DNA 序列翻译

dna = "ATGCACGTGCGCTCACTGCGAGCTGCGGCGCCGCACAGCTTCGTGGCGCTCTGGGCACCCCTGTTCCTGCTGCGCTCCGCCCTGGCCGACTTCAGCCTGGACAACGAGGTGCACTCGAGCTTCATCCACCGGCGCCTCCGCAGCCAGGAGCGGCGGGAGATGCAGCGCGAGATCCTCTCCATTTTGGGCTTGCCCCACCGCCCGCGCCCGCACCTCCAGGGCAAGCACAACTCGGCACCCATGTTCATGCTGGACCTGTACAACGCCATGGCGGTGGAGGAGGGCGGCGGGCCCGGCGGCCAGGGCTTCTCCTACCCCTACAAGGCCGTCTTCAGTACCCAGGGCCCCCCTCTGGCCAGCCTGCAAGATAGCCATTTCCTCACCGACGCCGACATGGTCATGAGCTTCGTCAACCTCGTGGAACATGACAAGGAATTCTTCCACCCACGCTACCACCATCGAGAGTTCCGGTTTGATCTTTCCAAGATCCCAGAAGGGGAAGCTGTCACGGCAGCCGAATTCCGGATCTACAAGGACTACATCCGGGAACGCTTCGACAATGAGACGTTCCGGATCAGCGTTTATCAGGTGCTCCAGGAGCACTTGGGCAGGGAATCGGATCTCTTCCTGCTCGACAGCCGTACCCTCTGGGCCTCGGAGGAGGGCTGGCTGGTGTTTGACATCACAGCCACCAGCAACCACTGGGTGGTCAATCCGCGGCACAACCTGGGCCTGCAGCTCTCGGTGGAGACGCTGGATGGGCAGAGCATCAACCCCAAGTTGGCGGGCCTGATTGGGCGGCACGGGCCCCAGAACAAGCAGCCCTTCATGGTGGCTTTCTTCAAGGCCACGGAGGTCCACTTCCGCAGCATCCGGTCCACGGGGAGCAAACAGCGCAGCCAGAACCGCTCCAAGACGCCCAAGAACCAGGAAGCCCTGCGGATGGCCAACGTGGCAGAGAACAGCAGCAGCGACCAGAGGCAGGCCTGTAAGAAGCACGAGCTGTATGTCAGCTTCCGAGACCTGGGCTGGCAGGACTGGATCATCGCGCCTGAAGGCTACGCCGCCTACTACTGTGAGGGGGAGTGTGCCTTCCCTCTGAACTCCTACATGAACGCCACCAACCACGCCATCGTGCAGACGCTGGTCCACTTCATCAACCCGGAAACGGTGCCCAAGCCCTGCTGTGCGCCCACGCAGCTCAATGCCATCTCCGTCCTCTACTTCGATGACAGCTCCAACGTCATCCTGAAGAAATACAGAAACATGGTGGTCCGGGCCTGTGGCTGCCACTAG"
 
 def trabslate_dna(sequence):
     start_codon = 'ATG'
     stop_codon = ('TAA', 'TAG', 'TGA' )
     codontable = {
         'ATA': 'I', 'ATC': 'I', 'ATT': 'I', 'ATG': 'M',
         'ACA': 'T', 'ACC': 'T', 'ACG': 'T', 'ACT': 'T',
         'AAC': 'N', 'AAT': 'N', 'AAA': 'K', 'AAG': 'K',
         'AGC': 'S', 'AGT': 'S', 'AGA': 'R', 'AGG': 'R',
         'CTA': 'L', 'CTC': 'L', 'CTG': 'L', 'CTT': 'L',
         'CCA': 'P', 'CCC': 'P', 'CCG': 'P', 'CCT': 'P',
         'CAC': 'H', 'CAT': 'H', 'CAA': 'Q', 'CAG': 'Q',
         'CGA': 'R', 'CGC': 'R', 'CGG': 'R', 'CGT': 'R',
         'GTA': 'V', 'GTC': 'V', 'GTG': 'V', 'GTT': 'V',
         'GCA': 'A', 'GCC': 'A', 'GCG': 'A', 'GCT': 'A',
         'GAC': 'D', 'GAT': 'D', 'GAA': 'E', 'GAG': 'E',
         'GGA': 'G', 'GGC': 'G', 'GGG': 'G', 'GGT': 'G',
         'TCA': 'S', 'TCC': 'S', 'TCG': 'S', 'TCT': 'S',
         'TTC': 'F', 'TTT': 'F', 'TTA': 'L', 'TTG': 'L',
         'TAC': 'Y', 'TAT': 'Y', 'TAA': '_', 'TAG': '_',
         'TGC': 'C', 'TGT': 'C', 'TGA': '_', 'TGG': 'W'
     }
     start = sequence.find(start_codon)
     codons = [] # Create a codon list to store codons generated from coding seq.
     for i in range(start, len(sequence), 3):
         if sequence[i:i+3] in stop_codons:
             break
         if sequence[i:i+3] in codontable.keys():
             codons.append(sequence[i:i+3])
     protein_sequence = ''.join([codontable[codon] for codon in codons]) #Translate condons to protein seq.
     return "{0}_".format(protein_sequence)
 
 protein_seq = translate_DNA(dna)
 print(protein_seq)

