src/hg/makeDb/doc/hg19.txt 1.33

Index: src/hg/makeDb/doc/hg19.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg19.txt,v
retrieving revision 1.32
retrieving revision 1.33
diff -b -B -U 4 -r1.32 -r1.33
--- src/hg/makeDb/doc/hg19.txt	22 Jul 2009 18:40:28 -0000	1.32
+++ src/hg/makeDb/doc/hg19.txt	29 Jul 2009 06:49:17 -0000	1.33
@@ -5314,4 +5314,35 @@
 
 see doc/builds.txt for specific details.
 ############################################################################
 testing
+
+
+############################################################################
+# AGILENT PROBES LIFTED FROM HG18 (DONE, 2009-07-28 Andy)
+
+ssh hgwdev
+bash
+mkdir /hive/data/genomes/hg19/bed/agilentProbes
+cd /hive/data/genomes/hg19/bed/agilentProbes
+for table in `echo show tables like \'agilent%\' | hgsql hg18 | tail -n +2 | grep -v Probe`; do
+    echo $table; echo "select * from $table" | hgsql hg18 | \
+        tail -n +2 | cut -f2- > ${table}.hg18.bed; liftOver ${table}.hg18.bed \
+          /gbdb/hg18/liftOver/hg18ToHg19.over.chain.gz ${table}.hg19.{bed,unmapped};
+    hgLoadBed hg19 $table ${table}.hg19.bed; 
+    echo done with $table; 
+done
+for unmap in *.unmapped; do
+   table=${unmap%.hg19.unmapped}
+   grep Deleted -A1 $unmap | grep -v Deleted | grep -v "^--" > agilentProbesHg18Unmapped/${table}.deleted.bed
+   grep Split -A1 $unmap | grep -v Split | grep -v "^--" > agilentProbesHg18Unmapped/${table}.split.bed
+   grep Partially -A1 $unmap | grep -v Partially | grep -v "^--" > agilentProbesHg18Unmapped/${table}.partiallyDeleted.bed
+done
+find agilentProbesHg18Unmapped/ -size 0b | xargs rm
+rm *hg18.bed *.unmapped bed.tab
+gzip *.bed
+tar cfz agilentProbesHg18Unmapped.tar.gz agilentProbesHg18Unmapped
+cd /usr/local/apache/htdocs/goldenPath/hg19
+mkdir agilentProbes
+cd agilentProbes/
+ln -s /hive/data/genomes/hg19/bed/agilentProbes/agilentProbesHg18Unmapped beds
+ln -s /hive/data/genomes/hg19/bed/agilentProbes/agilentProbesHg18Unmapped.tar.gz