#!/usr/bin/perl -w
use File::Temp;
use Carp qw(cluck croak);

# popularity contest
if( system('pp_popcon_cnt', '-p', 'norsnet') == -1 ){ warn("The Rost Lab recommends you install the pp-popularity-contest package that provides pp_popcon_cnt:\n\nsudo apt-get install pp-popularity-contest\n"); }

$DEF_MODE=1;
if (@ARGV<1)  {
	#                   0       1      2          3          4               5            6      7
	die "\nUsage: $0 [fasta] [prof] [hssp] [output_file] [target_name] [profbval_file] [mode] [debug]\n";
}
$seq_file=$ARGV[0];
$rdbProf_file=$ARGV[1];
$hssp_file=$ARGV[2];
$output_file=$ARGV[3];
#$target_name=$ARGV[4];
$profbval_file=$ARGV[5];
$mode=$ARGV[6]||$DEF_MODE;
my $dbg = $ARGV[7] || 0;

if( $mode eq '-' ){ $mode = $DEF_MODE; }

if( $mode ne '1' && $mode ne '2' && $mode ne '3' ) { die( "invalid mode, must be one of 1, 2 or 3" ); }

$dir = $ENV{NORSNET_ROOT} ||  "__pkgdatadir__";
$resultsdir = File::Temp::tempdir( CLEANUP => !$dbg );

$createDataFile_exe = "$dir/scr/createDataFile.pl";
$norsnet_exe = "$dir/scr/NORSnet.pl";


{
	#                                    0           1              2           3        4
	my @cmd = ( $createDataFile_exe, $seq_file, $rdbProf_file, $hssp_file, $resultsdir, $dbg );
	if( $dbg ){ warn( "@cmd" ); }
	system( @cmd ) && die( "@cmd failed: $!, ".( $? >> 8 ) );
}
{
	#                             0            1          2         3               4        5     6
	my @cmd = ( $norsnet_exe, $seq_file, $output_file, $mode, $profbval_file, $resultsdir, $dir, $dbg );
	if( $dbg ){ warn( "@cmd" ); }
	system( @cmd ) && die( "@cmd failed: $!, ".( $? >> 8 ));
}