src/hg/makeDb/doc/hg19.txt 1.116

Index: src/hg/makeDb/doc/hg19.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg19.txt,v
retrieving revision 1.115
retrieving revision 1.116
diff -b -B -U 4 -r1.115 -r1.116
--- src/hg/makeDb/doc/hg19.txt	27 May 2010 23:52:00 -0000	1.115
+++ src/hg/makeDb/doc/hg19.txt	2 Jun 2010 23:01:10 -0000	1.116
@@ -8365,29 +8365,31 @@
     featureBits hg19 vegaPseudoGene
     # 6885145 bases of 2897316137 (0.238%) in intersection
 
 ########################################################################
-# NHGRI GWAS CATALOG (DONE 5/12/10 angie)
+# NHGRI GWAS CATALOG (DONE 6/2/10 angie)
+# Updated 5/12/10 (last one to use snp130)
 # Updated 4/1/10
 # Updated 3/1/10
 # Originally done 1/19/10
     mkdir /hive/data/genomes/hg19/bed/gwasCatalog
     cd /hive/data/genomes/hg19/bed/gwasCatalog
     # Done once, don't need to redo:
-    cut -f 1-4 ../snp130/snp130.bed \
+    cut -f 1-4 ../snp131/snp131.bed \
     | sort -k4,4 \
-      > snp130Coords.bed
-    mkdir /hive/data/genomes/hg19/bed/gwasCatalog/100512
-    cd /hive/data/genomes/hg19/bed/gwasCatalog/100512
+      > snp131Coords.bed
+    set today = `date +%y%m%d`
+    mkdir /hive/data/genomes/hg19/bed/gwasCatalog/$today
+    cd /hive/data/genomes/hg19/bed/gwasCatalog/$today
 
     # Mapping to hg19 by joining hg19 SNP coords with catalog flatfile (see hg18.txt)
-    join -t "	" -1 4 ../snp130Coords.bed /hive/data/genomes/hg18/bed/gwasCatalog/100512/noCoords.tab \
+    join -t "	" -1 4 ../snp131Coords.bed /hive/data/genomes/hg18/bed/gwasCatalog/$today/noCoords.tab \
         -o 1.1,1.2,1.3,1.4,2.2,2.3,2.4,2.5,2.6,2.7,2.8,2.9,2.10,2.11,2.12,2.13,2.14,2.15,2.16,2.17,2.18,2.19 \
     | sort -k1,1 -k2n,2n \
         > gwasCatalog.bed
     hgLoadBed hg19 gwasCatalog gwasCatalog.bed \
       -tab -sqlTable=$HOME/kent/src/hg/lib/gwasCatalog.sql -notItemRgb -allowStartEqualEnd
-#Loaded 3277 elements of size 22
+#Loaded 3852 elements of size 22
 
 
 ######################################################################## 
 # ailMel1 Panda alignment (DONE - 2010-02-04 - Hiram)