src/hg/makeDb/doc/mm9.txt 1.106

Index: src/hg/makeDb/doc/mm9.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/mm9.txt,v
retrieving revision 1.105
retrieving revision 1.106
diff -b -B -U 4 -r1.105 -r1.106
--- src/hg/makeDb/doc/mm9.txt	20 Aug 2009 22:51:18 -0000	1.105
+++ src/hg/makeDb/doc/mm9.txt	23 Aug 2009 04:14:30 -0000	1.106
@@ -9493,8 +9493,14 @@
 # VEGA GENES UPDATE TO BUILD 35 (DONE, 2009-07-30, hartera)
 # Needs updating as the current version is build 31 from May 2008.
 # 2009-08-03 (hartera) - Added code to register track handler for
 # vegaGeneComposite.
+# 2009-08-15 - 2009-08-16 (hartera) - Added code to allow use of radio buttons
+# on the configuratio page for the track item labels. Modified code so it 
+# can be shared with Ensembl to create the links to Vega transcript, gene
+# and protein reports on the details pages. 
+# 2009-08-22 - Finished code for adding Vega report URLs to the details pages.
+# Loaded the vegaGtp table.
 
    # Download the VEGA genes for mouse from the ftp site
    # This file is from 03/17/09.
    wget --timestamping \
@@ -9541,5 +9547,35 @@
    # handler for vegaGeneComposite that is now used for this data. This used
    # vegaGeneMethods to display the name2 field (gene) as the item label in
    # the track.
 
+   # 2009-08-15 - 2009-08-16 (hartera)
+   # Information extracted the attributes in the GTF file as ensGtp so 
+   # change name to vegaGtp.
+   mv ensGtp.tab vegaGtp.tab
+   # ensGtp table definition is in ~/kent/src/hg/lib/ensGtp.sql
+   # There is an index on the protein field so it can not be NULL. 
+   # If there is no protein, the gene name is given.
+   # Added code to hgTracks.c and hgTrackUi.c to allow the use of 
+   # radio buttons on the track configuratioin page to select the
+   # gene name, accession or both to be displayed in the track.
+   # The gene name is displayed by default.
+   # Added code to hgc.c so that Ensembl and Vega can share code to 
+   # create links on the details pages to the Vega reports for transcript, 
+   # gene and protein through these IDs. Created new function
+   # printEnsemblOrVegaCustomUrl(). 
+
+   # 2009-08-22 (hartera)
+   # Loaded the vegaGtp table. Use ensGtp.sql to create the table.
+   # vegaGtp associates geneId/transcriptId/proteinId 
+   # for the links to Vega reports from the details page.
+   cd /hive/data/genomes/mm9/bed/vega35
+   cp ~/kent/src/hg/lib/ensGtp.sql .
+   # 11 of the gene names for noncoding transcripts are too long for the 
+   # protein ID field so change this field in ensGtp.sql to allow 40 chars 
+   # instead of 20 and re-load the table.
+   hgsql -e 'drop table vegaGtp;' mm9
+   hgLoadSqlTab mm9 vegaGtp ensGtp.sql vegaGtp.tab
+   # Loaded succesfully
+   # Added code to hgc.c to use printEnsemblOrVegaCustomUrl() in 
+   # doVegaGene() to add the links to Vega reports on the details pages.
 ############################################################################