#!/usr/bin/perl

$|++;

use strict;

use lib '/home/lairdm/bioperl/bioperl-live';

use Bio::SeqIO;
use Bio::Seq;
use Data::Dumper;

my $filename = $ARGV[0];

unless(-r $filename) {
    die "Can't open filename $filename for reading";
}

my $in = Bio::SeqIO->new( -file => $filename,
			  -format => 'GENBANK') 
    or die "Error opening $filename";

while( my $seq = $in->next_seq() ) {
    print "New sequence: " . $seq->display_id() . "\n";

    my @cds = grep { $_->primary_tag eq 'CDS' } $seq->get_SeqFeatures;

    foreach my $feat (@cds) {
	printf "%s\t%s\t%s\t%s\n", $feat->start, $feat->end, $feat->strand, $feat->length;

	my $ffn_seq = $seq->trunc($feat->start, $feat->end);
#	print Dumper \$ffn_seq;

    }
}

print "Done\n";