分割 fasta 文件

---

一、分割 fasta 文件

效果：对 fasta 文件进行分割，每个 > 的序列作为一个文件保存，并以 > 后的字符作为文件名。

# -*- coding: utf-8 -*-
"""
Created on Fri Jul 17 09:00:59 2020

@author: dujidan
"""
import sys

file_fasta = sys.argv[1] #fna 文件
out_path = sys.argv[2]  # 输出路径

f_fa = open (file_fasta) 

flag = True
while flag is True:
    line_fa = f_fa.readline()
    if line_fa.startswith('>'):
        #name = line_fa.replace('\n','').replace('>','').replace('|','-').replace('/','_').replace('/','_').replace(' ','_')
        name = line_fa.replace('>','')
        f_out = open(out_path + "'" + name.split(' ')[0] + ".fna'",'w')
        f_out.write(line_fa)
    else:
        f_out.write(line_fa)
                
    if not line_fa :
        flag = False


f_out.close()
f_fa.close()