#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sat Dec 26 11:51:15 2020

@author: lewis
"""

from sys import argv
import subprocess as sb

genome = argv[1]
prot1 = argv[2]
prot2 = argv[3]
prot3 = argv[4]
prots = [prot1, prot2, prot3]

sb.call(['makeblastdb',
         '-in', genome, 
         '-dbtype', 'nucl',
         '-out', 'genome_db',
         '-logfile', 'genome_db_log'])

i = 0
for elem in prots:
    i += 1
    usain = 'sw:{}'.format(elem)
    usaout = '{}.fasta'.format(elem)
    sb.call(['seqret', usain, usaout, '-filter'])
    sb.call(['tblastn', 
             '-word_size', '3',
             '-query', usaout, 
             '-db', 'genome_db',
             '-max_target_seqs', '10',
             '-outfmt', '7',
             '-out', 'output{}.tsv'.format(i)])