orf.py

CODON_PROTEIN_MAP = {
    'TTT': 'F',     'CTT': 'L',     'ATT': 'I',     'GTT': 'V',
    'TTC': 'F',     'CTC': 'L',     'ATC': 'I',     'GTC': 'V',
    'TTA': 'L',     'CTA': 'L',     'ATA': 'I',     'GTA': 'V',
    'TTG': 'L',     'CTG': 'L',     'ATG': 'M',     'GTG': 'V',
    'TCT': 'S',     'CCT': 'P',     'ACT': 'T',     'GCT': 'A',
    'TCC': 'S',     'CCC': 'P',     'ACC': 'T',     'GCC': 'A',
    'TCA': 'S',     'CCA': 'P',     'ACA': 'T',     'GCA': 'A',
    'TCG': 'S',     'CCG': 'P',     'ACG': 'T',     'GCG': 'A',
    'TAT': 'Y',     'CAT': 'H',     'AAT': 'N',     'GAT': 'D',
    'TAC': 'Y',     'CAC': 'H',     'AAC': 'N',     'GAC': 'D',
    'TAA': 'Stop',  'CAA': 'Q',     'AAA': 'K',     'GAA': 'E',
    'TAG': 'Stop',  'CAG': 'Q',     'AAG': 'K',     'GAG': 'E',
    'TGT': 'C',     'CGT': 'R',     'AGT': 'S',     'GGT': 'G',
    'TGC': 'C',     'CGC': 'R',     'AGC': 'S',     'GGC': 'G',
    'TGA': 'Stop',  'CGA': 'R',     'AGA': 'R',     'GGA': 'G',
    'TGG': 'W',     'CGG': 'R',     'AGG': 'R',     'GGG': 'G'
}

def reverse_complement(s):
    complements = {'A':'T', 'T':'A', 'G':'C', 'C':'G'}
    list = [complements[c] for c in reversed(s)]
    return ''.join(list)

def translate_codon(codon):
    if codon in CODON_PROTEIN_MAP and len(codon) == 3:
        return CODON_PROTEIN_MAP[codon]
    
def transcribe_anywhere(s):
    proteins = []

    for i in range(len(s)):
        protein = translate_codon(s[i:i+3])
        if protein == 'M':
            protein_string = protein

            for j in range(i+3,len(s), 3):
                    protein = translate_codon(s[j:j+3])
                    if protein == 'Stop':
                        proteins.append(protein_string)
                        break
                    protein_string += protein
    return proteins

if __name__ == "__main__":
    s = "AGCCATGTAGCTAACTCAGGTTACATGGGGATGACCCCGCGACTTGGATTAGAGTCTCTTTTGGAATAAGCCTGAATGATCCGAGTAGCATCTCAG"
    l = transcribe_anywhere(s)
    l += transcribe_anywhere(reverse_complement(s))
    x = set()
    for seq in l:
        x.add(seq)
    print(x)