#!/usr/bin/perl
# Description: This script runs the NetNES 1.1.ws0 Web Service. It reads FASTA file from STDIN and produces predictions in a simple table.
# Author: Edita Bartaseviciute
# Email: edita@cbs.dtu.dk
# Version: 1.1 ws0
# Date: 2010-03-24
# usage: perl netnes.pl < example.fsa

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 NetNES Web Service
my $netnes = WSDL2proxy ( 'http://www.cbs.dtu.dk/ws/NetNES/NetNES_1_1_ws0.wsdl' );

# append schema definitions
$netnes = appendSchemas ( $netnes , 
	"http://www.cbs.dtu.dk/ws/common/ws_common_1_0b.xsd" ,
	"http://www.cbs.dtu.dk/ws/NetNES/ws_netnes_1_1_ws0.xsd",
	"http://bioxsd.org/BioXSD-1.0.xsd"
);

# create hash of operations from proxy
my %ops = addOperations ( $netnes ) ;

# Get sequence in fasta format from STDIN
my @fasta;
my $entry = -1;

while (<STDIN>) {
	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 , { sequence => $fasta[$i]->{seq}, formalReference => {accession => $fasta[$i]->{id} }};
}

# Do the request
my $response = $ops{runService}->(
	 parameters => {
	  parameters => {
	   sequenceRecord => [@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";;
	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 ($id, $pos, $score_ANN, $score_HMM, $score_NES, $finding);

foreach my $annotatedSequence (@{$response->{parameters}->{annotatedSequence}}) {
	if (exists $annotatedSequence->{sequenceRecord}->{formalReference}) {
		$id = $annotatedSequence->{sequenceRecord}->{formalReference}->{accession};
	}
	print ">$id - netNES 1.1 prediction\n",
	      "#Seq-Pos-Residue\tANN\tHMM\tNES\tPredicted\n",
	      "#---------------------------------------------------------\n";
	foreach my $cho (@{$annotatedSequence->{cho_annotation}}) {
	   foreach my $occurence (@{$cho->{annotation}->{occurence}}) {
	   	$pos = $occurence->{position}->{point}->{_};
	   	foreach my $evidence (@{$occurence->{evidence}}){
			if ($evidence->{predicted}->{verdict} eq "Impossible") {
				$finding = "-";
			}
			elsif ($evidence->{predicted}->{verdict} eq "Present") {
				$finding = "Yes";
			}
			foreach my $score (@{$evidence->{predicted}->{score}}) {
				if ($score->{type} eq "ANN") {
					$score_ANN = sprintf ("%.3f", $score->{value});
				}
				elsif ($score->{type} eq "HMM") {
					$score_HMM = sprintf ("%.3f", $score->{value});
				}
				elsif ($score->{type} eq "NES") {
					$score_NES = sprintf ("%.3f", $score->{value});
				}
			
				
			}
			
		}
		print "$id-$pos\t\t$score_ANN\t$score_HMM\t$score_NES\t$finding\n";
		}
	}
	print "\n";
}