#!/usr/bin/perl
# Description: Calculate DNA properties
# Author: Peter Fischer Hallin
# Email: pfh@cbs.dtu.dk
# Version: Genome Atlas 3.0.ws2
# Date: 2009-02-14

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

use strict;

# read DNA from stdin
my @fasta;
my $entry=-1;
my $method = $ARGV[0];

while (<STDIN>) {
	if ( /^>(\S+)\s*(.*)/) {
		$entry++;
		$fasta[$entry]{id} = $1;
		$fasta[$entry]{comment} = $2;
	}  elsif (/([A-Z]+)/) {
		$fasta[$entry]{seq} .= $1;
	}
}

# usage getseq.pl [genbank accession no.]


# create proxy to genome atlas
my $proxy_genomeatlas = WSDLclient ( 'http://www.cbs.dtu.dk/ws/GenomeAtlas/GenomeAtlas_3_0_ws2.wsdl');
use Data::Dumper;
foreach my $entry (0 .. $#fasta) {
	my $response = $proxy_genomeatlas->{DNApropertyRun}->(  parameters => { parameters => { method => $method   , sequence => {id => $fasta[$entry]{id} ,comment => $fasta[$entry]{comment} , seq => $fasta[$entry]{seq}  }}});
	die "error obtaining jobid\n" unless defined ( $response->{queueentry}->{queueentry});
	my $jobid = $response->{queueentry}->{queueentry}->{jobid};
	wait_job($proxy_genomeatlas->{pollQueue},$jobid);
	print ">$fasta[$entry]{id} $fasta[$entry]{comment}\n";
	$response = $proxy_genomeatlas->{DNApropertyFetchResult}->( job => { jobid => $jobid });
	print $response->{parameters}->{output}->{values}."\n";	
}