#!/bin/sh
##convert output of CAPS detection tool to GFF3
## usage 
# sh CAPS2gff.sh <input tabular CAPS output> <output file>
#Copyright 2012 John McCallum
#New Zealand Institute for Plant and Food Research

#This program is free software: you can redistribute it and/or modify
#     it under the terms of the GNU General Public License as published by
#    the Free Software Foundation, either version 3 of the License, or
#    (at your option) any later version.
#
#    This program is distributed in the hope that it will be useful,
#    but WITHOUT ANY WARRANTY; without even the implied warranty of
#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#    GNU General Public License for more details.
#
#    You should have received a copy of the GNU General Public License
#    along with this program.  If not, see <http://www.gnu.org/licenses/>.

inputfile=$1
outputfile=$2
awk -F '\t' 'split($4,ID,":") {print ID[1], "FINDCAPS",ID[3],ID[4],ID[4],".",".",".","ID="$1";Enzyme="$5";Phase="$6}' $inputfile > $outputfile