python - 组合字符串，提取子串

Question

(我用的是python)

我正在处理一个大的 RNA 序列文件，我正在尝试重新格式化它以便在聚类程序中使用。我的文件由两种类型的“线条”组成。 1) 细菌的登录号，(句点)该序列开始的核苷酸，(句点)它结束的核苷酸。 2) 实际序列本身的行(跨越多行，即使它是一个连续的序列):

>A45315.1.1521\n GACGAACGCUGGCGGCGUGCCUAAUACAUGCAAGUCGAGCGCAGGAAGCCGGCGGAUCCC\n UUCGGGGUGAANCCGGUGGAAUGAGCGGCGGACGGGUGAGUAACACGUGGGCAACCUACC\n UUGUAGACUGGGAUAACUCCGGGAAACCGGGGCUAAUACCGGAUGAUCAUUUGGAUCGCAU\n GAUCCGAAUGUAAAAGUGGGGAUUUAUCCUCACACUGCAAGAUGGGCCCGCGGCGCA….. >A93610.15.1301\n CCACUGCUAUGGGGGUCCGACUAAGCCAUGCGAGUCAUGGGGUCCCUCUGGGACACCACC\n GGCGGACGGCUCAGUAACACGUCGGUAACCUACCCUCGGGAGGGGGAUAACCCCGGGAAA\n CUGGGGCUAAUCCCCCAUAGGCCUGAGGUACUGGAAGGUCCUCAGGCCGAAAGGGGCUU….

我需要创建一些东西来查看以 > 开头的行，然后转到第一个小数点后的数字(因此高于该数字将是 1 和 15)。从那个数字开始计数(在上面的例子中是 1 或 15)，它需要提取从 69 开始到 497 的核苷酸(As、Cs、Gs 或 Us)(注意这个例子我取出了一堆的核苷酸)。

因此，对于我的尝试，我认为将核苷酸序列做成一个长串，然后尝试提取核苷酸是有意义的。但我似乎无法将 RNA 序列的行变成一个长字符串(见下文了解我的尝试)。一旦我有了大字符串，我就不确定如何提取正确的核苷酸。我需要写类似 s = [x:497] 的内容，其中 x 是 69-(在第一个小数点前插入该数字)。

 #!/usr/bin/env python
 #Make a program that takes SSURef_NR99 file of sequences, makes a new file of 
 #Accession numbers and size of 16S.
 import re
 infilename = 'SSUtestdata.txt'
 outfilename = 'SSUtestdata3.txt'

 #Here I'm trying to search for one of the nucleotides, an end of line character and     another nucleotide, trying to make a long string.

 replace = re.compile(r'([A|C|G|U])(\n)([A|C|G|U])')

 #remove extra letters and spaces
 with open(infilename, 'r') as infile, open(outfilename, 'w') as outfile:
     for line in infile:
          line = replace.sub(r'\1\3', line)

 #Write to OutFile
          outfile.write(line)   

感谢您的任何想法!

Answer 1

如果我正确理解你的问题，应该这样做:

with open('path/to/input') as infile:
  while 1:
    try:
      line = infile.readline()
      _, start, end = line.strip().split('.')
      start, end = int(start), int(end)
      beg = infile.read(start-1)
      infile.read(beg.count('\n'))
      seq = infile.read(end-start)
      extra = infile.read(seq.count('\n'))
      seq = seq.replace('\n') + extra
      print seq  # print(seq) in python3
    except:
      break