如何使用 Python 根据给定数据过滤掉序列？

Question

我会根据给定的文件过滤掉不需要的序列 A.fasta。原始文件包含所有序列，而 fasta 文件实际上是一个以序列 ID 开头的文件，后跟由 A、T、C、G 表示的核苷酸。有人可以帮我吗？

A.fasta

>chr12:15747942-15747949
TGACATCA
>chr2:130918058-130918065
TGACCTCA

Original.fasta

>chr3:99679938-99679945
TGACGTAA
>chr9:135822160-135822167
TGACCTCA
>chr12:15747942-15747949
TGACATCA
>chr2:130918058-130918065
TGACCTCA
>chr2:38430457-38430464
TGACCTCA
>chr1:112381724-112381731
TGACATCA

C.fasta

的预期输出

>chr3:99679938-99679945
TGACGTAA
>chr9:135822160-135822167
TGACCTCA
>chr2:38430457-38430464
TGACCTCA
>chr1:112381724-112381731
TGACATCA

代码

import sys
import warnings
from Bio import SeqIO
from Bio import BiopythonDeprecationWarning
warnings.simplefilter('ignore',BiopythonDeprecationWarning)

fasta_file = sys.argv[1]  # Input fasta file
remove_file = sys.argv[2] # Input wanted file, one gene name per line
result_file = sys.argv[3] # Output fasta file

remove = set()
with open(remove_file) as f:
    for line in f:
        line = line.strip()
        if line != "":
            remove.add(line)

fasta_sequences = SeqIO.parse(open(fasta_file),'fasta')

with open(result_file, "w") as f:
    for seq in fasta_sequences:
        nuc = seq.seq.tostring()
        if nuc not in remove and len(nuc) > 0:
            SeqIO.write([seq], f, "fasta")

上面的代码会过滤掉重复序列，但如果重复序列确实出现在输出中，我想保留它

Answer 1

看看BioPython。这是一个使用它的解决方案：

from Bio import SeqIO

input_file = 'a.fasta'
merge_file = 'original.fasta'
output_file = 'results.fasta'
exclude = set()
fasta_sequences = SeqIO.parse(open(input_file),'fasta')
for fasta in fasta_sequences:
    exclude.add(fasta.id)

fasta_sequences = SeqIO.parse(open(merge_file),'fasta')
with open(output_file, 'w') as output_handle:
   for fasta in fasta_sequences:
        if fasta.id not in exclude:
            SeqIO.write([fasta], output_handle, "fasta")

如何使用 Python 根据给定数据过滤掉序列？

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