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# Bioconvert is a project to facilitate the interconversion #
# of life science data from one format to another. #
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"""Convert :term:`FASTA` to :term:`NEXUS` format"""
import colorlog
from bioconvert import ConvBase
from bioconvert.core.decorators import compressor, requires
_log = colorlog.getLogger(__name__)
__all__ = ["FASTA2NEXUS"]
[docs]class FASTA2NEXUS(ConvBase):
"""Converts a sequence alignment in :term:`FASTA` format to :term:`NEXUS` format
Methods available are based on squizz [GOALIGN]_.
"""
#: Default value
_default_method = "goalign"
def __init__(self, infile, outfile=None, alphabet=None, *args, **kwargs):
""".. rubric:: constructor
:param str infile: input :term:`FASTA` file.
:param str outfile: (optional) output :term:`NEXUS` file
"""
super(FASTA2NEXUS, self).__init__(infile, outfile)
[docs] @requires("goalign")
@compressor
def _method_goalign(self, *args, **kwargs):
"""Convert fasta file in Nexus format using goalign tool.
`goalign documentation <https://github.com/fredericlemoine/goalign>`_
The fasta file must be an alignemnt file, yhis mean all the sequences must
have the same length (with the gap) otherwise an error will be raised.
"""
self.install_tool("goalign")
cmd = "goalign reformat nexus -i {infile} -o {outfile}".format(infile=self.infile, outfile=self.outfile)
self.execute(cmd)