使用循环将特定长度的连字符序列添加到序列中 [英] Adding in sequences of hyphens, of a specific length, into sequences using loops

问题描述

我有三个文本文件:

>xx_oneFish |xxx
AAAAAAA
>xx_twoFish |xxx
CCCCCC
>xx_redFish |xxx
TTTTTT
>xx_blueFish |xxx
GGGGGG

>xx_oneFish |xxx
aaaa
>xx_twoFish |xxx
cccc

>xx_redFish |xxx
tt
>xx_blueFish |xxx
gg

我正在尝试获得一个输出，其中每种物种(redFish，blueFish等)的字母序列以列表中出现的顺序排列在列表中，顺序与它们在目录中文件中出现的顺序相同储存.每个物种都有一个嵌套列表.

I am trying to get an output, where the sequences of letters for each species (redFish, blueFish etc.) are put together in a list, in the same order as they appear in the files in my directory where the sequences are stored. There will be one nested list for each of the species.

如果文件不包含某个物种的序列，我想添加一串连字符，其长度与文件中其他物种的序列相同.

If a file contains no sequence for a species, I want to add in a string of hyphens that is the same length as the sequence present in the file for other species.

即对于此数据集，输出应如下所示:

i.e. for this dataset the output should look like this:

[['--', 'aaaa', 'AAAAAAA'], ['--', 'cccc', 'CCCCCC'], [ 'tt', '----', 'TTTTTT'], ['gg', '----', 'GGGGGG']]

这是我当前的代码:

differentNames =  ['oneFish', 'twoFish', 'redFish', 'blueFish']
concatSeq = [[], [], [], []]

import os
testSequences = []
testNames = []
for filename in os.listdir("./"): #go to directory where aligned files are kept
    if filename.endswith(".txt"): #open files which have been aligned with MAFFT
        fastaFile = open(filename, 'r') 
        temp_sub_list_names = []
        temp_sub_list_seq = []
        for line in fastaFile:
            line = line.strip()
            if line:
                if not line.startswith('>'):
                    temp_sub_list_seq.append(line)
                else:
                    temp_sub_list_names.append(line)
        testSequences.append(temp_sub_list_seq)
        testNames.append(temp_sub_list_names)

for i in range(len(testNames)):
    for k in range(len(testNames[i])):
        for j in range(len(differentNames)):
            if differentNames[j] in testNames[i][k]: #check whether the sequence names match up
                concatSeq[j].append(testSequences[i][k]) #if they do, add the sequence to the corresponding list
        c = 1
        for a in range(len(concatSeq)):
        #   for b in range(len(concatSeq[a]):
            if len(concatSeq[a]) < c:
                hyphenString = "-" * len(testSequences[c-1][0])
                concatSeq[a].append(hyphenString)
        c+=1


print concatSeq

在最终循环中出了点问题，因为这是我的输出:

Something is going wrong in the final loop, as this is my output:

[['aaaa', 'AAAAAAA'], ['----', 'cccc', 'CCCCCC'], ['----', 'tt', 'TTTTTT'], ['----', 'gg', 'GGGGGG']]

推荐答案

如果您不介意使用re模块来解析文件，则可以使用以下示例:

If you don't mind using re module for parsing the files, you can use this example:

file_1 = '''>xx_oneFish |xxx
AAAAAAA
>xx_twoFish |xxx
CCCCCC
>xx_redFish |xxx
TTTTTT
>xx_blueFish |xxx
GGGGGG'''

file_2 = '''>xx_oneFish |xxx
aaaa
>xx_twoFish |xxx
cccc'''

file_3 = '''>xx_redFish |xxx
tt
>xx_blueFish |xxx
gg'''

import re
from collections import OrderedDict

f1 = OrderedDict(re.findall(r'>.*?_(.*?)\s.*?\n(.*?)(?=\n|\Z)', file_1, flags=re.DOTALL))
f2 = OrderedDict(re.findall(r'>.*?_(.*?)\s.*?\n(.*?)(?=\n|\Z)', file_2, flags=re.DOTALL))
f3 = OrderedDict(re.findall(r'>.*?_(.*?)\s.*?\n(.*?)(?=\n|\Z)', file_3, flags=re.DOTALL))

differentNames = {'oneFish', 'twoFish', 'redFish', 'blueFish'}

d = OrderedDict()
for i, f in enumerate([f1, f2, f3]):
    for k, v in f.items():
        if k in differentNames: # <-- comment this out if you want to check for all species in files
            d.setdefault(k, []).append((i, v))

lengths = dict(i for v in d.values() for i in v)

vals = []
for k, v in d.items():
    dd = dict(v)
    vals.append([dd.get(i, '-' * len(lengths[i])) for i in range(len(lengths))][::-1])

from pprint import pprint
pprint(vals)

打印:

[['--', 'aaaa', 'AAAAAAA'],
 ['--', 'cccc', 'CCCCCC'],
 ['tt', '----', 'TTTTTT'],
 ['gg', '----', 'GGGGGG']]

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