src/hg/makeDb/doc/hg19.txt 1.69

Index: src/hg/makeDb/doc/hg19.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg19.txt,v
retrieving revision 1.68
retrieving revision 1.69
diff -b -B -U 4 -r1.68 -r1.69
--- src/hg/makeDb/doc/hg19.txt	15 Dec 2009 18:48:27 -0000	1.68
+++ src/hg/makeDb/doc/hg19.txt	28 Dec 2009 19:38:30 -0000	1.69
@@ -8239,6 +8239,21 @@
     hgsql hg19 < ~/src/hg/lib/geneNetworkId.sql
     hgsql hg19 -e \
     'load data local infile "GN_human_RefSeq.txt" into table geneNetworkId'
 
-#########################################################################
+######################################################################## EXONIPHY (2009-12-28, hartera, DONE)
 
+    # New predictions for hg19 run by Melissa Hubisz 
+    # (mjhubisz at gmail.com) for hg19 and sent by 
+    # Adam Siepel (acs4 at cornell.edu) on 2009-12-18
+    mkdir -p /hive/data/genomes/hg19/bed/exoniphy.2009-12-18
+    cd /hive/data/genomes/hg19/bed/exoniphy.2009-12-18
+    # Download predictions file, exoniphy.gff
+    wget --timestamping \
+         "http://compgen.bscb.cornell.edu/~acs/exoniphy.gff.gz"
+    gunzip exoniphy.gff.gz
+    # Remove table of lifted predictions from hg18
+    hgsql -e 'drop table exoniphy;' hg19
+    ldHgGene -genePredExt -gtf hg19 exoniphy exoniphy.gff
+    # Read 620689 transcripts in 647299 lines in 1 files
+    # 620689 groups 24 seqs 1 sources 4 feature types
+    # 186601 gene predictions