python实现根据序列ID从提取fasta文件序列

当序列少的时候，我习惯用 grep -A 1 -f seq.lst seq.fas | sed ‘/^–$/d’ > out.fas提取，可是此次遇到了一个大文件，用grep就太费时了，而后又试了一下TBtools的提取序列功能，发现时间也很长，因此就写了个python。提取将近100万条reads耗时也就须要10s左右python

#!/usr/bin/python
# -*- coding: utf-8 -*-
# Usage: python script.py lstFile seqFile outfile
import argparse
parser = argparse.ArgumentParser()
parser.add_argument("lstFile", help="input a list file", type=str)
parser.add_argument("seqFile", help="input a sequence file", type=str)
parser.add_argument("outfile", help="output a file", type=str)
args = parser.parse_args()
lst = args.lstFile
seq = args.seqFile
out = args.outfile

frLst = open(lst, 'r')
frSeq = open(seq, 'r')
fwOut = open(out, 'w')

query = []
database = {}
for i in frLst.readlines():
    query.append(i.strip())
for i in frSeq.readlines():
    if i.startswith('>'):
        keys = i.lstrip('>').strip()
        database[keys] = []
    else:
        database[keys].append(i.strip())
for line in query:
    fwOut.write('>' + str(line) + '\n' + str(''.join(database[line])) + '\n')
fwOut.close()