def degenerate(self, method=None):
"""
Parameters:
method (str): S, Z, SZ, normal
Returns:
(str): Degenerated sequence using Zwick et al methods.
"""
self._check_reading_frame()
self._correct_seq_based_on_reading_frame()
if not method:
table = self.table
method = 'normal'
else:
table = 1
method = method
res = Degenera(dna=str(self.seq), table=table, method=method)
res.degenerate()
return res.degenerated
#
# Author: Gregory Mendez
#
# This script uses the degenerate_dna python library from https://github.com/carlosp420/degenerate-dna
#
# This script takes an input fasta file and converts the third codon position to
# degenerate code that could produce the same amino acid for that codon.
#
# 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 ) )
class TestApi(unittest.TestCase):
def setUp(self):
self.dna = "AGTTCTTTACTACGTAGA"
self.res = Degenera(dna=self.dna)
def test_standard_code_normal(self):
self.res.table = 1
self.res.method = "normal"
self.res.degenerate()
result = self.res.degenerated
expected = "AGYTCNYTNYTNMGNMGN"
self.assertEqual(expected, result)
def test_standard_code_S(self):
self.res.table = 1
self.res.method = "S"
self.res.degenerate()
result = self.res.degenerated
expected = "AGYAGYYTNYTNMGNMGN"
self.assertEqual(expected, result)
def test_standard_code_Z(self):
self.res.table = 1
self.res.method = "Z"
self.res.degenerate()
result = self.res.degenerated
expected = "TCNTCNYTNYTNMGNMGN"
self.assertEqual(expected, result)
def test_standard_code_SZ(self):
self.res.table = 1
self.res.method = "SZ"
self.res.degenerate()
result = self.res.degenerated
expected = "NNNNNNYTNYTNMGNMGN"
self.assertEqual(expected, result)
def test_degenerate_code_nt1(self):
self.res.dna = "ANN"
self.res.table = 1
self.res.method = "SZ"
self.res.degenerate()
result = self.res.degenerated
expected = "NNN"
self.assertEqual(expected, result)
def test_long_seq_table_1_normal(self):
self.res.dna = "??????????aAGACGTGTTGGATGAG?TTGCCGACCTTCCGATCTGTCGGCGACGCCTTGAAAGATGCCTTCGAyGGAGCGTCGCGGGTCATGATGCCC---AACACAGAGTTGGAAGCGCCC---GCT---CAGCGGAACGAT---GCGGCTCCGCACAGAGTCCCGCGAAGAGATCGATACAGATTCCAACTTCGACCGCACAATCCTGACCATAAAACACCCGGGGACAAGGACCTAGTATACTTGGAATCATCGCCGGGTTTCTGCGAAAAGAACCCGAGACTGGGCATTCCCGGTACGCACGGGCGTTCCTGCAACGACACGAGCATCGGCGTCGATGGCTGCGACCTGATGTGCTGTGGCCGGGGGTACCGGACTGAGACGATGTTTGTCGTCGA"
self.res.table = 1
self.res.method = "normal"
self.res.degenerate()
result = self.res.degenerated
