src/hg/makeDb/doc/hg18.txt 1.369

Index: src/hg/makeDb/doc/hg18.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg18.txt,v
retrieving revision 1.368
retrieving revision 1.369
diff -b -B -U 4 -r1.368 -r1.369
--- src/hg/makeDb/doc/hg18.txt	17 Jul 2009 06:48:58 -0000	1.368
+++ src/hg/makeDb/doc/hg18.txt	17 Jul 2009 16:08:43 -0000	1.369
@@ -28374,8 +28375,34 @@
   # 4 = strand
   # 5 = start
   # 6 = end
 
+# Pull the raw scores into a single file
+cat h*_mapping.tbl.txt | grep -v '^#' | grep -v 'library_count' | grep 'chr' | perl -ne '$l=$_; @w = split /\t/, $l; print "$w[3]\t$w[5]\t$w[6]\t$w[0]\t$w[1]\t$w[4]\n";' > all.wscores.bed
+
+    cat << '_EOF_' > toBed.pl
+#!/usr/bin/perl
+
+$prefix = shift(@ARGV);
+$prefix =~ s/h/H/g;
+while($l = <>) {
+ if(!($l=~ /^\#/) && !($l=~/^id/)) { 
+      chomp($l); 
+      @w = split /\t/, $l; 
+      $score = 100 * $w[1];
+      if($score > 1000) {
+	  $score = 1000;
+      }
+      $name = $prefix; 
+      $size  = $w[6] - $w[5];
+      print "$w[3]\t$w[5]\t$w[6]\t$prefix\t$score\t$w[4]\t$w[5]\t$w[6]\t0\t1\t$size,\t0,\n";
+  }
+}
+'_EOF_'
+    # << happy emacs
+
+chmod 755 toBed.pl
+
 # Make the top level bed track
 for f in `ls *mapping.tbl.txt`; do 
   root=`basename $f .txt`;
   prefix=`basename $f _mapping.tbl.txt`;