src/hg/makeDb/doc/h1n1.txt 1.3

Index: src/hg/makeDb/doc/h1n1.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/h1n1.txt,v
retrieving revision 1.2
retrieving revision 1.3
diff -b -B -U 4 -r1.2 -r1.3
--- src/hg/makeDb/doc/h1n1.txt	29 Apr 2009 17:09:49 -0000	1.2
+++ src/hg/makeDb/doc/h1n1.txt	6 May 2009 19:27:46 -0000	1.3
@@ -209,4 +209,44 @@
 
 # load the psl result into h1n1_0429Seq table
     hgLoadPsl h1n1 h1n1_0429Seq.psl
 
+#################################
+# CREATE h1n1_0506Seq TRACK (DONE.  050609, Fan)
+
+    mkdir -p /hive/data/genomes/h1n1/bed/h1n1_0506Seq
+    cd /hive/data/genomes/h1n1/bed/h1n1_0506Seq
+
+
+# create .fa file
+
+    mkdir -p /gbdb/h1n1/h1n1_0506Seq
+    cp -p ../../download/0506/epiflu_0506_dna_sequence.fasta /gbdb/h1n1/h1n1_0506Seq
+
+    hgLoadSeq -replace h1n1 /gbdb/h1n1/h1n1_0506Seq/epiflu_0506_dna_sequence.fasta 
+
+# BLAT
+    gfClient -minScore=200 -minIdentity=80 -nohead hgwdev.cse.ucsc.edu 18892  /gbdb/h1n1/nib \
+    -out=psl -t=dna -q=dna /gbdb/h1n1/h1n1_0506Seq/epiflu_0506_dna_sequence.fasta h1n1_0506Seq.psl
+
+# load the psl result into h1n1_0506Seq table
+    hgLoadPsl h1n1 h1n1_0506Seq.psl
+
+# create CDS table
+
+    hgsql h1n1 -N -e \
+    'select qName, qStart+1,"xxx", qEnd from h1n1_0506Seq'|\
+    sed -e 's/\txxx\t/../' >h1n1_0506SeqCds.tab
+
+    hgLoadSqlTab h1n1 h1n1_0506SeqCds ~/hg/lib/cdsSpec.sql h1n1_0506SeqCds.tab
+
+# update h1n1SeqXref table
+
+    fgrep ">" /gbdb/h1n1/h1n1_0506Seq/epiflu_0506_dna_sequence.fasta|\
+    sed -e 's/ | /\t/g' |sed -e "s/>//" >j.tmp
+    rmLf j.tmp >h1n1SeqXref.tab
+
+    hgsql h1n1 -e 'delete from h1n1SeqXref'
+    hgsql h1n1 -e 'load data local infile "h1n1SeqXref.tab" into table h1n1SeqXref'
+
+#########################################################################################
+