use strict; use warnings;
use File::Basename qw(basename);
use File::Find::Rule;

my $origpairs = shift;
my @dbs = qw(ADMURimpQC2 ADNIimpQC2 GenADA_impQC2 NIA_AD_impQC2 TGEN_impQC2);
my $sel_template = '/home/data/Bonn_GWAS/selection_file_template.txt';
(my $test) = $origpairs =~ /listTEST(\d*)\.pairs/;
my $w_dir = 'intersnp_TEST'.$test;
mkdir $w_dir;
chdir $w_dir;
my $odir = 'outputs';
mkdir $odir;
my $tmpsel = 'selection_file_TEST'.$test.'.txt';
foreach my $dbname (@dbs){
	my $targetdb = '/home/data/Variomics/'.$dbname;
	my $grpfile = 'listTEST'.$test.'_'.$dbname.'.grp';
	my $order ='grppairs.pl '.$origpairs.' '.$targetdb.'.bim > '.$grpfile;
	print "Grep $origpairs into $dbname...\n";
	system($order); 
	print "Done\n";
	open TEMPLATE, "<$sel_template" or die "Could not find template\n";
	open TMPS, ">$tmpsel";
	my $ofile = $odir.'/'.$dbname.'_TEST'.$test.'_';
	while (<TEMPLATE>){
		s/<Database>/$targetdb/;
		s/<Test>/$test/;
		s/<Pairs>/$grpfile/;
		s/<Output>/$ofile/;
		print TMPS "$_";
	}
	close TMPS;
	close TEMPLATE;
#	my $order = 'intersnpPN '.$tmpsel;
#	system($order);	
	$order = 'intersnp '.$tmpsel;
	print "$order\n";
	system($order);
}