Python拆分，字符串为delimi

Question

我有一个类似这样的文件：

AAACAACAGGGTACAAAGAGTCACGCTTATCCTGTTGATACT
TCTCAATGGGCAGTACATATCATCTCTNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNAAAACGTGTGCATGAACAAAAAA
CGTAGCAGATCGTGACTGGCTATTGTATTGTGTCAATTTCGCTTCGTCAC
TAAATCAACGGACATGTGTTGC

我需要把它分成“非N”序列，所以两个独立的文件如下：

^{pr2}$

我现在拥有的是：

UMfile = open ("C:\Users\Manuel\Desktop\sequence.txt","r")
contignumber = 1
contigfile = open ("contig "+str(contignumber), "w")

DNA = UMfile.read()
DNAstring = str(DNA)

for s in DNAstring:
    DNAstring.split("NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN",1)
contigfile.write(DNAstring)

contigfile.close()
contignumber = contignumber+1
contigfile = open ("contig "+str(contignumber), "w")

问题是我意识到在“Ns”之间有一个换行符，这就是为什么它没有拆分我的文件，但是我显示的“file”只是一个大得多的文件的一部分。因此，有时“Ns”看起来像“NNNNNN\n”，有时类似于“NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN”，但我的序列之间总有1000个Ns需要拆分。在

所以我的问题是：如果知道每行中有不同数量的n，如何告诉python每1000xNs将其拆分成不同的文件？在

非常感谢大家，我真的没有信息学背景，而且我的python技能充其量只是基本的。在

Answer 1

假设你可以一次读取整个文件

s=DNAstring.replace("\n","")         # first remove the nasty linebreaks
l=[x for x in s.split("N") if x]     # split and drop empty lines

for x in l:                          # print in chunks
    while x:
        print x[:10]
        x=x[10:]
    print                            # extra linebreak between chunks

Answer 2

您可以简单地将每个N和\N替换为一个空格，然后拆分。在

result = DNAstring.replace("\n", " ").replace("N", " ").split()

这将返回一个字符串列表，并且'ACGT'序列也将与每一个新行分割。在

如果这不是您的目标，您希望在“ACGT”中保留\n并且不沿着它拆分，则可以执行以下操作：

^{pr2}$

这只会在n序列的中间移除\n。在

要在1000 Ns之后拆分字符串，请执行以下操作：

# 1/ Get rid of line breaks in the N sequence
result = DNAstring.replace("N\n", "N")
# 2/ split every 1000 Ns
result = result.split(1000*"N")

Answer 3

只需在'N'上拆分字符串，然后删除所有空字符串，或者只包含新行。像这样：

#!/usr/bin/env python

DNAstring = '''AAACAACAGGGTACAAAGAGTCACGCTTATCCTGTTGATACT
TCTCAATGGGCAGTACATATCATCTCTNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNAAAACGTGTGCATGAACAAAAAA
CGTAGCAGATCGTGACTGGCTATTGTATTGTGTCAATTTCGCTTCGTCAC
TAAATCAACGGACATGTGTTGC'''

sequences = [u for u in DNAstring.split('N') if u and u != '\n']

for i, seq in enumerate(sequences):
    print i
    print seq.replace('\n', '') + '\n'

输出

^{pr2}$

上面的代码片段还使用.replace('\n', '')删除序列中的新行。在

---

以下是一些你可能会发现有用的程序。在

首先，一个行缓冲类。用文件名和行宽初始化它。然后你可以给它随机长度的字符串，它会自动保存到文本文件，一行一行，所有的行（可能除了最后一行）都有给定的长度。您可以在其他程序中使用这个类，使您的输出看起来整洁。在

将此文件另存为linebuffer.py到Python路径中的某个位置；最简单的方法是在保存Python程序的任何位置保存它，并在运行程序时将其作为当前目录。在

linebuffer.py

#! /usr/bin/env python

''' Text output buffer 

    Write fixed width lines to a text file

    Written by PM 2Ring 2015.03.23
'''

class LineBuffer(object):
    ''' Text output buffer

        Write fixed width lines to file fname
    '''
    def __init__(self, fname, width):
        self.fh = open(fname, 'wt')
        self.width = width
        self.buff = []
        self.bufflen = 0

    def write(self, data):
        ''' Write a string to the buffer '''
        self.buff.append(data)
        self.bufflen += len(data)
        if self.bufflen >= self.width:
            self._save()

    def _save(self):
        ''' Write the buffer to the file '''
        buff = ''.join(self.buff)

