use strict;
use warnings;
use Getopt::Long;
use Bio::SeqIO;

### perl /home/xiangyang/Chen_genome/perl_bin/extract_rRNA_dir.pl /home/xiangyang/Chen_genome/chen_gbk

my $path=$ARGV[0];
# my $filename=getcwd $path;
opendir DIR, $path or die $!;
my @dir = readdir DIR; 
closedir DIR;

foreach my $file(@dir){
     my $input="$path/$file";
     mkdir "$path/rRNA/";
     my $output="$path/rRNA/$file.fasta";
     open(OUTPUT, ">$output");

#######################################################################################
my %options = (
     cdsCount => 0,
);
#######################################################################################
my $in = new Bio::SeqIO( -file => $input, -format => 'genbank' );
my $out = new Bio::SeqIO( -file => $output , -format => 'fasta' );

    my @dna=();
    my $label_3;
    my %hash_0;
    my $i=0;
    while ( my $seqObject = $in->next_seq() ) {
        my @features = $seqObject->get_SeqFeatures();
#--------------------------------------------------------------------------------------------display organism name for each CDS		
	my $org = "";
        foreach (@features) {
        my $feat = $_;
		my @ar;
		if ($feat->primary_tag() eq "source"){
				@ar = $feat->get_tag_values('organism');
				$org = $ar[0];
				next;
		                                      }	
#---------------------------------------------------------------------------------------------xiangyang li addition 2013-01-25
        my $type = $feat->primary_tag;
        unless ( $type eq "rRNA") {
            next;
        }
        my @label = ();
        my @tag=();

        if ( $feat->has_tag('locus_tag') ) {
                    push( @label, join( ",", $feat->get_tag_values('locus_tag') ) );
        }
        if ( $feat->has_tag('product') ) {                    
            	    push (@tag, join(",",$feat->get_tag_values('product')));
            	    push (@label, join(",",$feat->get_tag_values('product')));
        }
            	    push (@label, join(",","[".$file."]"));                        ###xiangyang li addition 2013-01-25
         
        my $label = join( ";", @label );
        my $label_2=join(";",@tag);

        $label =~ s/\s+/_/g;
        $label =~ s/\n//g;
        $label =~ s/\t+/ /g;

    if ($label_2 eq "16S ribosomal RNA") {
                     $i++;
                     print "$label\n";
                     my $dna = $feat->spliced_seq->seq;
                     $dna=$i."_".$dna;
                     $hash_0{$dna}=$label;
                     print "$dna\n";
                     push @dna,$dna;
                     $options{cdsCount}++;
                                         }
}                                                                                                   # corrsponding to Line 37
}                                                                                                   # corrsponding to Line 33
    my $max=length $dna[0];
    foreach (@dna) {if ($max<=length $_){$max=length $_;}} 
      $max=$max-2;               
    my %hash;
    foreach (@dna) {$hash {length $_}=$_;}                  
       my @number = sort{$b <=> $a} (keys %hash);
       my $sequence = $hash {$number[0]};
       $label_3=$max."---".$hash_0{$sequence};
       $sequence=~s/(.+)_//g;
       print OUTPUT ">$label_3\n$sequence\n"; 
       print    "A total of $options{cdsCount} records were written to $file.\n";
}                                                                                                   # corrsponding to Line 15