test8: 从总fasta文件中提取指定蛋白列表的sub_fa

输入文件：
1、总fasta文件：rename.fa

>Gene.2::TRINITY_DN1000_c0_g1::g.2::m.2
SKYKYAIQRPDFSADDFESFITKHTGISVKSKGSAALDSNSLIKAITGIFAVISIITFVI
YYHWEKFHHFIYGQNYRHISVHDTIQTGYGRALLQHIIPYQLSRRKMAIAI
>Gene.3::TRINITY_DN10027_c0_g1::g.3::m.3
LYLHGLLSPIFPNIGATLNAVAEKPAFTLPAPLMSRLGRRPLLVGTMWLSAVFCVFGSLT
GKMATATLVQMVCGVLGIFGMAAAFNLLLIYTAELFPTAVRNAALGCVQQAVHFGAIAAP
MVVMTGGGVALGVFGVCGMVGGVLAVYLPETWNKPLYDTMAGMEEGEKGMVGV*
>Gene.5::TRINITY_DN10030_c0_g1::g.5::m.5
RLINMYAAAARSSQVIPPPPRVSAASAAARSSPAIPPPPHTTADRSSPAIPPPPPATAPS
DSDFTSDSSDSDSPAPNSALHDSILSAYLRTSASSSPDLAKIRSFLSSSVSCCLICLVRI
RPTDAVWSCSASCHALF

2、指定蛋白列表：pro_list.txt

Gene.2::TRINITY_DN1000_c0_g1::g.2::m.2
Gene.3::TRINITY_DN10027_c0_g1::g.3::m.3
Gene.5::TRINITY_DN10030_c0_g1::g.5::m.5
Gene.6::TRINITY_DN1005_c0_g2::g.6::m.6

3:输出文件：sub.fa

指定蛋白列表的fasta文件

二、代码

#! /usr/bin/env python
# _*_ coding: utf-8 _*_
##usage:python3 sub_fa.py -fa rename.fa -list pro_list.txt -o sub.fa

import argparse


#if len(sys.argv) !=3 :
#    print("enter 'python3 sub_fa.py -h' for help")
#    sys.exit()


parser = argparse.ArgumentParser(description='manual to this script')
parser.add_argument('-fa', '--fasta', type=str, default=None, help='all_fasta',required=True)
parser.add_argument('-list', '--prolist', type=str, default=None, help='proList',required=True)
parser.add_argument('-o', '--output', type=str, default=None, help='output_path',required=True)
args = parser.parse_args()

faAll = args.fasta
pro_list = args.prolist
fa_w = args.output

#faAll = "E:/Script/python/test8/rename.fa"
#pro_list = "E:/Script/python/test8/pro_list.txt"
#fa_w = "E:/Script/python/test8/sub.fa"

pro_1 = open(pro_list,"r")
pro_list = list(pro_1)
pro_1_list = [i.replace("\n","") for i in pro_list]
# print(pro_1_list)

all_fa = open(faAll,"r")
fa_1_w = open(fa_w,"w")
l = all_fa.read()
ls = l.split(">")

for line in ls:
    name = line.split("\n")[0]
    if name in pro_1_list:
        fa_1_w.write(">" + line)