expected = "NNNNNNNNNNNNGAYGTNYTNGAYGARNNNGCNGAYYTNCCNATHTGYMGNMGNMGNYTNGARMGNTGYYTNMGNNNNAGYGTNGCNGGNCAYGAYGCNC---AACAYMGNGTNGGNAGYGCNC---GCT---CAGCNGARMGNT---GCGGNTCNGCNCARAGYCCNGCNAARMGNTCNATHCARATHCCNACNTCNACNGCNCARTCNTGACCNTAAAAYACNMGNGGNCARGGNCCNAGYATHYTNGGNATHATHGCNGGNTTYYTNMGNAARGARCCNGARACNGGNCAYTCNMGNTAYGCNMGNGCNTTYYTNCARMGNCAYGARCAYMGNMGNMGNTGGYTNMGNCCNGAYGTNYTNTGGCCNGGNGTNCCNGAYTGAGAYGAYGTNTGYMGNMGN"
self.assertEqual(expected, result)
def test_long_seq_table_1_S(self):
self.res.dna = "??????????aAGACGTGTTGGATGAG?TTGCCGACCTTCCGATCTGTCGGCGACGCCTTGAAAGATGCCTTCGAyGGAGCGTCGCGGGTCATGATGCCC---AACACAGAGTTGGAAGCGCCC---GCT---CAGCGGAACGAT---GCGGCTCCGCACAGAGTCCCGCGAAGAGATCGATACAGATTCCAACTTCGACCGCACAATCCTGACCATAAAACACCCGGGGACAAGGACCTAGTATACTTGGAATCATCGCCGGGTTTCTGCGAAAAGAACCCGAGACTGGGCATTCCCGGTACGCACGGGCGTTCCTGCAACGACACGAGCATCGGCGTCGATGGCTGCGACCTGATGTGCTGTGGCCGGGGGTACCGGACTGAGACGATGTTTGTCGTCGA"
self.res.table = 1
self.res.method = "S"
self.res.degenerate()
result = self.res.degenerated
expected = "NNNNNNNNNNNNGAYGTNYTNGAYGARNNNGCNGAYYTNCCNATHTGYMGNMGNMGNYTNGARMGNTGYYTNMGNNNNAGYGTNGCNGGNCAYGAYGCNC---AACAYMGNGTNGGNAGYGCNC---GCT---CAGCNGARMGNT---GCGGNAGYGCNCARAGYCCNGCNAARMGNAGYATHCARATHCCNACNAGYACNGCNCARAGYTGACCNTAAAAYACNMGNGGNCARGGNCCNAGYATHYTNGGNATHATHGCNGGNTTYYTNMGNAARGARCCNGARACNGGNCAYAGYMGNTAYGCNMGNGCNTTYYTNCARMGNCAYGARCAYMGNMGNMGNTGGYTNMGNCCNGAYGTNYTNTGGCCNGGNGTNCCNGAYTGAGAYGAYGTNTGYMGNMGN"
self.assertEqual(expected, result)
def test_long_seq_table_1_Z(self):
self.res.dna = "??????????aAGACGTGTTGGATGAG?TTGCCGACCTTCCGATCTGTCGGCGACGCCTTGAAAGATGCCTTCGAyGGAGCGTCGCGGGTCATGATGCCC---AACACAGAGTTGGAAGCGCCC---GCT---CAGCGGAACGAT---GCGGCTCCGCACAGAGTCCCGCGAAGAGATCGATACAGATTCCAACTTCGACCGCACAATCCTGACCATAAAACACCCGGGGACAAGGACCTAGTATACTTGGAATCATCGCCGGGTTTCTGCGAAAAGAACCCGAGACTGGGCATTCCCGGTACGCACGGGCGTTCCTGCAACGACACGAGCATCGGCGTCGATGGCTGCGACCTGATGTGCTGTGGCCGGGGGTACCGGACTGAGACGATGTTTGTCGTCGA"
self.res.table = 1
self.res.method = "Z"
self.res.degenerate()
result = self.res.degenerated
expected = "NNNNNNNNNNNNGAYGTNYTNGAYGARNNNGCNGAYYTNCCNATHTGYMGNMGNMGNYTNGARMGNTGYYTNMGNNNNTCNGTNGCNGGNCAYGAYGCNC---AACAYMGNGTNGGNTCNGCNC---GCT---CAGCNGARMGNT---GCGGNTCNGCNCARTCNCCNGCNAARMGNTCNATHCARATHCCNACNTCNACNGCNCARTCNTGACCNTAAAAYACNMGNGGNCARGGNCCNTCNATHYTNGGNATHATHGCNGGNTTYYTNMGNAARGARCCNGARACNGGNCAYTCNMGNTAYGCNMGNGCNTTYYTNCARMGNCAYGARCAYMGNMGNMGNTGGYTNMGNCCNGAYGTNYTNTGGCCNGGNGTNCCNGAYTGAGAYGAYGTNTGYMGNMGN"
self.assertEqual(expected, result)
def test_long_seq_table_1_SZ(self):
self.res.dna = "??????????aAGACGTGTTGGATGAG?TTGCCGACCTTCCGATCTGTCGGCGACGCCTTGAAAGATGCCTTCGAyGGAGCGTCGCGGGTCATGATGCCC---AACACAGAGTTGGAAGCGCCC---GCT---CAGCGGAACGAT---GCGGCTCCGCACAGAGTCCCGCGAAGAGATCGATACAGATTCCAACTTCGACCGCACAATCCTGACCATAAAACACCCGGGGACAAGGACCTAGTATACTTGGAATCATCGCCGGGTTTCTGCGAAAAGAACCCGAGACTGGGCATTCCCGGTACGCACGGGCGTTCCTGCAACGACACGAGCATCGGCGTCGATGGCTGCGACCTGATGTGCTGTGGCCGGGGGTACCGGACTGAGACGATGTTTGTCGTCGA"
