###########################################################################
# 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. #
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# bioconvert is free software: you can redistribute it and/or modify #
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# Repository: https://github.com/bioconvert/bioconvert #
# Documentation: http://bioconvert.readthedocs.io #
###########################################################################
"""Convert :term:`FASTA` format to :term:`FAA` format"""
import textwrap
import colorlog
from bioconvert import ConvBase
from bioconvert.core.decorators import compressor
from bioconvert.io.fasta import Fasta
_log = colorlog.getLogger(__name__)
__all__ = ["FASTA2FAA"]
[docs]class FASTA2FAA(ConvBase):
"""
Methods available is a bioconvert implementation.
"""
#: Default value
_default_method = "bioconvert"
def __init__(self, infile, outfile):
"""
:param str infile: The path to the input FASTA file
:param str outfile: The path to the output FASTQ file
"""
super(FASTA2FAA, self).__init__(infile, outfile)
self.codons = {
"ATA": "I",
"ATC": "I",
"ATT": "I",
"ATG": "M",
"ACA": "T",
"ACC": "T",
"ACG": "T",
"ACT": "T",
"AAC": "N",
"AAT": "N",
"AAA": "K",
"AAG": "K",
"AGC": "S",
"AGT": "S",
"AGA": "R",
"AGG": "R",
"CTA": "L",
"CTC": "L",
"CTG": "L",
"CTT": "L",
"CCA": "P",
"CCC": "P",
"CCG": "P",
"CCT": "P",
"CAC": "H",
"CAT": "H",
"CAA": "Q",
"CAG": "Q",
"CGA": "R",
"CGC": "R",
"CGG": "R",
"CGT": "R",
"GTA": "V",
"GTC": "V",
"GTG": "V",
"GTT": "V",
"GCA": "A",
"GCC": "A",
"GCG": "A",
"GCT": "A",
"GAC": "D",
"GAT": "D",
"GAA": "E",
"GAG": "E",
"GGA": "G",
"GGC": "G",
"GGG": "G",
"GGT": "G",
"TCA": "S",
"TCC": "S",
"TCG": "S",
"TCT": "S",
"TTC": "F",
"TTT": "F",
"TTA": "L",
"TTG": "L",
"TAC": "Y",
"TAT": "Y",
"TAA": "_",
"TAG": "_",
"TGC": "C",
"TGT": "C",
"TGA": "_",
"TGG": "W",
}
[docs] @compressor
def _method_bioconvert(self, *args, **kwargs):
"""Internal method."""
data = Fasta(self.infile)
with open(self.outfile, "w") as fout:
for line in data.read():
fout.write(">{}\t{}\n".format(line["id"], line["comment"]))
seq = line["value"]
# translate the sequence
aa = "".join((self.codons.get(seq[i:i+3], "X") for i in range(0, len(seq), 3)))
fout.write("\n".join(textwrap.wrap(aa, 60)) + "\n")