#!/usr/bin/perl -w
use strict;
use Bio::Perl;
use Data::Dumper;

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

print "Enter the filename of your input file with the single columns of your gff file:= ";		
chomp ($gfffilename=<STDIN>);
open (GFFINPUT,'<',$gfffilename) or die ("$gfffilename Can not open file\n");
@gff=<GFFINPUT>;

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


#my @array = (
 #   'a1 a2 a3 a4 a5 a6',
#);

my @spalten = split m{ }, $gff[0];


# "datei" auslesen
while ( my $line = <GFFINPUT> ) {
    
    chomp $line;                # umbruch entfernen

    # Sollte 3 Felder (z.B. A,A1,A2) ergeben
    my @fields = split m{ }, $line;
    my @result = @spalten;
    splice(@result, 2, 0, @fields );

    print join( ', ', @result ), "\n";
}