#!/usr/bin/perl
# Description: This script runs the NetCTL 1.2.ws0 Web Service. It requires no input; to be used for testing in the EMBRACE WS Registry.
# Author: Edita Bartaseviciute
# Email: edita@cbs.dtu.dk
# Version: 1.2 ws0
# Date: 2009-05-29
# usage: perl test_netctl.pl [-s supertype] [-thr float] 

# include standard XML::Compile helper functions (used to initiate WSDL proxys)
use strict;
require "xml-compile.pl"; # downloadable from the same site as this script


#taking options from a command line
my ($supertype, $threshold);
for (my  $i = 0; $i  <= $#ARGV; $i ++) {
	if ($ARGV[$i] eq "-s") {
		$supertype = $ARGV[$i+1];
	}
	elsif ($ARGV[$i] eq "-thr") {
		$threshold = $ARGV[$i+1];
	}
}

# create proxy to NetCTL Web Service
my $netctl = WSDL2proxy ( 'http://www.cbs.dtu.dk/ws/NetCTL/NetCTL_1_2_ws0.wsdl' );

# append schema definitions
$netctl = appendSchemas ( $netctl , 
	"http://www.cbs.dtu.dk/ws/common/ws_common_1_0b.xsd" ,
	"http://www.cbs.dtu.dk/ws/NetCTL/ws_netctl_1_2_ws0.xsd"
);

my %ops = addOperations ( $netctl ) ;

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;
if ((defined $supertype) and (defined $threshold)) {
	$response = $ops{runService}->(
	 parameters => {
	  parameters => {
	   supertype => $supertype ,
	   threshold => $threshold ,
	    sequencedata => {sequence => [@sequence]} } });
}
elsif ((defined $supertype) and !(defined $threshold)) {
	$response = $ops{runService}->(
	 parameters => {
	  parameters => {
	   supertype => $supertype , 
	     sequencedata => {sequence => [@sequence]} } });
	$threshold = 0.75;
}
elsif (!(defined $supertype) and (defined $threshold)) {
	$response = $ops{runService}->(
	 parameters => {
	  parameters => {
	   threshold => $threshold ,
	    sequencedata => {sequence => [@sequence]} } });
	$supertype = "A1";
}
else {
	$response = $ops{runService}->(
	 parameters => {
	  parameters => {
	    sequencedata => {sequence => [@sequence]} } });
	$supertype = "A1";
	$threshold = 0.75;
}

my $jobid;

if ( ! defined ( $response->{parameters}->{queueentry}) ) {
	die "error obtaining jobid\n";
} else {
	$jobid = $response->{parameters}->{queueentry}->{jobid};
	print STDERR "# waiting for job $jobid";
	my $status = "UNKNOWN";;
	while ( $status =~ /ACTIVE|RUNNING|QUEUED|WAITING|PENDING|UNKNOWN/ ) {
		my $response = $ops{pollQueue}->( job => { job  => { jobid => $jobid }   }) ;
		$status = $response->{queueentry}->{queueentry}->{status};
		print STDERR  ".";
	}
	die "\nunexpected job status '$status'\n" unless $status eq "FINISHED";
	print STDERR "\n# job has finished\n";
}

$response = $ops{fetchResult}->(job => { jobid => $jobid });

#printing the results
print "NetCTL-1.2 predictions using MHC supertype $supertype. Threshold " . sprintf ("%.6f", $threshold) ."\n\n";

foreach my $ann (@{$response->{parameters}->{anndata}->{ann}}) {
	my $sequence = $sequence[0]->{seq};
	my $no_ligands = 0;
	my $no_peptides = 0;	
	foreach my $annrecord (@{$ann->{annrecords}->{annrecord}}) {
			my $pos = sprintf ("%4s", $annrecord->{range}->{begin}->numify);
			my $pep = substr($sequence, $annrecord->{range}->{begin}->numify-1, 9);
			my $aff_score = sprintf ("%.4f", $annrecord->{score}[0]->{value});
			my $rescale_score = sprintf ("%.4f", $annrecord->{score}[1]->{value});
			my $cle_score = sprintf ("%.4f", $annrecord->{score}[2]->{value});
			my $tap_score = sprintf ("%.4f", $annrecord->{score}[3]->{value});
			$tap_score = sprintf ("%7s", $tap_score);
			my $comb_score = sprintf ("%.4f", $annrecord->{score}[4]->{value});
			$comb_score = sprintf ("%7s", $comb_score);
			my $comment;
			if (defined ($annrecord->{comment})){
				$comment = "<-E";
				$no_ligands++;
			}
			$no_peptides++;				
			print "$pos ID $ann->{sequence}->{id} pep $pep $annrecord->{score}[0]->{key}   $aff_score $annrecord->{score}[1]->{key}   ",
			      "$rescale_score $annrecord->{score}[2]->{key} $cle_score $annrecord->{score}[3]->{key}  $tap_score $annrecord->{score}[4]->{key}  ",
			      "$comb_score $comment\n";
			
	}	
	print "\n----------------------------\n\n".
	"Number of MHC ligands $no_ligands identified. Number of peptides $no_peptides. Protein name $ann->{sequence}->{id}\n\n".
	"----------------------------\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