0

我有一个名为：

FirstSequenceToSplit

它包含一个项目，即 DNA 序列 说：

'ATTTACGTA'

我可以很容易地返回这个项目的长度，所以用户知道它是 10 个字符长，然后我想做的是让用户说他们想要提取索引的字符，比如 [0:6]，并且然后在新列表中生成两个项目。第一项具有用户定义索引的字符，后跟一个问号替换未提取的其他字符，第二项具有相反的字符。

所以为了说明我想要什么，如果用户说他们想要 [0:5] 你会得到一个包含以下项目的新列表：

['ATTTT?????','?????ACGTA']

这是一个更大问题的一部分，我有一组 FASTA 格式的 DNA 序列（'>Sequence1/nATTTTACGTA'、'>Sequence2/nATTGCACGTA' 等），我希望用户能够根据它的 ID 和用于根据预定义输入拆分该序列并称为 Sequence2a 和 Sequence2b ('>Sequence1a/n?????ACGTA', '>Sequence1b/nATTTT?????''>Sequence2/ nATTGCACGTA' 等）。我目前已经通过打印序列的名称解决了这个问题，让用户选择一个来拼接，只提取序列（没有 ID），然后一旦我解决了上面显示的问题，我将创建一个包含新项目的新列表。

由于我是初学者（我确信现在很明显！）我将不胜感激对给出的代码的任何解释。非常感谢您提供的任何可能的帮助

到目前为止，我的代码是：

import sys
import re

#Creating format so more user friendly

class color:
   PURPLE = '\033[95m'
   CYAN = '\033[96m'
   DARKCYAN = '\033[36m'
   BLUE = '\033[94m'
   GREEN = '\033[92m'
   YELLOW = '\033[93m'
   RED = '\033[91m'
   BOLD = '\033[94m'
   UNDERLINE = '\033[4m'
   END = '\033[0m'


fileName = raw_input("Give the name of the Fasta file you wish to divide up  ")
# i.e TopTenFasta

#Reading in the sequences splitting them by the > symbol
in_file = open(fileName,"r")
sequences = in_file.read().split('>')[1:] 
in_file.close() 


#Putting all these sequences into a list
allSequences = []
for item in sequences:
    allSequences.append(item)

#Letting you know how many sequences there are in total
NumberOfSequences = len(allSequences)
print color.BOLD + "The Number of Sequences in this list is: " +color.END, NumberOfSequences

#Returning the names of the IDs to allow you to decide which ones to split
SequenceIds = []
for x in allSequences:
    SequenceIds.append(x[0:10])

print color.BOLD + "With the following names: " + color.END, "\n", "\n".join(SequenceIds)

#-----------------------Starting the Splice ------------------------------------
#-----------------------------------------------------------------------------
#------------------------------------------------------------------------------



#Choosing the sequence you wish to splice 
FirstSequenceToSplitID = raw_input(color.BOLD + "Which sequence would you like to splice  " + color.END)

#Seeing whether that item is in the list
for x in SequenceIds:
    if FirstSequenceToSplitID == x:
        print "valid input"

FirstSequenceToSplit = []

#making a new list (FirstSequenceToSplit) and putting into it just the sequence (no ID)
for listItem in allSequences:
    if listItem[0:10]==FirstSequenceToSplitID:
        FirstSequenceToSplit.append(listItem[11:])

#Printing the Length of the sequence to splice
for element in FirstSequenceToSplit:
    print color.BOLD + "The Length of this sequence is" + color.END, len(element)
4

2 回答 2

1

我会使用理解和压缩。我已经评论了代码，但如果有不清楚的地方，请随时询问。

my_str = 'ATTTTACGTA'

# This loop will check that 
#  - the casting to int is ok
#  - there are only two numbers inputted
#  - stop >= start
#  - start > 0
#  - stop < len(my_str)
while True:
    try:
        start, stop = map(int, raw_input(
            'Please enter start and stop index separated by whitespace\n').split())
        if stop < start or start < 0 or stop > len(my_str):
            raise ValueError
        break
    except ValueError:
        print 'Bad input, try again'


# Loop over all chars, check if the current index is inside range(start, stop).
# If it is, add (char, '?') to the array, if not, add ('?', char) to the array.
#
# This would give you an array of something like this:
# [('?', 'A'), ('?', 'T'), ('T', '?'), ('T', '?'), ('?', 'T'), ('?', 'A'),
#  ('?', 'C'), ('?', 'G'), ('?', 'T'), ('?', 'A')]
#
# By using zip(*array), we unpack each element, and saves the first indexes as
# one list, and the second indexes as another, giving you a list like this:
#
# [('?', '?', 'T', 'T', '?', '?', '?', '?', '?', '?'),
#  ('A', 'T', '?', '?', 'T', 'A', 'C', 'G', 'T', 'A')]

chars = zip(*((c, '?') if i in range(start, stop) else ('?', c)
              for i, c in enumerate(my_str)))

# ''.join is used to concencate all chars into two strings
my_lst = [''.join(s) for s in chars]
print my_lst

样本输出：

Please enter start and stop index separated by whitespace
4
Bad input, try again
Please enter start and stop index separated by whitespace
5 4
Bad input, try again
Please enter start and stop index separated by whitespace
e 3
Bad input, try again
Please enter start and stop index separated by whitespace
4 5
['????T?????', 'ATTT?ACGTA']
于 2014-04-10T18:21:27.103 回答
0

此表达式将起作用：

[ c[0:n] + '?' * (len(c)-n), '?' * n + c[n:] ]
于 2014-04-10T18:08:29.707 回答