tool."""
cmd = "squizz -c CLUSTAL {infile} > {outfile}".format(infile=self.infile, outfile=self.outfile)
self.execute(cmd)