#
# Example:
# degenerate.py /home/mendezg/greenalgae/translations/cds/env10972015_1.cds
from Bio import SeqIO
from degenerate_dna import Degenera
import argparse
# Argument Parser
parser = argparse.ArgumentParser(
description=
'This script uses the degenerate_dna python library to substitute the third codon position of input DNA sequences with degenerate codes for the same codon.'
)
parser.add_argument(
'--dna',
required=True,
help='The full file path to the desired input DNA sequence in FASTA format.'
)
args = parser.parse_args()
DNA = args.dna
OUTPUT_FILE = ("%s.deg.fas" % DNA.split("/")[-1].split(".")[0])
INPUT_HANDLE = open(DNA, "rU")
FASTA_SEQUENCES = SeqIO.parse(INPUT_HANDLE, 'fasta')
with open(OUTPUT_FILE, 'a') as FILE:
for SeqRecord in FASTA_SEQUENCES:
res = Degenera(dna=SeqRecord.seq, table=1, method='S')
res.degenerate()
DEG = res.degenerated
FILE.write(">%s\n%s\n" % (SeqRecord.id, DEG))