　　

hhh

import os
import re


F_path= os.getcwd()
print(F_path)


def trabslate_dna(sequence):
    codontable = {
     'ATA': 'I', 'ATC': 'I', 'ATT': 'I', 'ATG': 'M',
     'ACA': 'T', 'ACC': 'T', 'ACG': 'T', 'ACT': 'T',
     'AAC': 'N', 'AAT': 'N', 'AAA': 'K', 'AAG': 'K',
     'AGC': 'S', 'AGT': 'S', 'AGA': 'R', 'AGG': 'R',
     'CTA': 'L', 'CTC': 'L', 'CTG': 'L', 'CTT': 'L',
     'CCA': 'P', 'CCC': 'P', 'CCG': 'P', 'CCT': 'P',
     'CAC': 'H', 'CAT': 'H', 'CAA': 'Q', 'CAG': 'Q',
     'CGA': 'R', 'CGC': 'R', 'CGG': 'R', 'CGT': 'R',
     'GTA': 'V', 'GTC': 'V', 'GTG': 'V', 'GTT': 'V',
     'GCA': 'A', 'GCC': 'A', 'GCG': 'A', 'GCT': 'A',
     'GAC': 'D', 'GAT': 'D', 'GAA': 'E', 'GAG': 'E',
     'GGA': 'G', 'GGC': 'G', 'GGG': 'G', 'GGT': 'G',
     'TCA': 'S', 'TCC': 'S', 'TCG': 'S', 'TCT': 'S',
     'TTC': 'F', 'TTT': 'F', 'TTA': 'L', 'TTG': 'L',
     'TAC': 'Y', 'TAT': 'Y', 'TAA': '*', 'TAG': '*',
     'TGC': 'C', 'TGT': 'C', 'TGA': '*', 'TGG': 'W' }
 #start = sequence.find(start_codon)
    codons = [] # Create a codon list to store codons generated from coding seq.
    for i in range(0, len(sequence), 3):
        codons.append(sequence[i:i+3])
    protein_sequence = ''.join([codontable[codon] for codon in codons]) #Translate condons to protein seq.
    return "{0}".format(protein_sequence)



dna = "ATGCACGTGCGCTCACTGCGAGCTGCGGCGCCGCACAGCTTCGTGGCGCTCTGGGCACCCCTGTTCCTGCTGCGCTCCGCCCTGGCCGACTTCAGCCTGGACAACGAGGTGCACTCGAGCTTCATCCACCGGCGCCTCCGCAGCCAGGAGCGGCGGGAGATGCAGCGCGAGATCCTCTCCATTTTGGGCTTGCCCCACCGCCCGCGCCCGCACCTCCAGGGCAAGCACAACTCGGCACCCATGTTCATGCTGGACCTGTACAACGCCATGGCGGTGGAGGAGGGCGGCGGGCCCGGCGGCCAGGGCTTCTCCTACCCCTACAAGGCCGTCTTCAGTACCCAGGGCCCCCCTCTGGCCAGCCTGCAAGATAGCCATTTCCTCACCGACGCCGACATGGTCATGAGCTTCGTCAACCTCGTGGAACATGACAAGGAATTCTTCCACCCACGCTACCACCATCGAGAGTTCCGGTTTGATCTTTCCAAGATCCCAGAAGGGGAAGCTGTCACGGCAGCCGAATTCCGGATCTACAAGGACTACATCCGGGAACGCTTCGACAATGAGACGTTCCGGATCAGCGTTTATCAGGTGCTCCAGGAGCACTTGGGCAGGGAATCGGATCTCTTCCTGCTCGACAGCCGTACCCTCTGGGCCTCGGAGGAGGGCTGGCTGGTGTTTGACATCACAGCCACCAGCAACCACTGGGTGGTCAATCCGCGGCACAACCTGGGCCTGCAGCTCTCGGTGGAGACGCTGGATGGGCAGAGCATCAACCCCAAGTTGGCGGGCCTGATTGGGCGGCACGGGCCCCAGAACAAGCAGCCCTTCATGGTGGCTTTCTTCAAGGCCACGGAGGTCCACTTCCGCAGCATCCGGTCCACGGGGAGCAAACAGCGCAGCCAGAACCGCTCCAAGACGCCCAAGAACCAGGAAGCCCTGCGGATGGCCAACGTGGCAGAGAACAGCAGCAGCGACCAGAGGCAGGCCTGTAAGAAGCACGAGCTGTATGTCAGCTTCCGAGACCTGGGCTGGCAGGACTGGATCATCGCGCCTGAAGGCTACGCCGCCTACTACTGTGAGGGGGAGTGTGCCTTCCCTCTGAACTCCTACATGAACGCCACCAACCACGCCATCGTGCAGACGCTGGTCCACTTCATCAACCCGGAAACGGTGCCCAAGCCCTGCTGTGCGCCCACGCAGCTCAATGCCATCTCCGTCCTCTACTTCGATGACAGCTCCAACGTCATCCTGAAGAAATACAGAAACATGGTGGTCCGGGCCTGTGGCTGCCACTAG"

print(trabslate_dna(dna))

AA_FL=trabslate_dna(dna)
aa_feature='AAAPHSFVALWAPLFLLRSALAD'




match = re.search(aa_feature, AA_FL)
if match:
    matchstart = match.start()

    matchend = match.end()

    matchlength = matchend - matchstart

    matchtext = AA_FL[matchstart:matchend]

    print (matchstart,matchend,matchtext)
else:
    print ('match fail!')


kk='''     CDS        87..166
                     /locus_tag="5555666ppp"
                     /label="5555666ppp"
                     /ApEinfo_label="5555666ppp"
                     /ApEinfo_fwdcolor="#346ee0"
                     /ApEinfo_revcolor="#ff80c0"
                     /ApEinfo_graphicformat="arrow_data {{0 0.5 0 1 2 0 0 -1 0
                     -0.5} {} 0} width 5 offset 0"'''

print(kk)