1 #!/usr/bin/env python
   2 import sys, os
   3 import subprocess
   4 from Bio.Emboss import Primer3
   5 
   6 args = sys.argv[1:]
   7 new_args = []
   8 outfile = ''
   9 for i, arg in enumerate(args):
  10     if arg == '-outfile':
  11         outfile = args[i+1]
  12     if arg == outfile:
  13         arg += '.raw'
  14     new_args.append(arg)
  15 
  16 os.system('eprimer3 %s > /dev/null 2> /dev/null' % ' '.join(new_args))
  17 
  18 tabular_outfile = open(outfile.replace('.raw', ''), 'w')
  19 tabular_outfile.write('\t'.join((
  20     'Name', 'Primer number', 'Product size', 
  21     'Forward start', 'Forward length', 'Forward tm', 'Forward GC%', 'Forward sequence',
  22     'Reverse start', 'Reverse length', 'Reverse tm', 'Reverse GC%', 'Reverse sequence',
  23     )) + '\n')
  24 for record in Primer3.parse(open(outfile + '.raw')):
  25     name = record.comments.split()[4].strip()
  26     for i, p in enumerate(record.primers):
  27         tabular_outfile.write('\t'.join(map(str, (
  28             name, i+1, p.size,
  29             p.forward_start, p.forward_length, p.forward_tm, p.forward_gc, p.forward_seq,
  30             p.reverse_start, p.reverse_length, p.reverse_tm, p.reverse_gc, p.reverse_seq,
  31             ))) + '\n')