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

use Bio::SeqIO;
use Bio::DB::GenBank;
use Bio::Seq;

my $db = new Bio::DB::GenBank;
my $file = shift @ARGV;

my $in = new Bio::SeqIO(-format => 'genbank', -file => $file);
my $out = new Bio::SeqIO(-format => 'fasta');
my %seqs;

while( my $seq = $in->next_seq ) {
    my $num = 1;
    foreach my $feature ( $seq->get_SeqFeatures ) {
	if( $feature->primary_tag eq 'CDS' ) {
	    my $cdsseq; 
	    my $strand = 1;
	    if( $feature->has_tag('coded_by') ) {
		my ($tag) = $feature->get_tag_values('coded_by');
		print "tag is $tag\n";
		
		if( $tag =~ /complement/ ) {
		    $strand = -1;
		}
		if( $tag =~ /join\(([^)]+)\)/ ) {
		  my @pieces = split(/\s*\,\s*/,$1);
		  foreach my $piece ( @pieces ) {
		      my ($acc,$loc) = split(/\:/,$piece);
		      print "$acc $loc\n";
		      my ($start,$stop) = ($loc =~ /(\d+)\.\.(\d+)/ );
		      print "want $acc $start $stop\n";
		      my $ntseq = $seqs{$acc};
		      if( ! $ntseq ) {
			  $ntseq = $db->get_Seq_by_acc($acc);
			  $seqs{$acc} = $ntseq;
		      }
		      my $subseqobj = $ntseq->trunc($start,$stop);
		      my $subseq = $subseqobj->seq();
		      $cdsseq .= $subseq;
		  }
	      }
	    my $cdseqobj = new Bio::Seq(-seq        => $cdsseq,
					-display_id => "CDS$num");
	    $num++;
	    if( $strand < 0 ) {
		$cdseqobj = $cdseqobj->revcom;
	    }
	    $out->write_seq($cdseqobj);
	    $out->write_seq($cdseqobj->translate());
	    $out->write_seq($seq);
	}

    }
}
}