src/hg/makeDb/doc/hg19.txt 1.28

Index: src/hg/makeDb/doc/hg19.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg19.txt,v
retrieving revision 1.27
retrieving revision 1.28
diff -b -B -U 4 -r1.27 -r1.28
--- src/hg/makeDb/doc/hg19.txt	19 Jun 2009 21:54:43 -0000	1.27
+++ src/hg/makeDb/doc/hg19.txt	24 Jun 2009 01:22:17 -0000	1.28
@@ -5077,4 +5077,25 @@
     nice -n +19 featureBits hg18 exoniphy
     #	27475705 bases of 2881515245 (0.954%) in intersection
 
 #########################################################################
+nscanGene (2009-06-22 markd)
+   # nscanGene track from WUSTL
+   cd /cluster/data/hg19/bed/nscan
+   wget http://mblab.wustl.edu/~jeltje/hg19_tracks/hg19.updated.gtf
+   wget http://mblab.wustl.edu/~jeltje/hg19_tracks/hg19.readme
+   wget -r -np -l 1 http://mblab.wustl.edu/~jeltje/hg19_tracks/hg19_proteins
+   bzip2 hg19.updated.gtf hg19_proteins/*.fa
+
+   # load track
+   gtfToGenePred -genePredExt hg19.updated.gtf.bz2 stdout| hgLoadGenePred -genePredExt hg19 nscanGene stdin
+   bzcat hg19_proteins/chr*.fa.bz2 | hgPepPred hg19 generic nscanPep stdin
+   rm *.tab
+
+   # validate same number of transcripts and peptides are loaded
+   hgsql -Ne 'select count(*) from nscanGene' hg19
+   hgsql -Ne 'select count(*) from nscanPep' hg19
+
+   # validate search expression
+   hgc-sql -Ne 'select name from nscanGene' hg19 | egrep -v -e '^chr[0-9a-zA-Z_]+\.([0-9]+|pasa)((\.[0-9a-z]+)?\.[0-9a-z]+)?$' |wc -l
+
+#########################################################################