1.	#!/usr/bin/perl -w
2.	use strict;
3.	
4.	use ANNOserver;
5.	
6.	# Parms are FASTA input file name, genus, species.
7.	# Produce geneID, type, contig, begin, strand, len on STDOUT.
8.	
9.	my $annoObject = ANNOserver->new();
10.	my ($file, $genus, $species) = @ARGV;
11.	
12.	open FASTAIN, "<$file";
13.	my $geneCalls = $annoObject->call_genes(\*FASTAIN);
14.	# We throw away the FASTA string returned by call_genes.
15.	my (undef, $geneList) = @$geneCalls;
16.	for my $geneData (@$geneList) {
17.	    my ($gene, $contig, $begin, $strand, $len) = @$geneData;
18.	    print join("\t", $gene, 'peg', $contig, $begin, $strand, $len);
19.	}
20.	close FASTAIN;
21.	open FASTAIN, "<$file";
22.	my $rnaCalls = $annoObject->find_rnas(\*FASTAIN, $genus, $species, 'Bacteria');
23.	# We throw away the FASTA string returned by find_rnas.
24.	my (undef, $rnaList) = @$rnaCalls;
25.	for my $rnaData (@$rnaList) {
26.	    my ($rna, $contig, $begin, $strand, $len) = @$rnaData;
27.	    print join("\t", $rna, 'rna', $contig, $begin, $strand, $len);
28.	}