#!/usr/bin/perl -w
use strict;

use Bio::SeqIO;
use Bio::Seq;

# the input arguments are 
# 1. a directory of genbank genome files (*.gbk)
# 2. a filename for our coding sequences to be written to
my $dir = $ARGV[0];
my $outfile = $ARGV[1];

my $output = Bio::SeqIO->new(-format => 'fasta',
			     -file   => ">$outfile.cds");
my $output_protein = Bio::SeqIO->new(-format => 'fasta',
				     -file   => ">$outfile.pep");
opendir(DIR, $dir) || die("cannot open directory '$dir': $!");
my @files = readdir(DIR);

my %unique_loci;
foreach my $file ( @files ) {
    print "file is $file\n";
    # ABC.gbk.HIJ <-- don't want these
    # ABC.gbk <-- we want these
    if( $file =~ /\.gbk$/) {
	print "Opening $dir/$file...\n";
	my $input = Bio::SeqIO->new(-format => 'genbank',
				    -file   => "$dir/$file");
	while( my $seq = $input->next_seq ) { 
	    # get all the feature from the sequence object
	    my @features = $seq->get_SeqFeatures;
	    foreach my $f ( @features ) {
		# test if the feature TYPE is 'CDS'
		if( $f->primary_tag eq 'CDS' ) {
		    my $name;
		    if( $f->has_tag('locus_tag') ) {
			($name) = $f->get_tag_values('locus_tag');
                    } else {
			warn("cannot find a locus tag for this feature ", $f->gff_string, "\n");
 		    }
		    $unique_loci{$name}++;
		    if( $unique_loci{$name} > 1 ) {
			warn("Locus $name has been seen $unique_loci{$name} times\n");
			$name .= ".". $unique_loci{$name};
		    }
		    my ($desc) = $f->get_tag_values('product');
		    my $cds_seq = $f->spliced_seq;
		    $cds_seq->display_id($name);
	            $cds_seq->description($desc);
		    $output->write_seq($cds_seq); 
		    $output_protein->write_seq($cds_seq->translate);
		}
	    } 
	}
    }
}