src/hg/utils/automation/doEnsGeneUpdate.pl 1.21

Index: src/hg/utils/automation/doEnsGeneUpdate.pl
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/utils/automation/doEnsGeneUpdate.pl,v
retrieving revision 1.20
retrieving revision 1.21
diff -b -B -U 4 -r1.20 -r1.21
--- src/hg/utils/automation/doEnsGeneUpdate.pl	15 Jan 2010 22:25:55 -0000	1.20
+++ src/hg/utils/automation/doEnsGeneUpdate.pl	15 Jan 2010 23:43:32 -0000	1.21
@@ -500,12 +500,20 @@
   my $runDir = "$buildDir";
   my $whatItDoes = "It cleans up or compresses intermediate files.";
   my $bossScript = new HgRemoteScript("$runDir/doCleanup.csh", $dbHost,
 				      $runDir, $whatItDoes);
+  if ($opt_vegaGene) {
+    $bossScript->add(<<_EOF_
+rm -f pseudo.name not.pseudo.name vegaGene.name vegaPepAll.$db.fa.tab vegaPep.name
+gzip vegaPep.$db.fa.tab
+_EOF_
+    );
+  } else {
   $bossScript->add(<<_EOF_
 rm -f bed.tab ensPep.txt.gz ensPep.$db.fa.tab ensPep.name ensGene.name
 _EOF_
   );
+  }
   $bossScript->execute();
 } # doCleanup
 
 #########################################################################
@@ -519,25 +527,48 @@
   $updateTime =~ s/ .*//;	#	removes time
   my $organism = `hgsql -N -e 'select organism from dbDb where name = "$db";' hgcentraltest`;
   chomp $organism;
 
+  my $vegaOpt = "";
+  my $trackName = "Ensembl";
+  my $tableName = "ensGene";
+  my $workDir = "ensGene";
+  $tableName = "vegaGene" if ($opt_vegaGene);
+  $trackName = "Vega" if ($opt_vegaGene);
+  $vegaOpt = "-vegaGene" if ($opt_vegaGene);
+  $workDir = "vega" if ($opt_vegaGene);
+  if ($opt_vegaGene) {
   print <<_EOF_
 ############################################################################
-#  $db - $organism - Ensembl Genes version $ensVersion  (DONE - $updateTime - $ENV{'USER'})
+#  $db - $organism - $trackName Genes version $ensVersion  (DONE - $updateTime - $ENV{'USER'})
     ssh $dbHost
     cd /hive/data/genomes/$db
-    cat << '_EOF_' > $db.ensGene.ra
+_EOF_
+  ;
+  } else {
+    print <<_EOF_
+############################################################################
+#  $db - $organism - $trackName Genes version $ensVersion  (DONE - $updateTime - $ENV{'USER'})
+    ssh $dbHost
+    cd /hive/data/genomes/$db
+    cat << '_EOF_' > $db.$tableName.ra
 _EOF_
   ;
   print `cat $db.ensGene.ra`;
   print "'_EOF_'\n";
   print "#  << happy emacs\n\n";
-  print "    doEnsGeneUpdate.pl -ensVersion=$ensVersion $db.ensGene.ra\n";
+  }
+  print "    doEnsGeneUpdate.pl ${vegaOpt} -ensVersion=$ensVersion $db.$tableName.ra\n";
   print "    ssh hgwdev\n";
-  print "    cd /hive/data/genomes/$db/bed/ensGene.$ensVersion\n";
-  print "    featureBits $db ensGene\n";
+  print "    cd /hive/data/genomes/$db/bed/$workDir.$ensVersion\n";
+  print "    featureBits $db $tableName\n";
+  print "    # ";
+  print `featureBits $db $tableName`;
+  if ($opt_vegaGene) {
+    print "    featureBits $db vegaPseudoGene\n";
   print "    # ";
-  print `featureBits $db ensGene`;
+    print `featureBits $db vegaPseudoGene`;
+  }
   print "############################################################################\n";
 
 } # doMakeDoc