src/hg/makeDb/doc/h1n1.txt 1.4

Index: src/hg/makeDb/doc/h1n1.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/h1n1.txt,v
retrieving revision 1.3
retrieving revision 1.4
diff -b -B -U 4 -r1.3 -r1.4
--- src/hg/makeDb/doc/h1n1.txt	6 May 2009 19:27:46 -0000	1.3
+++ src/hg/makeDb/doc/h1n1.txt	15 May 2009 22:44:54 -0000	1.4
@@ -187,66 +187,5 @@
     -out=psl -t=dna -q=dna swineHA.fa swineHA.psl
 
 # load the psl result into humanHA table
     hgLoadPsl h1n1 swineHA.psl
-#################################
-# CREATE h1n1_0429Seq TRACK (DONE.  4/29/09, Fan)
-
-    mkdir –p /hive/data/genomes/h1n1/bed/h1n1_0429Seq
-    cd /hive/data/genomes/h1n1/bed/h1n1_0429Seq
-
-
-# create .fa file
-
-    mkdir -p /gbdb/h1n1/h1n1_0429Seq
-    cp –p ../../download/epiflu_0429_dna_sequence.fasta /gbdb/h1n1/h1n1_0429Seq
-
-    hgLoadSeq –replace h1n1 /gbdb/h1n1/h1n1_0429Seq/epiflu_0429_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_0429Seq/epiflu_0429_dna_sequence.fasta h1n1_0429Seq.psl
-
-# 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'
-
-#########################################################################################