src/hg/makeDb/doc/hg19.txt 1.42

Index: src/hg/makeDb/doc/hg19.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg19.txt,v
retrieving revision 1.41
retrieving revision 1.42
diff -b -B -U 4 -r1.41 -r1.42
--- src/hg/makeDb/doc/hg19.txt	1 Oct 2009 10:01:27 -0000	1.41
+++ src/hg/makeDb/doc/hg19.txt	1 Oct 2009 18:39:47 -0000	1.42
@@ -6284,9 +6284,9 @@
 # Make mapping between known genes and allenBrain
    hgMapToGene hg19 allenBrainAli -type=psl knownGene knownToAllenBrain
 
 ############################################################################
-# AFFY U133AB (Done - 2009-09-31 - Jim)
+# AFFY U133AB (Done - 2009-09-30 - Jim)
     # Align probes 
     ssh swarm
     cd /cluster/data/hg19/bed
     mkdir -p affyProbes/affyU133/run
@@ -6328,9 +6328,9 @@
     hgLoadPsl hg19 affyU133.psl
     hgLoadSeq hg19 /gbdb/hgFixed/affyProbes/HG-U133AB_all.fa
 
 ##########################################################################
-# GNF ATLAS 2 (In progress - 2009-09-31 - Jim)
+# GNF ATLAS 2 (In progress - 2009-09-30 - Jim)
     # Align probes from GNF1H chip.
     ssh swarm
     cd /cluster/data/hg19/bed
     mkdir -p geneAtlas2/run/psl
@@ -6383,5 +6383,28 @@
 
     hgLoadBed hg19 gnfAtlas2 gnfAtlas2.bed
     # Loaded 36357 elements of size 15
 
+##########################################################################
+# make new grp table to match hg18 (DONE  2009-10-01 kuhn)
+# to split regulation from expression 
+# phenDis group is also missing in hg19
+# and add one more column: defaultIsClosed
+
+# get the hg18.grp table into hg19 
+
+# copy the hg18.grp table into hg19.grpNew and edit 
+   hgsql hg19
+   CREATE TABLE grpNew SELECT * FROM hg18.grp;
+   # 24 rows in set (0.00 sec)
+   
+   DELETE FROM grpNew WHERE name LIKE "encode%";
+   DELETE FROM grpNew WHERE name LIKE "remc%"; 
+   DELETE FROM grpNew WHERE name LIKE "tcga%";
+   DELETE FROM grpNew WHERE name LIKE "cancer%"; 
+   DELETE FROM grpNew WHERE name LIKE "jk%";
+   # 10 rows in set (0.00 sec)
+   
+# move the new table into place quickly
+   DROP TABLE grp;
+   RENAME TABLE grpNew TO grp;