#!/usr/bin/perl
# Description: Use eFetch to retrieve a protein sequence given its id and predict if it's a signalling peptide
# Author: Francisco Roque
# Email: chico@cbs.dtu.dk
# Version: SignalP 3.1
# Date: 2008-01-23
# test with sequence Q9BS26

use SOAP::Lite;

# create SOAP services entry points
my $efetch = SOAP::Lite
	-> service('http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/efetch.wsdl')
	->on_fault(
				sub { my($self, $res) = @_;
					die
					 "faultcode:", ref $res ? $res->faultcode : $self->transport->status, "\n" ,
					 "faultstring:", ref $res ? $res->faultstring : $self->transport->status, "\n";
				}
			);
my $signalp = SOAP::Lite
	-> service('http://www.cbs.dtu.dk/ws/SignalP/SignalP_3_1.wsdl')
	->on_fault(
				sub { my($self, $res) = @_;
					die
					 "faultcode:", ref $res ? $res->faultcode : $self->transport->status, "\n" ,
					 "faultstring:", ref $res ? $res->faultstring : $self->transport->status, "\n";
				}
			);

my $protid = shift;

# method which will retrieve the sequences					
my $sequence = $efetch -> run_eFetch(
										SOAP::Data->name(db => "protein"),
										SOAP::Data->name(id => $protid));

print "Got sequence ".$sequence->{GBSeq}->{'GBSeq_primary-accession'}."\n";

# build the sequences array which will serve as input for SignalP
my @SEQUENCES;
my ($seq,$ident) = ($sequence->{GBSeq}->{GBSeq_sequence}, $sequence->{GBSeq}->{'GBSeq_primary-accession'});
push @SEQUENCES , ( SOAP::Data->name('entry' => \SOAP::Data->value(  
					SOAP::Data->name('ident' => "SEQ$nameid") ,
					SOAP::Data->name('seq' => $seq)
					))) ;


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



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

print "SignalP service launched with jobid: $job->{jobid}\n";

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

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

print "The job is: $job->{status}, fetching results\n";

#when job is done fetch results
my $signalout = $signalp->fetchResult($jobid);


if (ref ( $signalout->{prediction}->{gff_record} ) eq 'ARRAY') {
	@SIGNALOUT = @{$signalout->{prediction}->{gff_record}};
} else {
	@SIGNALOUT = ($signalout->{prediction}->{gff_record});
}

#get the predicted peptides' sequence
foreach $prediction (@SIGNALOUT) {
	#if predicted as signal peptide
	if ($prediction->{comment} =~ /Y/) {
		print "seqname: $sequence->{GBSeq}->{'GBSeq_primary-accession'}\n";
		print "score: $prediction->{score}\n";
		print "seq: ".uc($sequence->{GBSeq}->{GBSeq_sequence})."\n";
		print "start: $prediction->{start}\n";
		print "end: $prediction->{end}\n";
	}
};