cd52f66464cce415303d7ae24ba28603c927ee4f
hiram
  Thu Mar 6 15:39:33 2025 -0800
better names in ncbiRefSeq track fields and updated related trackDb URLs refs #32704

diff --git src/hg/utils/automation/doNcbiRefSeq.pl src/hg/utils/automation/doNcbiRefSeq.pl
index a7ff0a18a67..e2899b22bf1 100755
--- src/hg/utils/automation/doNcbiRefSeq.pl
+++ src/hg/utils/automation/doNcbiRefSeq.pl
@@ -608,96 +608,103 @@
 export db="$db"
 export asmId="$asmId"
 export verString="$verString"
 
 _EOF_
   );
   if (! $dbExists) {
     $bossScript->add(<<_EOF_
 export target2bit=$dbTwoBit
 
 twoBitInfo \$target2bit stdout | sort -k2,2nr > \$db.chrom.sizes
 wget -O bigGenePred.as 'https://raw.githubusercontent.com/ucscGenomeBrowser/kent/refs/heads/master/src/hg/lib/bigGenePred.as'
 wget -O bigPsl.as 'https://raw.githubusercontent.com/ucscGenomeBrowser/kent/refs/heads/master/src/hg/lib/bigPsl.as'
 
 ### overall gene track with both predicted and curated
-genePredToBigGenePred process/\$db.ncbiRefSeq.gp stdout | sort -k1,1 -k2,2n > \$db.ncbiRefSeq.bigGp
+\$HOME/kent/src/hg/utils/automation/updateName2.pl process/\$db.attrs.txt \\
+       process/\$db.ncbiRefSeq.gp | sort -k1,1 -k2,2n > \$db.ncbiRefSeq.bigGp
 genePredToBed -tab -fillSpace process/\$db.ncbiRefSeq.gp stdout \\
     | bedToExons stdin stdout | bedSingleCover.pl stdin > \$asmId.exons.bed
 export baseCount=`awk '{sum+=\$3-\$2}END{printf "%d", sum}' \$asmId.exons.bed`
 export asmSizeNoGaps=`grep sequences ../../\$asmId.faSize.txt | awk '{print \$5}'`
 export perCent=`echo \$baseCount \$asmSizeNoGaps | awk '{printf "%.3f", 100.0*\$1/\$2}'`
 bedToBigBed -type=bed12+8 -tab -as=bigGenePred.as -extraIndex=name \\
   \$db.ncbiRefSeq.bigGp \$db.chrom.sizes \\
     \$db.ncbiRefSeq.bb
 bigBedInfo \$db.ncbiRefSeq.bb | egrep "^itemCount:|^basesCovered:" \\
     | sed -e 's/,//g' > \$db.ncbiRefSeq.stats.txt
 LC_NUMERIC=en_US /usr/bin/printf "# ncbiRefSeq %s %'d %s %'d\\n" `cat \$db.ncbiRefSeq.stats.txt` | xargs echo
 ~/kent/src/hg/utils/automation/gpToIx.pl process/\$db.ncbiRefSeq.gp \\
     | sort -u > \$db.ncbiRefSeq.ix.txt
 ixIxx \$db.ncbiRefSeq.ix.txt \$db.ncbiRefSeq.ix{,x}
 rm -f \$db.ncbiRefSeq.ix.txt
 
