gff文件提取cds

 #!/usr/bin/perl

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

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

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

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

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

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

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

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

 sub cut
 {
     my %gene;

     my $exon = ;my $start = ;my $length = ;

     my $gff = shift;open GFF,"$gff"; 

     while(my $line = <GFF>)
     {
         chomp $line;

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

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

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

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

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