src/hg/makeDb/doc/mm9.txt 1.106
1.106 2009/08/23 04:14:30 hartera
Documented adding new code to handle Vega Genes track and loaded a vegaGtp table.
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.
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