从文件中读取序列作为字符串而不是单个字母 python

Question

I have three files, they look like this:

>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

I am trying to read these files using python to get this result:

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

Here is my code:

testNames = []
testSequences = []
counter = 0
for filename in os.listdir("/PATH/TO/FILE"): #go to directory where aligned files are kept
    if filename.endswith(".txt"): #open files which have been aligned with MAFFT
        fastaFile = open(filename, 'r') 
        testNames.append([])
        testSequences.append([])
        for line in fastaFile: 
            line = line.strip() 
            if len(line)>0: 
                if line[0] == '>':  
                    testNames[counter].append(line[1:]) 
                    testSequences.append("") 
                    currentTaxon = len(testSequences)-1 
                else: 
                    testSequences[currentTaxon] += line 
        counter +=1

print testSequences

This gives me this result:

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

I tried to change my code to but the strings inside the brackets by taking out the 14th line:

testNames = []
testSequences = []
counter = 0
for filename in os.listdir("/PATH/TO/FILE"): #go to directory where aligned files are kept
    if filename.endswith(".txt"): #open files which have been aligned with MAFFT
        fastaFile = open(filename, 'r') 
        testNames.append([])
        testSequences.append([])
        for line in fastaFile: 
            line = line.strip() 
            if len(line)>0: 
                if line[0] == '>':  
                    testNames[counter].append(line[1:]) 
                    currentTaxon = len(testSequences)-1 
                else: 
                    testSequences[currentTaxon] += line 
        counter +=1

print testSequences

Now I get this result:

[['a', 'a', 'a', 'a', 'c', 'c', 'c', 'c'], ['t', 't', 'g', 'g'], ['A', 'A', 'A', 'A', 'A', 'A', 'A', 'C', 'C', 'C', 'C', 'C', 'C', 'T', 'T', 'T', 'T', 'T', 'T', 'G', 'G', 'G', 'G', 'G', 'G']]

How can I fix my code to get sequences read in as strings, inside the nested list?

I want to keep the contents of the list testNames as is:

[['xx_oneFish |xxx', 'xx_twoFish |xxx'], ['xx_redFish |xxx', 'xx_blueFish |xxx'], ['xx_oneFish |xxx', 'xx_twoFish |xxx', 'xx_redFish |xxx', 'xx_blueFish |xxx']]

Answer 1

Try this :

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)

print (testSequences)
print (testNames)

Output :

[['tt', 'gg'], ['AAAAAAA', 'CCCCCC', 'TTTTTT', 'GGGGGG'], ['aaaa', 'cccc']]
[['>xx_redFish |xxx', '>xx_blueFish |xxx'], ['>xx_oneFish |xxx', '>xx_twoFish |xxx', '>xx_redFish |xxx', '>xx_blueFish |xxx'], ['>xx_oneFish |xxx', '>xx_twoFish |xxx']]

Note : 1. This would work if you had the script in the same folder where the text files are. 2. This doesn't check for the expected values in the lines exactly happening after those lines starting with '>' . That being said, if one of your .txt file is like this :

>xx_oneFish |xxx
aaaa
bbbb
dddd
>xx_twoFish |xxx
cccc

For that file, the sub-list produced inside testSequences would be ['aaaa', 'bbbb', 'dddd', 'cccc']