#!/usr/bin/perl
# Description: Extract a genome sequences using the GenomeAtlas 3.0 WSDL getSeq operation, and submit sequences to RNAmmer services to predict rRNA genes.
# Author: Peter Fischer Hallin
# Email: pfh@cbs.dtu.dk
# Version: 1.2a
# Date: 2007-01-27 

use SOAP::Lite;
use Data::Dumper;

# create SOAP services entry points
my $getseq = SOAP::Lite
	-> service('http://www.cbs.dtu.dk/ws/GenomeAtlas/GenomeAtlas_3_3.wsdl')
	->on_fault(
				sub { my($self, $res) = @_;
					die
					 "faultcode:", ref $res ? $res->faultcode : $self->transport->status, "\n" ,
					 "faultstring:", ref $res ? $res->faultstring : $self->transport->status, "\n";
				}
			);
my $rnammer = SOAP::Lite
	-> service('http://www.cbs.dtu.dk/ws/RNAmmer/RNAmmer_1_2a.wsdl')
	->on_fault(
				sub { my($self, $res) = @_;
					die
					 "faultcode:", ref $res ? $res->faultcode : $self->transport->status, "\n" ,
					 "faultstring:", ref $res ? $res->faultstring : $self->transport->status, "\n";
				}
			);


# input parameters for retrieving the sequence information
my $input = SOAP::Data->name(
			'parameters' => \SOAP::Data->value(
				SOAP::Data->name('accession' => "L43967")
				)
);

# method which will retrieve the sequences
die "unable to fetch sequence\n" unless my $sequences = $getseq -> getSeq($input);

my @SEQ_REQUEST;
my ($seq,$ident) = ($sequences->{contig}->{sequencedata}->{sequence}->{seq},$sequences->{contig}->{sequencedata}->{sequence}->{id});
	push @SEQ_REQUEST , ( SOAP::Data->name('entry' => \SOAP::Data->value(  
		SOAP::Data->name('ident' => $ident) ,
		SOAP::Data->name('seq' => $seq)
))) ;

#input for finding signaling peptides
$input = SOAP::Data->name(
			'parameters' => \SOAP::Data->value(
				SOAP::Data->name('kingdom' => "bac"),
				SOAP::Data->name('sequences' => \SOAP::Data->value(@SEQ_REQUEST))
				)
			);

my $job = $rnammer->runService($input);


# this method returns a jobid, which can be used to get the results later
my $jobid = SOAP::Data->name(
 'job' => \SOAP::Data->value(
 SOAP::Data->name('jobid' => $job->{jobid})
));

#set a loop for checking job status
$job = $rnammer -> pollQueue($jobid);

while ($job->{status} !~ /FINISHED/) {
	print  "The job is: $job->{status}\n";
	$job = $rnammer->pollQueue($jobid);
	sleep 5;
}

my $out = $rnammer->fetchResult($jobid);


my @RESULT;
if (ref ( $out->{entries}->{entry} ) eq 'ARRAY') {
	@RESULT = @{$out->{entries}->{entry}};
} else {
	@RESULT = ( $out->{entries}->{entry});
}

foreach my $gene (@RESULT) {
	print join("\t",($gene->{sequenceEntry},$gene->{start},$gene->{stop},$gene->{direction},$gene->{feature},$gene->{score}))."\n";
}