        #Split buff into lines
        lines = []
        while len(buff) >= self.width:
            lines.append(buff[:self.width])
            buff = buff[self.width:]

        #Add an empty line so we get a trailing newline
        lines.append('')
        self.fh.write('\n'.join(lines))  

        self.buff = [buff]
        self.bufflen = len(buff)

    def close(self):
        ''' Flush the buffer & close the file '''
        if self.bufflen > 0:
            self.fh.write(''.join(self.buff) + '\n')
        self.fh.close()


def testLB():
    alpha = 'abcdefghijklmnopqrstuvwxyz'
    fname = 'linebuffer_test.txt'
    lb = LineBuffer(fname, 27)
    for _ in xrange(30):
        lb.write(alpha)
    lb.write(' bye.')
    lb.close()


if __name__ == '__main__':
    testLB()

这是一个程序，它可以按照你在问题中描述的形式随机生成DNA序列。它使用linebuffer.py来处理输出。我写这个是为了能正确地测试我的DNA序列拆分器。在

随机

#! /usr/bin/env python

''' Make random DNA sequences

    Sequences consist of random subsequences of the letters 'ACGT'
    as well as short sequences of 'N', of random length up to 200.
    Exactly 1000 'N's separate sequence blocks. 
    All sequences may contain newlines chars 

    Takes approx 3 seconds per megabyte generated and saved 
    on a 2GHz CPU single core machine.

    Written by PM 2Ring 2015.03.23
'''

import sys
import random
from linebuffer import LineBuffer

#Set seed to None to seed randomizer from system time
random.seed(37)

#Output line width
linewidth = 120

#Subsequence base length ranges
minsub, maxsub = 15, 300

#Subsequences per sequence ranges
minseq, maxseq = 5, 50

#random 'N' sequence ranges
minn, maxn = 5, 200

#Probability that a random 'N' sequence occurs after a subsequence
randn = 0.2

#Sequence separator
nsepblock = 'N' * 1000

def main():
    #Get number of sequences from the command line
    numsequences = int(sys.argv[1]) if len(sys.argv) > 1 else 2
    outname = 'DNA_sequence.txt'

    lb = LineBuffer(outname, linewidth)
    for i in xrange(numsequences):
        #Write the 1000*'N' separator between sequences
        if i > 0:
            lb.write(nsepblock)

        for j in xrange(random.randint(minseq, maxseq)):
            #Possibly make a short run of 'N's in the sequence
            if j > 0 and random.random() < randn:
                lb.write(''.join('N' * random.randint(minn, maxn)))

            #Create a single subsequence
            r = xrange(random.randint(minsub, maxsub))
            lb.write(''.join([random.choice('ACGT') for _ in r]))
    lb.close()


if __name__ == '__main__':
    main()

最后，我们有一个程序可以分割你的随机DNA序列。它再次使用linebuffer.py来处理输出。在

DNA拆分器0.py

#! /usr/bin/env python

''' Split DNA sequences and save to separate files

    Sequences consist of random subsequences of the letters 'ACGT'
    as well as short sequences of 'N', of random length up to 200.
    Exactly 1000 'N's separate sequence blocks. 
    All sequences may contain newlines chars 

    Written by PM 2Ring 2015.03.23
'''

import sys
from linebuffer import LineBuffer

#Output line width
linewidth = 120

#Sequence separator
nsepblock = 'N' * 1000

def main():
    iname = 'DNA_sequence.txt'
    outbase = 'contig'

    with open(iname, 'rt') as f:
        data = f.read()

    #Remove all newlines
    data = data.replace('\n', '')

    sequences = data.split(nsepblock)

    #Save each sequence to a series of files
    for i, seq in enumerate(sequences, 1):
        outname = '%s%05d' % (outbase, i)
        print outname

        #Write sequence data, with line breaks
        lb = LineBuffer(outname, linewidth)
        lb.write(seq)
        lb.close()


if __name__ == '__main__':
    main()