根据 csv 文件中的切片索引连接切片字符串

Question

好吧，我的挑战似乎很容易，但我已经没有选择了。因此，我们将不胜感激。

我有许多 fasta 格式的 DNA 序列，它们需要在特定位置切片，然后连接生成的部分。所以如果我的序列文件是这样的：

~$ cat seq_file
>Sequence1
This is now a sequence that must require a bit of slicing and concatenation to be useful
>Sequence2
I have many more uncleaned strings like this in the form of sequences

我希望输出是这样的：

>Sequence1
This is useful
>Sequence2
I have cleaned sequences

现在切片部分由单独 csv 文件中的切片索引确定。在这种情况下，切片位置是这样组织的：

~$ cat test.csv
Sequence1,0,9,66,74,,
Sequence2,0,5,15,22,48,57

我的代码：

from Bio import SeqIO
import csv

seq_dict = {}
for seq_record in SeqIO.parse('seq_file', 'fasta'):
    descr = seq_record.description
    seq_dict[descr] = seq_record.seq

with open('test.csv', 'rb') as file:
    reader = csv.reader(file)
    for row in reader:
        seq_id = row[0] 
        for n in range(1,7): 
            if n % 2 != 0:
                start = row[n] # all start positions for the slice occupy non-even rows
            else:
                end = row[n] 

                for key, value in sorted(seq_dict.iteritems()):
                    #print key, value
                    if key == string_id: # cross check matching sequence identities
                        try:
                            slice_seq = value[int(start):int(end)]
                            print key
                            print slice_seq
                        except ValueError:
                            print 'Ignore empty slice indices.. '

现在会打印出来：

Sequence1
Thisisnow
Sequence1
useful
Ignore empty slice indices.. 
Sequence2
Ihave
Sequence2
cleaned
Sequence2
sequences

到目前为止一切顺利，这是我所期望的。但是如何通过连接或连接或通过 python 中可能的任何操作将切片部分组合在一起达到我想要的目的？谢谢。

Answer 1

类似这样的：

import csv
from string import whitespace
with open('seq_file') as f1, open('test.csv')  as f2:
    for row in csv.reader(f2):
        it = iter(map(int, filter(None, row[1:])))
        slices = [slice(*(x,next(it))) for x in it]
        seq = next(f1)
        line = next(f1).translate(None, whitespace)
        print seq,
        print ' '.join(line[s] for s in slices)

输出：

>Sequence1
Thisisnow useful
>Sequence2
Ihave cleaned sequences

Answer 2

您可以通过一些修改来实现：

with open('test.csv', 'rb') as file:
    reader = csv.reader(file)
    for row in reader:
        seq_id = row[0]
        seqs = []
        for n in range(1,7):
            if n % 2 != 0:
                start = row[n] # all start positions for the slice occupy non-even rows
            else:
                end = row[n]

                for key, value in sorted(seq_dict.iteritems()):
                    #print key, value
                    if key == seq_id: # cross check matching sequence identities
                        try:
                            seqs.append(value[int(start):int(end)])
                        except ValueError:
                            print 'Ignore empty slice indices.. '
        print ' '.join(str(x) for x in seqs)