#!/usr/bin/perl
# Description: Reads a genomic sequence from STDIN and submits to RNAMmer to predict rRNA genes
# Author: Peter Fischer Hallin
# Email: pfh@cbs.dtu.dk
# Version: 1.2 ws0
# Date: 2008-11-19

# include standard XML::Compile helper functions (used to initiate WSDL proxys)
require "xml-compile.pl";
require "fasta.inc.pl";

my @fasta = read_fasta();
my $rnammer = WSDLclient ( 'http://www.cbs.dtu.dk/ws/RNAmmer/RNAmmer_1_2_ws0.wsdl' );

my ($kingdom , $mol) = @ARGV;

$kingdom = "bac" unless defined $kingdom;

$mol = "ssu,lsu,tsu" unless defined $mol;

print STDERR "# kingdom: $kingdom\n";
print STDERR "# mol: $mol\n";

for ( my $i = 0 ; $i < scalar ( @fasta ) ; $i++ ) {
	my $ident = $fasta[$i]->{id};
	my $comment = $fasta[$i]->{comment};
	my $seq = $fasta[$i]->{seq};
	run_rnammer  ($ident,$comment,$seq,$kingdom,$mol) ;
}

sub run_rnammer {
	my ($jobid,$status,$expires);
	my ($ident,$comment,$seq,$kingdom,$mol) = @_;
	my $response;
	$response = $rnammer->{runService}->( parameters => { parameters => { mol => $mol ,kingdom => $kingdom , sequences => { entry => {  ident => $ident , seq => $seq}}}});
	die "error obtaining jobid\n" unless defined ( $response->{parameters}->{queueentry});
	$jobid = $response->{parameters}->{queueentry}->{jobid};
	wait_job($rnammer->{pollQueue},$jobid);
	$response = $rnammer->{fetchResult}->( job => { jobid => $jobid   }) ;
	print  STDERR "# parsing 'anndata' object\n";
	printf STDERR "# annotations from %s version %s\n" , 
	 $response->{parameters}->{anndata}->{annsource}->{method} , 
	 $response->{parameters}->{anndata}->{annsource}->{version};
	foreach my $ann (@{$response->{parameters}->{output}->{entries}->{entry}}) {
		my $inp_id = $ann->{sequenceEntry};
			my ( $begin , $end ) = ( $ann->{start} , $ann->{stop} );
			my $strand = $ann->{direction};
			my $mol = $ann->{mol};
			my $id;
			if ( $strand eq "+")  {
				$id = "rRNA_$begin-$end";
			} else {
				$id = "rRNA_$end-$begin";
			}
			my $gene = $ann->{sequence};
			my $comment = "/input_id=$inp_id /mol=$mol /score=$ann->{score}";
			print ">$id $comment\n";
			for (my $x=0 ; $x < length ( $gene ) ; $x += 60) {
				print substr($gene,$x,60),"\n";
		}
	}
}