胰蛋白酶消化(切割)不能使用正则表达式

Question

我试图在Python中编码蛋白质序列的理论性胰蛋白酶切割.胰蛋白酶的切割规则是:在R或K之后,但不在P之前(即胰蛋白酶在每个K或R之后切割(切割)蛋白质序列,除非(K或R)之后是P).

例子:序列的切割(切割)MVPPPPSRGGAAKPGQLGRSLGPLLLLLRPEEPEDGDREICSESK应产生这4个序列(肽):

MVPPPPSR
GGAAKPGQLGR
SLGPLLLLLRPEEPEDGDR
EICSESK 

注意,在第二肽中K后没有裂解(因为P在K之后出现)并且在第三肽中R之后没有裂解(因为P在R之后出现).

我用Python编写了这段代码,但效果不好.有没有办法更有意义地实现这个正则表达式？

    # Open the file and read it line by line.

    myprotein = open(raw_input('Enter input filename: '),'r')
    if  os.path.exists("trypsin_digest.txt"):
        os.remove("trypsin_digest.txt")
    outfile = open("trypsin_digest.txt",'w+')

    for line in myprotein:
        protein = line.rstrip()
        protein = re.sub('(?<=[RK])(?=[^P])','', protein)

    for peptide in protein:
        outfile.write(peptide)
    print 'results written to:\n', os.getcwd() +'\ trypsin_digest.txt'

这就是我让它为我工作的方式

   myprotein = open(raw_input('Enter input filename: '),'r')
   my_protein = []

   for protein in myprotein:
   myprotein = protein.rstrip('\n')
   my_protein.append(myprotein)
   my_pro = (''.join(my_protein))

   #cleaves sequence    
   peptides = re.sub(r'(?<=[RK])(?=[^P])','\n', my_pro)
   print peptides

蛋白质序列:

MVPPPPSRGGAAKPGQLGRSLGPLLLLLRPEEPEDGDREICSESK MVPPPPSRGGAAKPGQLGRSLGPLLLLLRPEEPEDGDREICSESK MVPPPPSRGGAAKPGQLGRSLGPLLLLLRPEEPEDGDREICSESK

输出(胰蛋白酶切割位点)或肽

MVPPPPSR
GGAAKPGQLGR
SLGPLLLLLRPEEPEDGDR
EICSESK
MVPPPPSR
GGAAKPGQLGR
SLGPLLLLLRPEEPEDGDR
EICSESK
MVPPPPSR
GGAAKPGQLGR
SLGPLLLLLRPEEPEDGDR
EICSESK

Answer 1

正则表达式很好,但这是一个使用常规python的解决方案.既然您正在寻找基础中的子序列,那么将其构建为生成器就可以生成片段.

example = 'MVPPPPSRGGAAKPGQLGRSLGPLLLLLRPEEPEDGDREICSESK'

def trypsin(bases):
    sub = ''
    while bases:
        k, r = bases.find('K'), bases.find('R')
        cut = min(k, r)+1 if k > 0 and r > 0 else max(k, r)+1
        sub += bases[:cut]
        bases = bases[cut:]
        if not bases or bases[0] != 'P':
            yield sub
            sub = ''


print list(trypsin(example))

Answer 2

编辑只需稍加修改，您的正则表达式就可以很好地工作：

在您的评论中，您提到您在一个文件中有多个序列（我们将其称为sequence.dat）：

$ cat sequences.dat
MVPPPPSRGGAAKPGQLGRSLGPLLLLLRPEEPEDGDREICSESK
MVPPPPSRGGAAKPGQLGRSLGPLLLLLRPEEPEDGDREICSESK
MVPPPPSRGGAAKPGQLGRSLGPLLLLLRPEEPEDGDREICSESK

>>> with open('sequences.dat') as f:
    s = f.read()

>>> print(s)
MVPPPPSRGGAAKPGQLGRSLGPLLLLLRPEEPEDGDREICSESK
MVPPPPSRGGAAKPGQLGRSLGPLLLLLRPEEPEDGDREICSESK
MVPPPPSRGGAAKPGQLGRSLGPLLLLLRPEEPEDGDREICSESK

>>> protein = re.sub(r'(?<=[RK])(?=[^P])','\n', s, re.DOTALL)

>>> protein.split()
['MVPPPPSR', 'GGAAKPGQLGR', 'SLGPLLLLLRPEEPEDGDR', 'EICSESK', 'MVPPPPSR', 'GGAAKPGQLGR', 'SLGPLLLLLRPEEPEDGDR', 'EICSESK', 'MVPPPPSR', 'GGAAKPGQLGR', 'SLGPLLLLLRPEEPEDGDR', 'EICSESK']

>>> print protein
MVPPPPSR
GGAAKPGQLGR
SLGPLLLLLRPEEPEDGDR
EICSESK

MVPPPPSR
GGAAKPGQLGR
SLGPLLLLLRPEEPEDGDR
EICSESK

MVPPPPSR
GGAAKPGQLGR
SLGPLLLLLRPEEPEDGDR
EICSESK