reverse_translate_amino-acids.py

"""
"""

import sys
from random import random, seed

table={"TTT": "F", "TTC": "F", "TTA": "L", "TTG": "L",
       "TCT": "S", "TCC": "S", "TCA": "S", "TCG": "S",
       "TAT": "Y", "TAC": "Y", "TGT": "C", "TGC": "C",
       "TGG": "W", "CTT": "L", "CTC": "L", "CTA": "L",
       "CTG": "L", "CCT": "P", "CCC": "P", "CCA": "P",
       "CCG": "P", "CAT": "H", "CAC": "H", "CAA": "Q",
       "CAG": "Q", "CGT": "R", "CGC": "R", "CGA": "R",
       "CGG": "R", "ATT": "I", "ATC": "I", "ATA": "I",
       "ATG": "M", "ACT": "T", "ACC": "T", "ACA": "T",
       "ACG": "T", "AAT": "N", "AAC": "N", "AAA": "K",
       "AAG": "K", "AGT": "S", "AGC": "S", "AGA": "R",
       "AGG": "R", "GTT": "V", "GTC": "V", "GTA": "V",
       "GTG": "V", "GCT": "A", "GCC": "A", "GCA": "A",
       "GCG": "A", "GAT": "D", "GAC": "D", "GAA": "E",
       "GAG": "E", "GGT": "G", "GGC": "G", "GGA": "G",
       "GGG": "G"}

fnam, seed_num = sys.argv[1:]

seed(int(seed_num))

reverse = {}
for aa in set(list(table.values())):
    codons = [c for c, a in table.items() if a == aa]
    lena = len(codons)
    reverse[aa] = [codons[int(random() * lena)] if random() < 0.2 else codons[0]
                   for i in range(100)]

sequences = {}
for l in open(fnam):
    if l.startswith('>'):
        name = l[1:].strip()
        sequences[name] = ''
    else:
        sequences[name] += l.strip()

line_len = 60
for name, seq in sequences.items():
    print('>{}'.format(name))
    tr_seq = ''.join(reverse[a][int(random() * 100)] for a in seq)
    print('\n'.join(tr_seq[i:i + line_len] for i in range(0, len(tr_seq), line_len)))