src/hg/makeDb/doc/hg19.txt 1.96

Index: src/hg/makeDb/doc/hg19.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg19.txt,v
retrieving revision 1.95
retrieving revision 1.96
diff -b -B -U 4 -r1.95 -r1.96
--- src/hg/makeDb/doc/hg19.txt	2 Apr 2010 17:25:47 -0000	1.95
+++ src/hg/makeDb/doc/hg19.txt	7 Apr 2010 17:42:44 -0000	1.96
@@ -8937,4 +8937,32 @@
     cat fb.susScr2.chainHg19Link.txt 
     #	1272785114 bases of 2231298548 (57.042%) in intersection
 
 #########################################################################
+# Vega gene update (DONE - 2010-04-07 - Hiram)
+    #	lookup version number at the Vega WEB site:
+    #	http://vega.sanger.ac.uk/index.html
+    #	and FTP site:
+    #	ftp://ftp.sanger.ac.uk/pub/vega/
+    cd /hive/data/genomes/hg19
+    #	step wise to verify operation
+    doEnsGeneUpdate.pl -vegaGene -ensVersion=38 -stop=download hg19.ensGene.ra
+    doEnsGeneUpdate.pl -vegaGene -ensVersion=38 \
+	-continue=process -stop=process hg19.ensGene.ra
+# genePredCheck -db=hg19 vegaPseudo.gp.gz
+# checked: 11590 failed: 0
+# genePredCheck -db=hg19 not.vegaPseudo.gp.gz
+# checked: 96345 failed: 0
+# genePredCheck -db=hg19 hg19.allGenes.gp.gz
+# checked: 107935 failed: 0
+    doEnsGeneUpdate.pl -vegaGene -ensVersion=38 \
+	-continue=load -stop=load hg19.ensGene.ra
+# zcat: download/Homo_sapiens.VEGA.38.pep.all.fa.gz: unexpected end of file
+    #	they changed their file name convention ...
+    doEnsGeneUpdate.pl -vegaGene -ensVersion=38 \
+	-continue=cleanup hg19.ensGene.ra
+    featureBits hg19 vegaGene
+    # 74206453 bases of 2897316137 (2.561%) in intersection
+    featureBits hg19 vegaPseudoGene
+    # 8494715 bases of 2897316137 (0.293%) in intersection
+
+########################################################################