gff文件提取cds

#!/usr/bin/perl

use strict;
use warnings;
########input########

my $gff = $ARGV[0];my $cut = &cut($gff);my %cut = %$cut;

my ($gene_number,$gene_id,$gene_name)  = ($ARGV[1],$ARGV[2],$ARGV[3]);

#########main#######

my %hash_2 = %{$cut{$gene_name}};

foreach my $key_2(keys %hash_2)
{
    my @arr = $hash_2{$key_2};my $exon_start = $arr[0][0]+30-1;my $exon_end =$arr[0][1]-30+1;

    print "$gene_name	$key_2	$arr[0][0]	$exon_start
$gene_name	$key_2	$exon_end	$arr[0][1]
";
}

#############sub################

sub cut
{
    my %gene;

    my $exon = 1;my $start = 0;my $length = 0;

    my $gff = shift;open GFF,"$gff"; 
    
    while(my $line = <GFF>)
    {
        chomp $line;

        my @q = split /s/,$line;

        if($q[2] =~ /mRNA/)
        {
            $exon = 1;$start = $q[3];$length = 0;
        }
        elsif($q[2] =~ /CDS/)
        {
            $q[8] =~ /Parent=(.*);S/m;my $key = $1;  

            my $new_length = $q[4]-$q[3]; 

            $exon =~/(w*)/; $gene{$key}{$1} = [$length+1,$length+$new_length];

            $exon++; $length += $new_length;
        }    
    }   
    return %gene;
}