src/hg/makeDb/doc/hg18.txt 1.379

Index: src/hg/makeDb/doc/hg18.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg18.txt,v
retrieving revision 1.378
retrieving revision 1.379
diff -b -B -U 4 -r1.378 -r1.379
--- src/hg/makeDb/doc/hg18.txt	23 Aug 2009 04:14:05 -0000	1.378
+++ src/hg/makeDb/doc/hg18.txt	3 Sep 2009 15:39:14 -0000	1.379
@@ -28626,8 +28626,10 @@
 # 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.
+# 2009-09-01 - 2009-09-02 (hartera). Loaded a vegaPep table for the protein
+# sequence link on the details pages.
 
     mkdir /hive/data/genomes/hg18/bed/vega35
     cd /hive/data/genomes/hg18/bed/vega35
     wget --timestamping "ftp://ftp.sanger.ac.uk/pub/vega/human/*" \
@@ -28698,6 +28700,23 @@
     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.
-
+    # Code was added so that there is no protein sequence link on the details
+    # page if it there is none available e.g. noncoding.
+    # 2009-09-01 - 2009-09-02 (hartera)
+    # Coding genes are displaying the message that there is no protein
+    # prediction available. Need to add a vegaPep table.
+    cd /hive/data/genomes/hg18/bed/vega35
+    # from the Ensembl process:
+    zcat Homo_sapiens.VEGA.mar.pep.tot.fa.gz  \
+        | sed -e 's/^>.* Transcript:/>/;' | gzip > vegaPep.txt.gz
+    zcat vegaPep.txt.gz \
+         | ~/kent/src/utils/faToTab/faToTab.pl /dev/null /dev/stdin \
+         | sed -e '/^$/d; s/*$//' | sort > vegaPep.hg18.fa.tab
+    # Load table
+    hgPepPred hg18 tab vegaPep vegaPep.hg18.fa.tab
+    # Add vegaPep to the trackDb.ra entry for the vegaGeneComposite track 
+    # in the type line for src/hg/makeDb/trackDb/human/hg18/trackDb.ra.
+    # Check that the vegaPep table looks ok and then check protein-coding and 
+    # noncoding transcript details pages for protein links.
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