src/hg/makeDb/doc/hg18.txt 1.407

Index: src/hg/makeDb/doc/hg18.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg18.txt,v
retrieving revision 1.406
retrieving revision 1.407
diff -b -B -U 4 -r1.406 -r1.407
--- src/hg/makeDb/doc/hg18.txt	25 Mar 2010 21:35:39 -0000	1.406
+++ src/hg/makeDb/doc/hg18.txt	30 Mar 2010 17:08:49 -0000	1.407
@@ -29900,4 +29900,50 @@
 
 
 # stop here pending answer for seraching with newest version id 
 
+#########################################################################
+# UPDATE snpArrayIllumina HumanCytoSNP-12 SUB-TRACK (DONE 3/23/10, Fan)
+
+# Received raw data file HumanCytoSNP-12_v2_1_forUCSC.csv
+# from Illumina,  Jennifer L. Stone Ph.D., jstone@illumina.com 
+
+    mkdir -p /hive/data/genomes/gs.19/build36/bed/snp/illumina/032210
+    cd /hive/data/genomes/gs.19/build36/bed/snp/illumina/032210
+
+    cat HumanCytoSNP-12_v2_1_forUCSC.csv |\
+    sed -e 's/,/\t/g' >HumanCytoSNP.tab
+
+    hgsql hg18 -e 'drop table snpArrayIlluminaHumanCytoSNP_12Raw'
+    hgsql hg18 < ~/src/hg/lib/snpArrayIlluminaHumanCytoSNP_12Raw.sql
+    hgsql hg18 -e 'load data local infile "HumanCytoSNP.tab" into table snpArrayIlluminaHumanCytoSNP_12Raw ignore 1 lines'
+
+    ~/src/hg/snp/snpLoad/illuminaLookup1M hg18 snpArrayIlluminaHumanCytoSNP_12Raw snp130
+
+# The illuminaLookup1M generate two files:
+#
+#	illuminaLookup.out  contains all probes found in snp130
+#	illuminaLookup.err  contains all probes not found in snp130
+
+    mv illuminaLookup.out illuminaLookupHumanCytoSNP_12a.out
+
+    cut -f 1 illuminaLookup.err >j.1
+    cat j.1 |sed -e 's/chrMt/chrM/' |\
+    sed -e 's/XY/X/'  >j.chr
+
+    cut -f 2-5 illuminaLookup.err >j.2
+
+    cut -f 6 illuminaLookup.err >j.3
+    cat j.3 |sed -e 's/F/+/' |sed -e 's/R/-/' >j.strand
+
+    cut -f 7 illuminaLookup.err |sed -e "s/\[//" |sed -e "s/\]//" >j.observed
+
+    paste j.chr j.2 j.strand j.observed >illuminaLookupHumanCytoSNP_12b.out
+
+# combine two parts
+    cat illuminaLookupHumanCytoSNP_12a.out illuminaLookupHumanCytoSNP_12b.out >snpArrayIlluminaHumanCytoSNP_12.tab
+
+# load the table
+# hgLoadBed -allowStartEqualEnd hg18 snpArrayIlluminaHumanCytoSNP_12 snpArrayIlluminaHumanCytoSNP_12.tab -tab -sqlTable=~/scratch/tip201/kent/src/hg/lib/snpArrayIlluminaHumanCytoSNP_12.sql
+    hgLoadBed -allowStartEqualEnd hg18 snpArrayIlluminaHumanCytoSNP_12 snpArrayIlluminaHumanCytoSNP_12.tab -tab -sqlTable=/cluster/home/fanhsu/scratch/tip201/kent/src/hg/lib/snpArrayIlluminaHumanCytoSNP_12.sql
+
+#############################################################################