--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/TAP4.pl	Fri Dec 09 11:56:56 2011 -0500
@@ -0,0 +1,128 @@
+#This is the TAp2.pl script 
+#The goal of this is to count the number of CIS present in a NR set
+# one file is required nr.txt sorted in chromosome order!
+# Aaron Lyman Sarver Oct 21, 2010
+# This script takes over following the bowtie mapping and generates CIS.
+# Update NOV15,2010 to pass library information through 
+#$Fully modified december 1 2010i
+
+require 'config.pl';
+require 'lib/feature_finder_methods.pl';
+my $path = $0;
+$path =~ s/\/\w*\.pl$//g;
+require "$path/project_man.pl";
+unless (-d "CIS") {
+    mkdir("CIS");
+}
+unless (-d "results") {
+    mkdir("results");
+}
+
+$proj_all = $proj."_all";
+
+$sth = $dbh->prepare("drop table if exists lib_mappable_$proj_all");
+$sth->execute;
+
+$sth = $dbh->prepare("drop table if exists lib_mappable_$proj");
+$sth->execute;
+
+$sth = $dbh->prepare("drop table if exists illumina_hist_$proj_all");
+$sth->execute;
+
+$sth = $dbh->prepare("drop table if exists illumina_hist_$proj");
+$sth->execute;
+
+$sth = $dbh->prepare("drop table if exists bowtie_lib_$proj_all");
+$sth->execute;
+
+$sth = $dbh->prepare("drop table if exists bowtie_lib_$proj");
+$sth->execute;
+
+$sth = $dbh->prepare("drop table if exists metadata_$proj_all");
+$sth->execute;
+
+
+open DIN, "< data/meta.tab";
+@met;
+while (defined($line = <DIN>)) {
+    chomp $line;
+    @field= split(/\t/, $line);
+    push (@met,$line);
+}
+
+$proj_all = $proj."_all";
+$var=shift(@met);
+
+$sth = $dbh->prepare("create table lib_mappable_$proj_all select * from lib_mappable_$var");
+$sth->execute;
+$sth = $dbh->prepare("create table illumina_hist_$proj_all select * from illumina_hist_$var");
+$sth->execute;
+$sth = $dbh->prepare("create table bowtie_lib_$proj_all select * from bowtie_lib_$var");
+$sth->execute;
+$sth = $dbh->prepare("create table metadata_$proj_all select * from metadata_$var");
+$sth->execute;
+
+foreach $var(@met) {
+$sth = $dbh->prepare("insert into lib_mappable_$proj_all select * from lib_mappable_$var");
+$sth->execute;
+$sth = $dbh->prepare("insert into  illumina_hist_$proj_all select * from illumina_hist_$var");
+$sth->execute;
+$sth = $dbh->prepare("insert into  bowtie_lib_$proj_all select * from bowtie_lib_$var");
+$sth->execute;
+$sth = $dbh->prepare("insert into metadata_$proj_all select * from metadata_$var");
+$sth->execute;
+}
+
+unless(-e "data/metadata.tab") {
+    $sth = $dbh->prepare("select library, descriptor, type from metadata_$proj_all");
+    $sth->execute;
+    open(my $meta_out, ">", "data/metadata.tab") || die "Unable to open data/metadata.tab for output. $!\n";
+    while ((@row) = $sth->fetchrow_array) {
+	print $meta_out join("\t", @row) . "\n";
+    }
+    close($meta_out);
+}
+
+
+$sth = $dbh->prepare("create table lib_mappable_$proj select distinct library, sum(total) as total from lib_mappable_$proj_all group by library;");
+$sth->execute;
+
+$sth = $dbh->prepare("create table illumina_hist_$proj select distinct library, chromo, start, sum(count) as count,orient from illumina_hist_$proj_all group by library,chromo,start,orient;");
+$sth->execute;
+
+$sth = $dbh->prepare("create table bowtie_lib_$proj select distinct library,chromo, start,stop, pos, sum(count) as count,strand, orient from bowtie_lib_$proj_all group by library,chromo,start,stop,pos,strand order by chromo,start+0,orient ;");
+$sth->execute;
+
+$sth = $dbh->prepare("select chromo, start, stop, concat(library,'-',count),count,strand,start,stop from bowtie_lib_$proj");
+$sth->execute;
+#7.2
+open OUT, "> results/raw_$proj.BED";
+print OUT "track type ='BED' name='raw$proj' description='all$proj' visibility=2 itemRgb='On'";
+while ((@row) = $sth->fetchrow_array) {
+ print OUT "\n$row[0]\t$row[1]\t$row[2]\t$row[3]\t$row[4]\t$row[5]\t$row[6]\t$row[7]";}
+close OUT;
+#7.3
+$sth = $dbh->prepare("drop table if exists convert_2_hex_$proj");
+$sth->execute;
+$sth = $dbh->prepare("create table convert_2_hex_$proj (orient varchar(5), hex varchar(20))");
+$sth->execute;
+$sth = $dbh->prepare("insert into convert_2_hex_$proj VALUES(\"A\", \"255,0,0\")");
+$sth->execute;
+$sth = $dbh->prepare("insert into convert_2_hex_$proj VALUES(\"B\", \"0,0,255\")");
+$sth->execute;
+$sth = $dbh->prepare("insert into convert_2_hex_$proj VALUES(\"U\", \"0,0,0\")");
+$sth->execute;
+
+$sth = $dbh->prepare("select chromo, start, stop, concat(library,'-',count),count,strand,start,stop from bowtie_lib_$proj where count > 9");
+### JJE
+#$sth = $dbh->prepare("select chromo, start, start+1, concat(library,count),count,'+',start,start+1, hex from bowtie_lib_$proj A, convert_2_hex_$proj B where A.orient = B.orient and count > 9");
+###
+$sth->execute;
+open OUT, "> results/raw10_$proj.BED";
+print OUT "track type ='BED' name='raw10$proj' description='10$proj' visibility=2 itemRgb='On'";
+while ((@row) = $sth->fetchrow_array) {
+ print OUT "\n$row[0]\t$row[1]\t$row[2]\t$row[3]\t$row[4]\t$row[5]\t$row[6]\t$row[7]\t$row[8]";}
+close OUT;
+
+&set_project_status($proj, 1, 0);
+