#!/usr/bin/python
# -*- coding:utf-8 -*-
'''Convert primers in RTPrimerDB into FASTA format

The CSV file wad downloaded from: http://medgen.ugent.be/rtprimerdb/index.php?downloads

PATTYN, F., SPELEMAN, F., DE PAEPE A. & VANDESOMPELE, J. (2003). 
RTPrimerDB: the Real-Time PCR primer and probe database. 
Nucleic Acids Research, 31(1): 122-123.


by Wubin Qu <quwubin@gmail.com>,
Copyright @ 2010, All Rights Reserved.
'''

Author  = 'Wubin Qu  <quwubin@gmail.com> CZlab, BIRM, China'
Date    = 'Mar-08-2011 09:39:27'
License = 'New-BSD License'
Version = '1.0'

import sys
import os
import re
from optparse import OptionParser


def get_opt():
    '''Handle options'''
    usage = 'Usage: %prog -i InFile -o OutFile'

    version = '%prog Version: ' + '%s [%s]' % (Version, Date)
    parser = OptionParser(usage=usage, version=version)
    parser.add_option('-i', '--infile', dest='infile', help='Input file name. [String]')
    parser.add_option('-o', '--outfile', dest='outfile', help='Output file name. [String]')
    [options, args] = parser.parse_args()

    if len(args) > 1:
        parser.error('Incorrect argument, add" "-h" for help.')

    if not options.infile:
        parser.error('Infile needed, add" "-h" for help.')

    if not options.outfile:
        parser.error('OutFile needed, add" "-h" for help.')

    return options

def main ():
    '''Main'''
    options = get_opt()
    fh = open(options.outfile, 'w')
    for line in open(options.infile):
        line = line.strip()
        if not re.match('(\d+)', line):
            continue
        fields = line.split('\t')
        rt_id = fields[0]
        fp = fields[8]
        rp = fields[7]
        if not (fp and rp):
            continue
        fh.write('>%s_fp\n%s\n>%s_rp\n%s\n' % (rt_id, fp, rt_id, rp))
    
    fh.close()


if __name__ == '__main__':
    main()