#!/usr/bin/perl
# Description: Runs SignalP Web Service. 
#It requires no input; to be used for testing in the EMBRACE WS Registry.
# Author: Peter Fischer Hallin
# Email: pfh@cbs.dtu.dk
# Version: 3.1 ws0
# Date: 2008-06-15
# usage: perl signalp.pl

# include standard XML::Compile helper functions (used to initiate WSDL proxys)
use Data::Dumper;
use strict;
require "xml-compile.pl";

# create proxy to genome atlas
my $signalp = WSDLclient ( 'http://www.cbs.dtu.dk/ws/SignalP/SignalP_3_1_ws0.wsdl' );

my @fasta;
my $entry = -1;

while (<DATA>) {
	if (/^>(.*)/) {
		my ($id , $comment) = split (" ",$1);
		$entry++;
		$fasta[$entry]->{id} = $id;
		$fasta[$entry]->{comment} = $comment if defined $comment;
	} elsif (/^([A-Za-z]+)/) {
		$fasta[$entry]->{seq} .= $1;
	}
}
my @sequence;
for ( my $i = 0 ; $i < scalar ( @fasta ) ; $i ++ ) {
	push @sequence , { id => $fasta[$i]->{id} , comment => $fasta[$i]->{comment} , seq => $fasta[$i]->{seq} };
}

my $response = $signalp->{runService}->(
	 parameters => {
	  parameters => {
	   organism => 'euk' ,
	   method => 'nn+hmm' ,
	   thnn => '0.43' ,
	   sequencedata => {sequence => [@sequence]} } });

my $jobid;

die "error obtaining jobid\n" unless defined $response->{parameters}->{queueentry};
$jobid = $response->{parameters}->{queueentry}->{jobid};
&wait_job($signalp->{pollQueue},$jobid);
$response = $signalp->{fetchResult}->(job => { jobid => $jobid });
print "method           : ".$response->{parameters}->{anndata}->{annsource}->{method}."\n";
print "version          : ".$response->{parameters}->{anndata}->{annsource}->{version}."\n";
foreach my $ann (@{$response->{parameters}->{anndata}->{ann}}) {
	print " sequence id      : $ann->{sequence}->{id}\n";
	print " sequence comment : $ann->{sequence}->{comment}\n";
	print " sequence         : $ann->{sequence}->{seq}\n";
	foreach my $annrecord (@{$ann->{annrecords}->{annrecord}}) {
			print join ( "\t", ( 
					$annrecord->{feature},
					$annrecord->{range}->{begin}->numify,
					$annrecord->{range}->{end}->numify,
					$annrecord->{score}[0]->{key}.':'.$annrecord->{score}[0]->{value},
				))."\n";
		}}

__DATA__
>EGFR_HUMAN  P00533 EPIDERMAL GROWTH FACTOR RECEPTOR PRECURSOR (EC 2.7.1.112). - Homo sapiens (Human).
MRPSGTAGAALLALLAALCPASRALEEKKVCQGTSNKLTQLGTFEDHFLSLQRMFNNCEV
VLGNLEITYVQRNYDLSFLKTIQEVAGYVLIALNTVERIPLENLQIIRGNMYYENSYALA
VLSNYDANKTGLKELPMRNLQEILHGAVRFSNNPALCNVESIQWRDIVSSDFLSNMSMDF
QNHLGSCQKCDPSCPNGSCWGAGEENCQKLTKIICAQQCSGRCRGKSPSDCCHNQCAAGC
TGPRESDCLVCRKFRDEATCKDTCPPLMLYNPTTYQMDVNPEGKYSFGATCVKKCPRNYV
VTDHGSCVRACGADSYEMEEDGVRKCKKCEGPCRKVCNGIGIGEFKDSLSINATNIKHFK
NCTSISGDLHILPVAFRGDSFTHTPPLDPQELDILKTVKEITGFLLIQAWPENRTDLHAF
ENLEIIRGRTKQHGQFSLAVVSLNITSLGLRSLKEISDGDVIISGNKNLCYANTINWKKL
FGTSGQKTKIISNRGENSCKATGQVCHALCSPEGCWGPEPRDCVSCRNVSRGRECVDKCN
LLEGEPREFVENSECIQCHPECLPQAMNITCTGRGPDNCIQCAHYIDGPHCVKTCPAGVM
GENNTLVWKYADAGHVCHLCHPNCTYGCTGPGLEGCPTNGPKIPSIATGMVGALLLLLVV
ALGIGLFMRRRHIVRKRTLRRLLQERELVEPLTPSGEAPNQALLRILKETEFKKIKVLGS
GAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGI
CLTSTVQLITQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAA
RNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSY
GVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPK
FRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQ
QGFFSSPSTSRTPLLSSLSATSNNSTVACIDRNGLQSCPIKEDSFLQRYSSDPTGALTED
SIDDTFLPVPEYINQSVPKRPAGSVQNPVYHNQPLNPAPSRDPHYQDPHSTAVGNPEYLN
TVQPTCVNSTFDSPAHWAQKGSHQISLDNPDYQQDFFPKEAKPNGIFKGSTAENAEYLRV
APQSSEFIGA