#!/usr/bin/perl
# Description: This script runs the TMHMM 2.0 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: 2.0 ws0
# Date: 2009-09-29
# usage: perl tmhmm.pl

use strict;

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

# create proxy to TMHMM Web Service
my $tmhmm = WSDL2proxy ( 'http://www.cbs.dtu.dk/ws/TMHMM/TMHMM_2_0_ws0.wsdl' );

# append schema definitions
$tmhmm = appendSchemas ( $tmhmm , 
	"http://www.cbs.dtu.dk/ws/common/ws_common_1_0b.xsd" ,
	"http://www.cbs.dtu.dk/ws/TMHMM/ws_tmhmm_2_0_ws0.xsd"
);
# create hash of operations from proxy
my %ops = addOperations ( $tmhmm ) ;

# Get sequence in fasta format from STDIN
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;
	}
}
# Create sequence for request
my @sequence;
for ( my $i = 0 ; $i < scalar ( @fasta ) ; $i ++ ) {
	push @sequence , { id => $fasta[$i]->{id} , comment => $fasta[$i]->{comment} , seq => $fasta[$i]->{seq} };
}

# Do the request
my $response = $ops{runService}->(
	 parameters => {
	  parameters => {
	   sequencedata => {sequence => [@sequence]} } });

# uncomment the two following lines to inspect the structure of $response
#use Data::Dumper;
#print Dumper($response);   

#get job id which can be used to get the results later
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";;
	# poll the queue
	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";
}
# when the job is done, fetch the result
$response = $ops{fetchResult}->(job => { jobid => $jobid });

# uncomment the two following lines to inspect the structure of $response
#use Data::Dumper;
#print Dumper($response); 

#printing the results 
my $method = substr ($response->{parameters}->{anndata}->{annsource}->{method}, 0, 5) . substr ($response->{parameters}->{anndata}->{annsource}->{version}, 0, 3);
print "_______________________________________________________________\n";
foreach my $ann (@{$response->{parameters}->{anndata}->{ann}}) {
	
	foreach my $annrecord (@{$ann->{annrecords}->{annrecord}}) {
		print "$ann->{sequence}->{id}\t$method\t$annrecord->{comment}\t\t$annrecord->{range}->{begin}\t$annrecord->{range}->{end}\n";
		
	}
	print "_______________________________________________________________\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