src/hg/makeDb/doc/hg18.txt 1.422

Index: src/hg/makeDb/doc/hg18.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg18.txt,v
retrieving revision 1.421
retrieving revision 1.422
diff -b -B -U 4 -r1.421 -r1.422
--- src/hg/makeDb/doc/hg18.txt	1 Jun 2010 17:56:24 -0000	1.421
+++ src/hg/makeDb/doc/hg18.txt	2 Jun 2010 23:00:02 -0000	1.422
@@ -29606,9 +29606,10 @@
 # load the table
     hgLoadBed -allowStartEqualEnd hg18 snpArrayIlluminaHumanOmni1_Quad snpArrayIlluminaHumanOmni1_Quad.tab -tab -sqlTable=snpArrayIlluminaHumanOmni1_Quad.sql
 
 #############################################################################
-# NHGRI GWAS CATALOG (DONE 5/12/10)
+# NHGRI GWAS CATALOG (DONE 6/2/10)
+# Updated 5/12/10
 # Updated 4/1/10
 # Updated 3/1/10
 # Originally done 1/19/10
 # Area of possible future improvement: for SNPs that can't be mapped via our SNP track,
@@ -29618,10 +29619,11 @@
     # Done once, don't need to redo:
     cut -f 1-4 ../snp130/snp130.bed \
     | sort -k4,4 \
     > snp130Coords.bed
-    mkdir /hive/data/genomes/hg18/bed/gwasCatalog/100512
-    cd /hive/data/genomes/hg18/bed/gwasCatalog/100512
+    set today = `date +%y%m%d`
+    mkdir /hive/data/genomes/hg18/bed/gwasCatalog/$today
+    cd /hive/data/genomes/hg18/bed/gwasCatalog/$today
     wget http://www.genome.gov/admin/gwascatalog.txt
     # Column headers:
 #  1 Date Added to Catalog
 #  2 PubMedID
@@ -29677,19 +29679,20 @@
     | sort -k1,1 -k2n,2n \
         > gwasCatalog.bed
     hgLoadBed hg18 gwasCatalog gwasCatalog.bed \
       -tab -sqlTable=$HOME/kent/src/hg/lib/gwasCatalog.sql -notItemRgb -allowStartEqualEnd
-#Loaded 3461 elements of size 22
+#Loaded 3545 elements of size 22
 
     # For David: find examples of risk alleles for which dbSNP observed
     # alleles are complementary (A/T or C/G) -- how do we know what strand the
     # risk allele is on??  -- asking corresp. author Teri Manolio.
-    hgsql hg18 -e 'select snp.name,gc.riskAllele,snp.strand,snp.refNcbi,snp.observed \
+    hgsql hg18 -NBe 'select snp.name,gc.riskAllele,snp.strand,snp.refNcbi,snp.observed \
                    from gwasCatalog as gc, snp130 as snp \
                    where gc.riskAllele rlike "^rs[0-9]+-[ACGT]" and \
                          gc.name = snp.name and snp.observed in ("C/G", "A/T") \
-                   order by gc.name limit 20;'
-    # count(*) = 170
+                     order by gc.name;' > ambigStrand.txt
+    wc -l ambigStrand.txt 
+#174 ambigStrand.txt
 
 
 #############################################################################
 # CRG MAPABILITY (2010-01-19 - 2010-01-28, hartera, DONE)