src/hg/makeDb/doc/hg18.txt 1.389

Index: src/hg/makeDb/doc/hg18.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg18.txt,v
retrieving revision 1.388
retrieving revision 1.389
diff -b -B -U 4 -r1.388 -r1.389
--- src/hg/makeDb/doc/hg18.txt	6 Nov 2009 23:06:53 -0000	1.388
+++ src/hg/makeDb/doc/hg18.txt	9 Dec 2009 19:24:40 -0000	1.389
@@ -28915,5 +28915,48 @@
     hgsql hg18 -e \
     'load data local infile "GN_human_RefSeq.txt" into table geneNetworkId'
 
 #########################################################################
+# BUILD snpArrayIllumina HumanCytoSNP-12 SUB-TRACK (DONE 12/4/09, Fan)
 
+# Received raw data file HumanCytoSNP-12_forUCSC.csv
+# from Illumina,  Jennifer L. Stone Ph.D., jstone@illumina.com 
+
+#    mkdir -p /hive/data/genomes/gs.19/build36/bed/snp/illumina/120309
+#    cd /hive/data/genomes/gs.19/build36/bed/snp/illumina/120309
+
+    cat HumanCytoSNP-12_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=snpArrayIlluminaHumanCytoSNP_12.sql
+
+#############################################################################