找到停止密码子

Question

我想在我的CD里找到起始密码子和终止密码子。我使用过正则表达式，但是当我运行这个python脚本时，我得到了一个空的stop密码子列表。非常感谢任何帮助。在

std_code = {"TTT":"F|Phe","TTC":"F|Phe","TTA":"L|Leu","TTG":"L|Leu","TCT":"S|Ser","TCC":"S|Ser",
            "TCA":"S|Ser","TCG":"S|Ser", "TAT":"Y|Tyr","TAC":"Y|Tyr","TAA":"*|Stp","TAG":"*|Stp",
            "TGT":"C|Cys","TGC":"C|Cys","TGA":"*|Stp","TGG":"W|Trp", "CTT":"L|Leu","CTC":"L|Leu",     
            "CTA":"L|Leu","CTG":"L|Leu","CCT":"P|Pro","CCC":"P|Pro","CCA":"P|Pro","CCG":"P|Pro",
            "CAT":"H|His","CAC":"H|His","CAA":"Q|Gln","CAG":"Q|Gln","CGT":"R|Arg","CGC":"R|Arg",
            "CGA":"R|Arg","CGG":"R|Arg", "ATT":"I|Ile","ATC":"I|Ile","ATA":"I|Ile","ATG":"M|Met",
            "ACT":"T|Thr","ACC":"T|Thr","ACA":"T|Thr","ACG":"T|Thr", "AAT":"N|Asn","AAC":"N|Asn",
            "AAA":"K|Lys","AAG":"K|Lys","AGT":"S|Ser","AGC":"S|Ser","AGA":"R|Arg","AGG":"R|Arg",
            "GTT":"V|Val","GTC":"V|Val","GTA":"V|Val","GTG":"V|Val","GCT":"A|Ala","GCC":"A|Ala",
            "GCA":"A|Ala","GCG":"A|Ala", "GAT":"D|Asp","GAC":"D|Asp","GAA":"E|Glu",
            "GAG":"E|Glu","GGT":"G|Gly","GGC":"G|Gly","GGA":"G|Gly","GGG":"G|Gly"}

cds = ("ATGCTAGCGGTAAATCGTGAATAGGCCTAA")
for i in range (0, len(cds),3):
    print cds[i:i+3]

def translate (cds, std_code):
    protein = ""
    for i in range (0,len(cds),3):
        codon = cds[i:i+3]
        protein = protein + std_code[codon]
    return protein
print translate(cds, std_code)
def codon_usage(cds):
    usage = {}
    for i in range(0,len(cds),3):
        codon = cds[i:i+3]
        if usage.has_key(codon):
            usage[codon] += 1
        else:
            usage[codon] = 1
    return usage
print codon_usage(cds)


import re
pat = '(ATG)+?(?:TAA|TGA|TAG)'
reg = re.compile(pat)
def stop_codons(cds, messages=None,s=0,reg=reg):
    stop_codons = []
    while True:
        ma = reg.search(cds[s:])
        if ma:
            if ma.group(1) == 'ATG':
                break
            else:
                stop_codons.append(ma.group.upper())
                s = s + ma.start() + 1
        else:
            break
    return stop_codons
print stop_codons(cds, messages=None, s=0,reg=reg)      

Answer 1

我看到你的stop_codons函数有几个问题。首先，您的正则表达式：

(ATG)+?(?:TAA|TGA|TAG)

正如它所写的，这是在寻找你的起始密码子的重复，然后是一个终止密码子。如果您的regex如它所写的那样匹配，它将只返回起始密码子，而不返回其他任何内容。如果您想在起始密码子之后找到第一个终止密码子，可以尝试：

^{pr2}$

第二，如果正则表达式与起始密码子匹配，它将中断循环并返回stop_codons的列表，假设传入此函数的每个序列在停止之前都包含一个起始密码子，则始终会返回一个空列表。希望这有帮助。在

Answer 2

你考虑过使用Biopython吗？它有各种处理序列的内置工具，如果你在做任何与生物信息学相关的事情，它可以为你节省很多时间。尤其是，^{}对象正是您要查找的对象：

>>> from Bio.Seq import Seq
>>> from Bio.Alphabet import generic_dna
>>> my_dna = Seq("AGTACACTGGT", generic_dna)
>>> my_dna
Seq('AGTACACTGGT', DNAAlphabet())
>>> my_dna.find("ACT")
5

我强烈建议您阅读tutorial和API documentation来查找字母表、密码子表（Bio.Data.CodonTable）等信息