#!/usr/local/bin/perl -w
# A program that accept an input file: Scorpion database from Gen Bank
# and will output the database in BioWare format

my $file1="$ARGV[0]";          #var to save the input database
my $result=">".$ARGV[1];
my $counter=1;
my $no='D000001';

open(INFO1,$file1) or die "Can't open $file1.\n";   #open file1
open(OUT,$result) or die "Can't open $result.\n";

#foreach line in the files
foreach(<INFO1>)
{
    if(/^DATE\s*(.*)-(.*)-(.*)/){
        print OUT "DBACC\t $no\n";
        print OUT "Date\t $1-$2-$3\n";
        $no++;
        }
    elsif(/\s*\/exon="(\d*-\d*)*"\n/){
        print OUT "Exon\t \{Translation\%$1\}\n";
        }
    elsif(/\s*\/intron="(\d*-\d*)*"\n/){
        print OUT "Intron\t \{Translation\%$1\}\n";
        }    
    else{
    print OUT "line $counter\n";
    }
    $counter++;
}
close(INFO1);
close(OUT);