self.res.table = 1
self.res.method = "SZ"
self.res.degenerate()
result = self.res.degenerated
expected = "NNNNNNNNNNNNGAYGTNYTNGAYGARNNNGCNGAYYTNCCNATHTGYMGNMGNMGNYTNGARMGNTGYYTNMGNNNNNNNGTNGCNGGNCAYGAYGCNC---AACAYMGNGTNGGNNNNGCNC---GCT---CAGCNGARMGNT---GCGGNNNNGCNCARNNNCCNGCNAARMGNNNNATHCARATHCCNACNNNNACNGCNCARNNNTGACCNTAAAAYACNMGNGGNCARGGNCCNNNNATHYTNGGNATHATHGCNGGNTTYYTNMGNAARGARCCNGARACNGGNCAYNNNMGNTAYGCNMGNGCNTTYYTNCARMGNCAYGARCAYMGNMGNMGNTGGYTNMGNCCNGAYGTNYTNTGGCCNGGNGTNCCNGAYTGAGAYGAYGTNTGYMGNMGN"
self.assertEqual(expected, result)
def test_long_seq_table_5(self):
self.res.dna = "??????????aAGACGTGTTGGATGAG?TTGCCGACCTTCCGATCTGTCGGCGACGCCTTGAAAGATGCCTTCGAyGGAGCGTCGCGGGTCATGATGCCC---AACACAGAGTTGGAAGCGCCC---GCT---CAGCGGAACGAT---GCGGCTCCGCACAGAGTCCCGCGAAGAGATCGATACAGATTCCAACTTCGACCGCACAATCCTGACCATAAAACACCCGGGGACAAGGACCTAGTATACTTGGAATCATCGCCGGGTTTCTGCGAAAAGAACCCGAGACTGGGCATTCCCGGTACGCACGGGCGTTCCTGCAACGACACGAGCATCGGCGTCGATGGCTGCGACCTGATGTGCTGTGGCCGGGGGTACCGGACTGAGACGATGTTTGTCGTCGA"
self.res.table = 5
self.res.degenerate()
result = self.res.degenerated
expected = "NNNNNNNNNNNNGAYGTNYTNGAYGARNNNGCNGAYYTNCCNATYTGYCGNCGNCGNYTNGARAGNTGYYTNCGNNNNAGNGTNGCNGGNCAYGAYGCNC---AACAYAGNGTNGGNAGNGCNC---GCT---CAGCNGARCGNT---GCGGNTCNGCNCARAGNCCNGCNAARAGNTCNATRCARATYCCNACNTCNACNGCNCARTCNTGRCCNTAAAAYACNCGNGGNCARGGNCCNAGNATRYTNGGNATYATYGCNGGNTTYYTNCGNAARGARCCNGARACNGGNCAYTCNCGNTAYGCNCGNGCNTTYYTNCARCGNCAYGARCAYCGNCGNCGNTGRYTNCGNCCNGAYGTNYTNTGRCCNGGNGTNCCNGAYTGRGAYGAYGTNTGYCGNCGN"
self.assertEqual(expected, result)
def test_long_seq_table_5_normal(self):
self.res.dna = "?ACTTTATATTTTATTTTTGGAATTTGAGCAG"
self.res.table = 5
self.res.method = "normal"
self.res.degenerate()
result = self.res.degenerated
expected = "NNNTTYATRTTYTAYTTYTGRAAYYTNAGNAG"
self.assertEqual(expected, result)
def test_incomplete_seq_table_5(self):
self.res.dna = "?ACTTTATATTTTATTTTTGGAATTTGAGCAG"
self.res.table = 5
self.res.degenerate()
result = self.res.degenerated
expected = "NNNTTYATRTTYTAYTTYTGRAAYYTNAGNAG"
self.assertEqual(expected, result)
def test_incomplete2_seq_table_5(self):
self.res.dna = "ACTTTATATTTTATTTTTGGAATTTGAGCAG"
self.res.table = 5
self.res.degenerate()
result = self.res.degenerated
expected = "ACNYTNTAYTTYATYTTYGGNATYTGRGCNG"
self.assertEqual(expected, result)
def setUp(self):
self.dna = "AGTTCTTTACTACGTAGA"
self.res = Degenera(dna=self.dna)
#
# 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))
