use strict;
use warnings;
use autodie;
use Data::Dump;
use Data::Dumper;
use Bio::SeqIO;
STDOUT->autoflush(1);

my $gbffpath='C:\My gbff path';

opendir(DIR, "$gbffpath");
my @files= grep {/\.gbff$/ } readdir(DIR);
closedir(DIR);
my $featc=0;

foreach my $gbfffile (@files){
	my $in = Bio::SeqIO->new(-file=>"<$gbffpath\\$gbfffile", -format=>"genbank");
	my @allpos;
	my $obj = $in->next_seq();
	my @features = $obj->get_SeqFeatures();
	my @two = shift @features;
	foreach my $fefe  (@features){
		my $pt = $fefe->primary_tag();
		if ($pt eq "CDS" or $pt eq "rRNA" or $pt eq "tRNA") {
			$featc++;
			last if $featc==4;
			push @two, $fefe;
			my $starti= $two[1]->start();
			my $endi; my $end; my $start;
			if($two[0]->primary_tag() eq "source"){
				$endi = $starti;
				$end = $endi +1;
				$start = $starti -1;
				shift @two;
			}
			else{
				$endi = $two[0]->end();
				$end = $endi +1;
				$start = $starti -1;
				#do something else
				# change $start to be -21 nucleotides
				# my $subseq = $obj->subseq($end,$start) unless ($end>=$start);
				my $subseq = $obj->subseq($end,$start) unless ($end>=$start);
				shift @two;

				dd ($gbfffile,$pt,"\$two\[0\]:","endi:$endi","\$two\[1\]:","starti:$starti","after:","end:$end","start:$start",$subseq);
			}
	}
}