#!/usr/bin/perl -w

use strict;
use Bio::Perl;
use Data::Dumper;



my @var;
my @gff;
my @fields;
my @results;
my $gff;
my $gfffilename;
my $string;
my $name;
my $line;
my $var;
my $score;
my $column;
@fields=();
@results=();
@var=();
@gff=();
my %score;
my $varfilename;
my $ref;


# sub routinen
###########################

sub read_gff_file {

print "Enter the filename of your input file with the single columns of your gff file:= ";          
chomp( my $gfffilename=<STDIN> );
open my $gff_fh, '<', $gfffilename or die "$gfffilename Can not open file\n";
# only read first line
chomp( my $gff = <$gff_fh> );
return $gff;
}

sub open_var_file {

print "Enter the filename of your input file with the variants:= ";         
chomp( my $varfilename=<STDIN> );
open my $var_fh, '<',$varfilename or die "$varfilename Can not open file\n";
return $var_fh;
}

sub do_my_job {

my @column = split(/\t/,&read_gff_file());
my $var_handle = open_var_file();
while ( my $line = <$var_handle> ) {
chomp $line;

 # should reveal 3 fields like (A,A1,A2) 
my @fields = split /\t/, $line;
my @result = @column;
splice(@result,2,0,@fields);
print join( ' ', @result ), "\n";
}

}


# main program

###########################

foreach (my $var_fh) 

{
 ($name,$score) = split; # get score
 $score{$_} = $score; # record it
}

print sort {

             $score{$a} <=> $score{$b};

           }
@var;


do_my_job();

NC_010109.1 NTRFinder motif_small_h 2298 2308 . . . ID=NTR-a1;Parent=NTR-a;Name=motif_small_b
NC_010109.1 NTRFinder motif_small_h 2309 2319 . . . ID=NTR-a1;Parent=NTR-a;Name=motif_small_b
NC_010109.1 NTRFinder motif_small_i 822 832 . . . ID=NTR-a1;Parent=NTR-a;Name=motif_small_b
NC_010109.1 NTRFinder motif_small_i 1598 1608 . . . ID=NTR-a1;Parent=NTR-a;Name=motif_small_b
NC_010109.1 NTRFinder motif_small_j 1723 1733 . . . ID=NTR-a1;Parent=NTR-a;Name=motif_small_b