--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/visualize.pl	Fri Dec 09 11:56:56 2011 -0500
@@ -0,0 +1,72 @@
+require 'config.pl';
+open OUT, "> FISH/library_cis_list.txt";
+open OUT2, ">FISH/multi_test.txt";
+
+$query1 = "select count(name) from cis_result_final_$proj where pvalueregion < $cocis_threshold and type = 'all_$library_percent' and gene_name not like '%BAD%' and region > 1 order by pvalueregion limit 100";
+$sth = $dbh->prepare("$query1");
+
+$sth->execute;
+
+while ((@row) = $sth->fetchrow_array) {
+$cis_number = $row[0];
+}
+
+$query2="select name,gene_name, library_name from cis_result_final_$proj where pvalueregion < $cocis_threshold and type = 'all_$library_percent' and gene_name not like '%BAD%' and region > 1 order by pvalueregion limit 100";
+
+$sth = $dbh->prepare("$query2");
+$sth->execute;
+
+while ((@row) = $sth->fetchrow_array) {
+#print $row[2];
+@chunks = split(/::/m, $row[2]);
+foreach $lib(@chunks) {
+if ($lib ne '') {
+print OUT "$row[0]::$row[1]\t$lib\t1\n";
+}
+} 
+}
+close OUT;
+
+$sth = $dbh->prepare("select count(distinct descriptor) from metadata_$proj where descriptor != 'all';");
+
+$sth->execute;
+
+while ((@row) = $sth->fetchrow_array) {
+$desc_number = $row[0];
+}
+$ann_cis_testing = $desc_number*$cis_number;
+$cis_cis_testing = $cis_number*($cis_number-3)/2;
+$ann_ann_testing = $desc_number*($desc_number-3)/2;
+print OUT2 "$cis_number\t$desc_number\t$ann_cis_testing\t$cis_cis_testing\t$ann_ann_testing\n";
+close OUT2;
+$sth = $dbh->prepare("select 'descriptor', descriptor, library from metadata_$proj;");
+$sth->execute;
+
+open OUT, "> FISH/library_descriptor_list.txt";
+
+while ((@row) = $sth->fetchrow_array) {
+print OUT "$row[0]::$row[1]\t$row[2]\t1\n";
+}
+
+close OUT;
+
+open (my $list, ">", "FISH/list.txt");
+open (my $cis_list, "<", "FISH/library_cis_list.txt");
+while(<$cis_list>) {
+    print $list $_;
+}
+close($cis_list);
+open (my $desc_list, "<", "FISH/library_descriptor_list.txt");
+while (<$desc_list>) {
+    print $list $_;
+}
+close($desc_list);
+close($list);
+#system ("cat FISH/library_cis_list.txt FISH/library_descriptor_list.txt > FISH/list.txt");
+system ("perl lib/list2tab.pl 1 2 3 0 FISH/list.txt  > FISH/cis4cluster.txt");
+system ("perl lib/list2tab.pl 1 2 3 0 FISH/library_cis_list.txt > results/Assoc/Cis.txt");
+system ("perl lib/list2tab.pl 1 2 3 0 FISH/library_descriptor_list.txt > results/Assoc/Ann.txt");
+
+print "generated the matrix file cis4cluster.txt";
+
+