src/hg/makeDb/doc/hg18.txt 1.378
1.378 2009/08/23 04:14:05 hartera
Documented adding new code to handle Vega Genes track and loaded a vegaGtp table.
Index: src/hg/makeDb/doc/hg18.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg18.txt,v
retrieving revision 1.377
retrieving revision 1.378
diff -b -B -U 4 -r1.377 -r1.378
--- src/hg/makeDb/doc/hg18.txt 18 Aug 2009 22:47:49 -0000 1.377
+++ src/hg/makeDb/doc/hg18.txt 23 Aug 2009 04:14:05 -0000 1.378
@@ -28615,11 +28615,20 @@
# Converted stdin, upper limit 11.63, lower limit -28.64
hgLoadWiggle -pathPrefix=/gbdb/hg18/wib hg18 sfrs1ConsensusSites sfrs1ConsensusSites.wig
ln -s $(pwd -P)/sfrs1ConsensusSites.wib /gbdb/hg18/wib/
############################################################################
-# VEGA GENES UPDATE TO BUILD 35 (DONE, 2009-07-04, hartera)
+# VEGA GENES UPDATE TO BUILD 35 (DONE, 2009-08-04, hartera)
# Needs updating as the current version is build 33.
# Download the human VEGA Genes posted on ftp site on 2009-03-31
+# 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.
+
mkdir /hive/data/genomes/hg18/bed/vega35
cd /hive/data/genomes/hg18/bed/vega35
wget --timestamping "ftp://ftp.sanger.ac.uk/pub/vega/human/*" \
"ftp://ftp.sanger.ac.uk/pub/vega/human/pep/*.tot.fa.gz"
@@ -28659,5 +28668,36 @@
# Added code to src/hg/hgTracks/simpleTracks.c to register a track 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.
+ # 2009-08-16 (hartera)
+ # 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)
+ # Create a vegaGtp table using the vegaGtp.tab file above. Use ensGtp.sql
+ # to create the table. vegaGtp associates geneId/transcriptId/proteinId
+ # for the links to Vega reports from the details page. If there is no
+ # protein ID because the transcript is noncoding, the gene name is used
+ # instead. This field can not be NULL in the table as there is an index
+ # on it.
+ cd /hive/data/genomes/hg18/bed/vega35
+ cp ~/kent/src/hg/lib/ensGtp.sql .
+ # One of the gene names is long for a noncoding gene so it does not fit
+ # in the protein ID field so change the protein field in ensGtp.sql
+ # to allow 40 chars instead of 20 and re-load the table.
+ hgsql -e 'drop table vegaGtp;' hg18
+ hgLoadSqlTab hg18 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.
+
############################################################################