修改python腳本以運行多個輸入文件

Question

我是python的新手，我有一個針對特定文件（input1.txt）運行的python腳本，並生成了輸出（output1.fasta），但我想針對多個文件運行此腳本，例如：input2 .txt，input3.txt ...並生成相應的輸出：output2.fasta，output3.fasta

from Bio import SeqIO

fasta_file = "sequences.txt" 
wanted_file = "input1.txt" 
result_file = "output1.fasta" 

wanted = set()
with open(wanted_file) as f:
    for line in f:
        line = line.strip()
        if line != "":
            wanted.add(line)
fasta_sequences = SeqIO.parse(open(fasta_file),'fasta')
with open(result_file, "w") as f:
    for seq in fasta_sequences:
        if seq.id in wanted:
            SeqIO.write([seq], f, "fasta")

我試圖添加glob函數，但是我不知道如何處理輸出文件名。

from Bio import SeqIO
import glob

fasta_file = "sequences.txt"

for filename in glob.glob('*.txt'):

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

    fasta_sequences = SeqIO.parse(open(fasta_file),'fasta')
    with open(result_file, "w") as f:
        for seq in fasta_sequences:
            if seq.id in wanted:
                SeqIO.write([seq], f, "fasta")

錯誤消息是：NameError：未定義名稱'result_file'

Answer 1

您的glob文件當前正在提取“序列”文件和輸入，因為*.txt包含sequences.txt文件。 如果“ fasta”文件始終相同，而您只想迭代輸入文件，則需要

for filename in glob.glob('input*.txt'):

另外，要遍歷整個過程，也許您想將其放入方法中。 而且，如果始終創建輸出文件名以與輸入相對應，則可以動態創建該文件名。

from Bio import SeqIO

def create_fasta_outputs(fasta_file, wanted_file):
    result_file = wanted_file.replace("input","output").replace(".txt",".fasta")

    wanted = set()
    with open(wanted_file) as f:
        for line in f:
            line = line.strip()
            if line != "":
                wanted.add(line)
    fasta_sequences = SeqIO.parse(open(fasta_file),'fasta')
    with open(result_file, "w") as f:
        for seq in fasta_sequences:
            if seq.id in wanted:
                SeqIO.write([seq], f, "fasta")

fasta_file = "sequences.txt"
for wanted_file in glob.glob('input*.txt'):
    create_fasta_outputs(fasta_file, wanted_file)