#!/usr/bin/env python
import sys, os
import subprocess
from Bio.Emboss import Primer3

args = sys.argv[1:]
new_args = []
outfile = ''
for i, arg in enumerate(args):
    if arg == '-outfile':
        outfile = args[i+1]
    if arg == outfile:
        arg += '.raw'
    new_args.append(arg)

os.system('eprimer3 %s > /dev/null 2> /dev/null' % ' '.join(new_args))

tabular_outfile = open(outfile.replace('.raw', ''), 'w')
tabular_outfile.write('\t'.join((
    'Name', 'Primer number', 'Product size', 
    'Forward start', 'Forward length', 'Forward tm', 'Forward GC%', 'Forward sequence',
    'Reverse start', 'Reverse length', 'Reverse tm', 'Reverse GC%', 'Reverse sequence',
    )) + '\n')
for record in Primer3.parse(open(outfile + '.raw')):
    name = record.comments.split()[4].strip()
    for i, p in enumerate(record.primers):
        tabular_outfile.write('\t'.join(map(str, (
            name, i+1, p.size,
            p.forward_start, p.forward_length, p.forward_tm, p.forward_gc, p.forward_seq,
            p.reverse_start, p.reverse_length, p.reverse_tm, p.reverse_gc, p.reverse_seq,
            ))) + '\n')