Problema 1 del folleto "A The first look at the Code of Life" de Cleopatra Kozlowski http://emblog.embl.de/ells/teachingbase/code-of-life-2/

Gene_finding_game.py

# coding: utf-8

import re
def secuencia_degenerada(sequencia):
    seq = []
    aa_degenerados = { 
                        'A': ['GC.'],
                        'C': ['TG[CT]'],
                        'D': ['GA[CT]'],
                        'E': ['GA[AG]'],
                        'F': ['TT[CT]'],
                        'G': ['GG.'],
                        'H': ['CA[CT]'],
                        'I': ['AT[CAT]'],
                        'K': ['AA[AG]'],
                        'L': ['[CT]T.'],
                        'M': ['ATG'],
                        'N': ['AA[CT]'],
                        'P': ['CC.'],
                        'Q': ['CA[AG]'],
                        'R': ['[AC]G.'],
                        'S': ['[AT][CG].'],
                        'T': ['AC.'],
                        'V': ['GT.'],
                        'W': ['TGG'],
                        'Y': ['TA[CT]'],
                        '*': ['T[AG][AG]']
    }

    for i in range(len(sequencia)):
      seq.append(aa_degenerados[sequencia[i]])
    regexp = ''.join(str(e) for e in seq)
    return regexp.replace("['", "").replace("']", "")

def encuentra_motivo(regexp, DNA_sequence):
    return re.search(regexp, DNA_sequence).group()

def main():
    #Met Ser Ile Leu Leu Tyr Stop
    peptido_1 = "MSILVER*"
    #Met Ser Ile Leu Val Glu Arg Stop
    peptido_2 = "MCRT*"
    #Met Cys Arg Thr Stop
    peptido_3 = "MSILLY*"
    peptidos = [peptido_1, peptido_2, peptido_3]
    for peptido in peptidos:
        regexp = secuencia_degenerada(peptido)
        DNA_sequence = "TGGTCCTGCAGTCCTCTCCTGGCGCCCCGGGGGCGAGCGGATGTCGATTCTCGTGGAAAGATAGTCCCGCTGCCTGCGGGCGGAGGGACCGTGCTGACCAAGATGTACCCGCGCGGCAACCACTGGGCGGTGGGGCACTTAATGGGGAAAAAGAGCACAGGGGAGTCTTCTTCTGTATGTTCTGAGAGAGGGAGCCTGAAGCAGCAGCTGAGAGATGTGTCGAACGTGAAGTACATCAGGTGGGAAGAAGCTGCAAGGAATTTGCTGGGTCTCATAGAAGCTAAAGGAGAACAGAAACCACCAGCCACCTCAACCCAAGATGTCGATTCTACTTTATTAAGCCCTGGGCAATCAGCAGCCTTCGTGGGATATGTCAGAGGATAGCAGCCAACTGAATAGC"
        match = encuentra_motivo(regexp, DNA_sequence)
        print(str(DNA_sequence.find(match) + 1 ) + " " + match + " " + str((DNA_sequence.find(match) + len(match))) + "\n")

if __name__ == '__main__':
    main()