Python：如何根据具有二进制内容的文本文件提取DNA序列？

Question

For example I have a fasta file with the following sequences:

>human1
AGGGCGSTGC
>human2
GCTTGCGCTAG
>human3
TTCGCTAG

How to use python to read a text file with the following content to extract the sequences? 1 represents true and 0 represents false. Only sequence with value 1 will be extracted.

Example text file:

0
1
1

Expected output:

>human2
GCTTGCGCTAG
>human3
TTCGCTAG

Answer 1

for this is better to use biopython

from Bio import SeqIO

mask = ["1"==_.strip() for _ in open("mask.txt")]
seqs = [seq for seq in SeqIO.parse(open("input.fasta"), "fasta")]
seqs_filter = [seq for flag, seq in zip(mask, seqs) if flag]
for seq in seqs_filter:
  print seq.format("fasta")

you get:

>human2
GCTTGCGCTAG
>human3
TTCGCTAG

explanation

parse fasta: the format fasta may to have several lines of sequences (check fasta format ), is better to use a specialized library to read (parser) and write the output

mask: I read de mask file and cast to boolean [False, True, True]

filter : use zip function for each sequence match with his mask, and following i use list Comprehensions to filter

Answer 2

I think this may help you and I really think you should take some time learn Python. Python is a good language for bioinformatics.

display = []
with open('test.txt') as f:
    for line in f.readlines():
        display.append(int(line.strip()))

output_DNA = []
with open('XX.fasta') as f:
    index = -1
    for line in f.readlines():
        if line[0] == '>':
            index = index + 1

        if display[index]:
            output_DNA.append(line)

print output_DNA

Answer 3

You can create an list to act like a mask for when you read your fasta file:

with open('mask.txt') as mf:
    mask = [ s.strip() == '1' for s in mf.readlines() ]

Then:

with open('seq.fasta') as f:
    for i, line in enumerate(f):
        if mask[i]:
            *something* line

or:

from itertools import izip

for b, line in izip(open(mask_file), open(seq_file)):
    if b.strip() == '1':
          *something* line

Answer 4

I am unfamiliar with the fasta file format specifically but hopefully this helps. You can open your file in python the following way and extract the valid line entries in a list.

valid = []
with open('test.txt') as f:
    all_lines = f.readlines() # get all the lines
    all_lines = [x.strip() for x in all_lines] # strip away newline chars
    for i in range(len(all_lines)):
        if all_lines[i] == '1': # if it matches our condition
            valid.append(i) # add the index to our list

    print valid # or get only the fasta file contents on these lines

I ran it with the following text file test.txt:

0
1
1
1
0
0
1
1

And got output when printing valid :

[1, 2, 3, 6, 7]

I think this will help you move along, but please let me know in the comments if you need an expanded answer.