src/hg/makeDb/doc/hg18.txt 1.360

Index: src/hg/makeDb/doc/hg18.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg18.txt,v
retrieving revision 1.359
retrieving revision 1.360
diff -b -B -U 4 -r1.359 -r1.360
--- src/hg/makeDb/doc/hg18.txt	19 Mar 2009 19:59:14 -0000	1.359
+++ src/hg/makeDb/doc/hg18.txt	8 May 2009 17:39:00 -0000	1.360
@@ -27288,4 +27288,43 @@
     genePredCheck -db=hg18 not.pseudo.gp
 #checked: 62958 failed: 0
     hgLoadGenePred -genePredExt hg18 vegaGene not.pseudo.gp
     hgLoadGenePred -genePredExt hg18 vegaPseudoGene pseudo.gp
+
+##############################################################################
+# UCSC to Ensembl chr name mapping (DONE - 2009-05-08 - Hiram)
+    mkdir /hive/data/genomes/hg18/bed/ucscToEnsembl
+    cd /hive/data/genomes/hg18/bed/ucscToEnsembl
+    awk '{printf "%s\t%s\n", $4, $2}' ../../jkStuff/ensGene.haplotype.lift \
+	> ucscToEnsembl.tab
+
+    cat << '_EOF_' > ucscToEnsembl.sql
+# UCSC to Ensembl chr name translation
+CREATE TABLE ucscToEnsembl (
+    ucsc varchar(255) not null,        # UCSC chromosome name
+    ensembl varchar(255) not null,     # Ensembl chromosome name
+              #Indices
+    PRIMARY KEY(ucsc(21))
+);
+'_EOF_'
+
+    hgsql hg18 < ucscToEnsembl.sql
+    hgsql hg18 \
+-e 'LOAD DATA LOCAL INFILE "ucscToEnsembl.tab" INTO TABLE ucscToEnsembl'
+
+    awk '{printf "%s\t%d\n", $2, -$1}' ../../jkStuff/ensGene.haplotype.lift \
+	> ensemblLift.tab
+
+    cat << '_EOF_' > ensemblLift.sql
+# UCSC offset to Ensembl coordinates
+CREATE TABLE ensemblLift (
+    chrom varchar(255) not null,      # Ensembl chromosome name
+    offset int unsigned not null,     # offset to add to UCSC position 
+              #Indices
+    PRIMARY KEY(chrom(6))
+);
+'_EOF_'
+
+    hgsql hg18 < ensemblLift.sql
+    hgsql hg18 \
+-e 'LOAD DATA LOCAL INFILE "ensemblLift.tab" INTO TABLE ensemblLift'
+##############################################################################