src/hg/makeDb/doc/hg18.txt 1.390

Index: src/hg/makeDb/doc/hg18.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg18.txt,v
retrieving revision 1.389
retrieving revision 1.390
diff -b -B -U 4 -r1.389 -r1.390
--- src/hg/makeDb/doc/hg18.txt	9 Dec 2009 19:24:40 -0000	1.389
+++ src/hg/makeDb/doc/hg18.txt	9 Dec 2009 20:54:34 -0000	1.390
@@ -28959,4 +28959,91 @@
 # load the table
     hgLoadBed -allowStartEqualEnd hg18 snpArrayIlluminaHumanCytoSNP_12 snpArrayIlluminaHumanCytoSNP_12.tab -tab -sqlTable=snpArrayIlluminaHumanCytoSNP_12.sql
 
 #############################################################################
+# BUILD snpArrayIllumina Human660W-Quad SUB-TRACK (DONE 12/9/09, Fan)
+
+# Received raw data file Human660W.ucsc.csv 
+# from Illumina,  Jennifer L. Stone Ph.D., jstone@illumina.com 
+
+    mkdir -p /hive/data/genomes/gs.19/build36/bed/snp/illumina/120809
+    cd /hive/data/genomes/gs.19/build36/bed/snp/illumina/120809
+
+    cat Human660W.ucsc.csv|\
+    sed -e 's/,/\t/g' >Human660W.tab
+
+    hgsql hg18 -e 'drop table snpArrayIlluminaHuman660W_QuadRaw'
+    hgsql hg18 < ~/src/hg/lib/snpArrayIlluminaHuman660W_QuadRaw.sql
+    hgsql hg18 -e 'load data local infile "Human660W.tab" into table snpArrayIlluminaHuman660W_QuadRaw ignore 1 lines'
+
+    ~/src/hg/snp/snpLoad/illuminaLookup1M hg18 snpArrayIlluminaHuman660W_QuadRaw 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 illuminaLookupHuman660W_Quada.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 >illuminaLookupHuman660W_Quadb.out
+
+# combine two parts
+    cat illuminaLookupHuman660W_Quada.out illuminaLookupHuman660W_Quadb.out >snpArrayIlluminaHuman660W_Quad.tab
+
+# load the table
+    hgLoadBed -allowStartEqualEnd hg18 snpArrayIlluminaHuman660W_Quad snpArrayIlluminaHuman660W_Quad.tab -tab -sqlTable=snpArrayIlluminaHuman660W_Quad.sql
+
+#############################################################################
+# BUILD snpArrayIllumina Human Omni1-Quad SUB-TRACK (DONE 12/9/09, Fan)
+
+# Received raw data file Omni.ucsc.txt
+# 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 Omni.ucsc.txt |\
+    sed -e 's/,/\t/g' >HumanOmni1.tab
+
+    hgsql hg18 -e 'drop table snpArrayIlluminaHumanOmni1_QuadRaw'
+    hgsql hg18 < ~/src/hg/lib/snpArrayIlluminaHumanOmni1_QuadRaw.sql
+    hgsql hg18 -e 'load data local infile "HumanOmni1.tab" into table snpArrayIlluminaHumanOmni1_QuadRaw ignore 1 lines'
+
+    ~/src/hg/snp/snpLoad/illuminaLookup1M hg18 snpArrayIlluminaHumanOmni1_QuadRaw 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 illuminaLookupHumanOmni1_Quada.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 >illuminaLookupHumanOmni1_Quadb.out
+
+# combine two parts
+    cat illuminaLookupHumanOmni1_Quada.out illuminaLookupHumanOmni1_Quadb.out >snpArrayIlluminaHumanOmni1_Quad.tab
+
+# load the table
+    hgLoadBed -allowStartEqualEnd hg18 snpArrayIlluminaHumanOmni1_Quad snpArrayIlluminaHumanOmni1_Quad.tab -tab -sqlTable=snpArrayIlluminaHumanOmni1_Quad.sql
+