#!/usr/bin/perl

# Task: Extract GeneID-Number and gene information

use strict;
use warnings;

my $in;
my $data;
my @array;
my $array;
my $GeneID;
my @BMB;
my $flag = 0;
my %hash;
my $hash;

# 1) open the .gff Inputfile and while reading line by line split $dat
+a at each tab and put them in the @array

open $in, '<', "Genomteil.gff" or die $!;
while ($data = <$in>) {
    @array = split (/\t/, $data);
    if ($flag == 0) {
        if ($array[2] =~ /gene/) {    #if you find the word 'gene' a textbloxk follows which contains some information I want to extract and put in an array)
            $flag = 1; # Set the flag. We will be expecting a 'CDS' or 'exon'-line next
            @BMB = ($array[3], $array[4], $array[6]);    #the array will be used as values for my hash later
        } ## end if ($array[2] =~ /gene/)
        if ($array[8] =~ /.*;db_xref=GeneID:(\d+)\n/) {    #if you find the word 'GeneID' extract the following number and put it in my hash (as key), then put the array in my hash
            $GeneID = $1;
        } ## end if ($array[8] =~ /.*;db_xref=GeneID:(\d+)\n/)
    } elsif ($flag == 1) {
        if ($array[2] =~ /CDS/) {
            push (@BMB, $array[2]);
            #put more data in my array
        } elsif ($array[2] =~ /exon/) {
            push (@BMB, $array[2]);
        }
        @{$hash{$GeneID}} = @BMB;
        $flag = 0; # Reset the flag. We will be expecting a 'gene'-line next
    }
} ## end while ($data = <$in>)

close $in;

my $BMB;
while (($GeneID, $BMB) = each %hash) {
    print "$GeneID => $BMB[0]\n";
}