#!/usr/bin/perl
use SOAP::Lite;
use strict;
# e.g. bac and ssu
my ($kingdom,$mol) = @ARGV;

my $rnammer = SOAP::Lite
		->service('http://www.cbs.dtu.dk/ws/RNAmmer/RNAmmer_1_2a.wsdl')
		->on_fault(
			sub { my($self, $res) = @_;
				die 
				"faultcode:", ref $res ? $res->faultcode : $self->transport->status, "\n" , 
				"faultstring:", ref $res ? $res->faultstring : $self->transport->status, "\n" , 
				;
});

# read first fasta entry from stdin
my $id;
my $seq;
my $genome = "";
while (<STDIN>) {
	chomp;
	last if /^>/ and defined $id;
	$id = $1 if /^>(.*)/;
	$genome .= $1 if /^([A-Za-z]+)$/;
}

#input for finding signaling peptides
my $input = SOAP::Data->name(
			'parameters' => \SOAP::Data->value(
				SOAP::Data->name('kingdom' => $kingdom),
				SOAP::Data->name('mol' => $mol),
				SOAP::Data->name('sequences' => \SOAP::Data->value(
					SOAP::Data->name('entry' => \SOAP::Data->value(  
						SOAP::Data->name('ident' => $id) ,
						SOAP::Data->name('seq' => $genome)))))));

my $job = $rnammer->runService($input);
print STDERR "# job submitted with jobid $job->{jobid}\n";

# this method returns a jobid, which can be used to get the results later
my $jobid = SOAP::Data->name(
 'job' => \SOAP::Data->value(
 SOAP::Data->name('jobid' => $job->{jobid})
));

while (my $jobid = $rnammer->pollQueue($jobid)) {
	if ( $jobid->{status} eq 'FINISHED' ) {
		print STDERR "# finished ... \n";
		last;
	} elsif ( $jobid->{status} =~  /ACTIVE|QUEUED/ ) {
		print STDERR "# status:$jobid->{status}\n";
		sleep 2;
	} else {
		print STDERR "# unexpected queue status: '$jobid->{status}'\n";
		exit 1;
	}
}

my $out = $rnammer->fetchResult($jobid);

my @RESULT;
if (ref ( $out->{entries}->{entry} ) eq 'ARRAY') {
	@RESULT = @{$out->{entries}->{entry}};
} else {
	@RESULT = ( $out->{entries}->{entry});
}

my @UNITS;
foreach my $gene (@RESULT) {
	my $sequence = $gene->{sequence};
	#if ( $gene->{direction} eq "+" ) {
	#	$sequence = substr($genome , ($gene->{start}-501),500);
	#} else {
	#	$sequence = substr($genome, $gene->{stop},500);
	#	$sequence = revcompl($sequence);
	#}
	print ">16SrRNA_$gene->{start}..$gene->{stop}\n";
	for ( my $i = 0 ; $i < length($sequence ) ; $i+=60 ) {
		print substr( $sequence , $i , 60)."\n";
	}
}

sub revcompl {
	# this function will do the reverse complement of the DNA
	$_[0] =~ tr/ATGC/TACG/;
	return reverse $_[0];
}