degen.py

import Bio
print(Bio.__version__)
from Bio.Seq import Seq


def degenerate_codon(codon):
    try:
        #translate codon
        seq = Seq(codon)
        aa = str(seq.translate())

        #dictionary relating aa to degnerate codon
        degen_dict = {'A': 'GCN', 'C': 'TGY', 'D': 'GAY', 'E': 'GAR',
                      'F': 'TTY', 'G': 'GGN', 'H': 'CAY', 'I': 'ATH',
                      'K': 'AAR', 'M': 'ATG', 'N': 'AAY', 'P': 'CCN',
                      'Q': 'CAR', 'T': 'ACN', 'V': 'GTN', 'W': 'TGG',
                      'X': 'NNN', 'Y': 'TAY'}

        #dealing with multiple serine codons
        if aa == 'S':
            if codon in ('AGT', 'ACG'):
                return('AGY')
            else:
                return('TCN')

        #dealing with multiple leucine codons
        if aa == 'L':
            if codon in ('TTA', 'TTG'):
                return('TTR')
            else:
                return('CTN')

        # dealing with multiple arginine codons
        if aa == 'R':
            if codon in ('AGA', 'AGG'):
                return('AGR')
            else:
                return('CGN')

        #main block to deal with most of the codons
        elif aa in degen_dict.keys():
            #convert back to string before returning the codon
            return(degen_dict[aa])
        else:
            #Return the stop codons
            return(codon.upper())

    #The except block allows the return of --- and ??? if those are the codons
    except:
        if codon == '???':
            return('NNN')
        else:
            return(codon)


def degenerate_sequence(seq):
    #if not divisible by 3, slice off end of sequence to make divisible by 3
    seq_length = len(seq)
    i=0
    degen_string=""
    while i < seq_length:
        degen_string += degenerate_codon(seq[i:i+3])
        i = i+3
    return degen_string


test_seq ='TTTTTCTTATTGCTTCTCCTACTGATTATCATAATGGTTGTTGTCGTAGTGTCTTCCTCATCGCCTCCCCCACCGACTACCACAACGGCTGCCGCAGCGTATTACTAATAGCATCACCAACAGAATAACAAAAAGGATGACGAAGAGTGTTGCTGATGGCGTCGCCGACGGAGTAGCAGAAGGGGTGGCGGAGGGNNN---???'
test_output=degenerate_sequence(test_seq)

#using the webtool @http://www.phylotools.com/ptdegenwebservice.htm I have the Perl output
#perl_output = 'TTYTTYYTNYTNYTNYTNYTNYTNATHATHATHATGGTNGTNGTNGTNGTNTCNTCNTCNTCNCCNCCNCCNCCNACNACNACNACNGCNGCNGCNGCNTAYTAYTAATAGCAYCAYCARCARAAYAAYAARAARGAYGAYGARGARTGYTGYTGATGGMGNMGNMGNMGNAGYAGYMGNMGNGGNGGNGGNGGNNNN---NNN'
#test_output = 'TTYTTYYTNYTNYTNYTNYTNYTNATHATHATHATGGTNGTNGTNGTNGTNTCNTCNTCNTCNCCNCCNCCNCCNACNACNACNACNGCNGCNGCNGCNTAYTAYTAATAGCAYCAYCARCARAAYAAYAARAARGAYGAYGARGARTGYTGYTGATGGMGNMGNMGNMGNAGYTCNMGNMGNGGNGGNGGNGGNNNN---NNN'

#print(test_output)
#print(perl_output)