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"""Converts :term:`PHYLIP` file to :term:`FASTA` format."""
import colorlog
from Bio import SeqIO
from bioconvert import ConvBase
from bioconvert.core.decorators import compressor, requires
_log = colorlog.getLogger(__name__)
__all__ = ["PHYLIP2FASTA"]
[docs]class PHYLIP2FASTA(ConvBase):
"""Converts a sequence alignment in :term:`PHYLIP` format to :term:`FASTA` format
Methods available are based on biopython [BIOPYTHON]_, squiz [SQUIZZ]_.
"""
#: default value
_default_method = "biopython"
def __init__(self, infile, outfile=None, alphabet=None, *args, **kwargs):
""".. rubric:: constructor
:param str infile: input :term:`PHYLIP` file.
:param str outfile: (optional) output :term:`FASTA` file
"""
super(PHYLIP2FASTA, self).__init__(infile, outfile)
self.alphabet = alphabet
[docs] @requires(python_library="biopython")
@compressor
def _method_biopython(self, *args, **kwargs):
"""For this method we use the biopython package Bio.SeqIO.
`Bio.SeqIO Documentation <https://biopython.org/docs/1.76/api/Bio.SeqIO.html>`_"""
sequences = list(SeqIO.parse(self.infile, "phylip", alphabet=self.alphabet))
_ = SeqIO.write(sequences, self.outfile, "fasta")
[docs] @requires("squizz")
@compressor
def _method_squizz(self, *args, **kwargs):
"""Convert Phylip inteleaved file in fasta format using squizz tool.
The fasta file is an alignemnt, that means the gap are conserved."""
cmd = "squizz -c FASTA {infile} > {outfile}".format(infile=self.infile, outfile=self.outfile)
self.execute(cmd)
[docs] @requires("goalign")
@compressor
def _method_goalign(self, *args, **kwargs):
"""Convert fasta file in Phylip interleaved 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 fasta -i {infile} -p -o {outfile}".format(infile=self.infile, outfile=self.outfile)
self.execute(cmd)