Aeembly parsing

parseAssembly.pl

sub parseAssembly{

	use Bio::Assembly::IO;
	 
	# Load a reference ACE assembly
	my $aio = Bio::Assembly::IO->new( -file => "output.all.cap.ace", -format => 'ace');
	my $assembly = $aio->next_assembly;

    foreach my $contig ($assembly->all_contigs) {
        print $contig->id . "(" . $contig->get_consensus_length . "b)" . ":\n";
		
		foreach my $seq ( $contig->each_seq ) {
			# $seq is a Bio::LocatableSeq object

			# $feature is a Bio::SeqFeature::Generic
			my $feature = $contig->get_seq_coord($seq);
			
			print "\t" . $seq->id . "\t" . $feature->start . "\t" . $feature->end . "\n";
		}
    }
}