 ### curated only if present
 if [ -s process/\$db.curated.gp ]; then
-  genePredToBigGenePred process/\$db.curated.gp stdout | sort -k1,1 -k2,2n > \$db.ncbiRefSeqCurated.bigGp
+  \$HOME/kent/src/hg/utils/automation/updateName2.pl process/\$db.attrs.txt \\
+     process/\$db.curated.gp | sort -k1,1 -k2,2n > \$db.ncbiRefSeqCurated.bigGp
   bedToBigBed -type=bed12+8 -tab -as=bigGenePred.as -extraIndex=name \\
   \$db.ncbiRefSeqCurated.bigGp \$db.chrom.sizes \\
     \$db.ncbiRefSeqCurated.bb
   rm -f \$db.ncbiRefSeqCurated.bigGp
   bigBedInfo \$db.ncbiRefSeqCurated.bb | egrep "^itemCount:|^basesCovered:" \\
     | sed -e 's/,//g' > \$db.ncbiRefSeqCurated.stats.txt
   LC_NUMERIC=en_US /usr/bin/printf "# ncbiRefSeqCurated %s %'d %s %'d\\n" `cat \$db.ncbiRefSeqCurated.stats.txt` | xargs echo
   ~/kent/src/hg/utils/automation/gpToIx.pl process/\$db.curated.gp \\
     | sort -u > \$db.ncbiRefSeqCurated.ix.txt
   ixIxx \$db.ncbiRefSeqCurated.ix.txt \$db.ncbiRefSeqCurated.ix{,x}
   rm -f \$db.ncbiRefSeqCurated.ix.txt
 ### and refseqSelect if exists (a subset of curated)
   if [ -s process/\$db.refseqSelect.curated.gp ]; then
-    genePredToBigGenePred process/\$db.refseqSelect.curated.gp stdout | sort -k1,1 -k2,2n > \$db.ncbiRefSeqSelectCurated.bigGp
+    \$HOME/kent/src/hg/utils/automation/updateName2.pl process/\$db.attrs.txt \\
+      process/\$db.refseqSelect.curated.gp | sort -k1,1 -k2,2n \\
+         > \$db.ncbiRefSeqSelectCurated.bigGp
     bedToBigBed -type=bed12+8 -tab -as=bigGenePred.as -extraIndex=name \\
     \$db.ncbiRefSeqSelectCurated.bigGp \$db.chrom.sizes \\
       \$db.ncbiRefSeqSelectCurated.bb
     rm -f \$db.ncbiRefSeqSelectCurated.bigGp
     bigBedInfo \$db.ncbiRefSeqSelectCurated.bb | egrep "^itemCount:|^basesCovered:" \\
       | sed -e 's/,//g' > \$db.ncbiRefSeqSelectCurated.stats.txt
     LC_NUMERIC=en_US /usr/bin/printf "# ncbiRefSeqSelectCurated %s %'d %s %'d\\n" `cat \$db.ncbiRefSeqSelectCurated.stats.txt` | xargs echo
     ~/kent/src/hg/utils/automation/gpToIx.pl process/\$db.refseqSelect.curated.gp \\
       | sort -u > \$db.ncbiRefSeqSelectCurated.ix.txt
     ixIxx \$db.ncbiRefSeqSelectCurated.ix.txt \$db.ncbiRefSeqSelectCurated.ix{,x}
     rm -f \$db.ncbiRefSeqSelectCurated.ix.txt
   fi
 ### and hgmd if exists (a subset of curated)
   if [ -s process/hgmd.curated.gp ]; then
-    genePredToBigGenePred process/hgmd.curated.gp stdout | sort -k1,1 -k2,2n > \$db.ncbiRefSeqHgmd.bigGp
+    \$HOME/kent/src/hg/utils/automation/updateName2.pl process/\$db.attrs.txt \\
+      process/hgmd.curated.gp | sort -k1,1 -k2,2n > \$db.ncbiRefSeqHgmd.bigGp
     bedToBigBed -type=bed12+8 -tab -as=bigGenePred.as -extraIndex=name \\
     \$db.ncbiRefSeqHgmd.bigGp \$db.chrom.sizes \\
       \$db.ncbiRefSeqHgmd.bb
     rm -f \$db.ncbiRefSeqHgmd.bigGp
     bigBedInfo \$db.ncbiRefSeqHgmd.bb | egrep "^itemCount:|^basesCovered:" \\
       | sed -e 's/,//g' > \$db.ncbiRefSeqHgmd.stats.txt
     LC_NUMERIC=en_US /usr/bin/printf "# ncbiRefSeqHgmd %s %'d %s %'d\\n" `cat \$db.ncbiRefSeqHgmd.stats.txt` | xargs echo
     ~/kent/src/hg/utils/automation/gpToIx.pl process/hgmd.curated.gp \\
       | sort -u > \$db.ncbiRefSeqHgmd.ix.txt
     ixIxx \$db.ncbiRefSeqHgmd.ix.txt \$db.ncbiRefSeqHgmd.ix{,x}
     rm -f \$db.ncbiRefSeqHgmd.ix.txt
   fi
 fi
 
 ### predicted only if present
 if [ -s process/\$db.predicted.gp ]; then
-  genePredToBigGenePred process/\$db.predicted.gp stdout | sort -k1,1 -k2,2n > \$db.ncbiRefSeqPredicted.bigGp
+  \$HOME/kent/src/hg/utils/automation/updateName2.pl process/\$db.attrs.txt \\
+      process/\$db.predicted.gp | sort -k1,1 -k2,2n \\
+        > \$db.ncbiRefSeqPredicted.bigGp
   bedToBigBed -type=bed12+8 -tab -as=bigGenePred.as -extraIndex=name \\
   \$db.ncbiRefSeqPredicted.bigGp \$db.chrom.sizes \\
     \$db.ncbiRefSeqPredicted.bb
   rm -f \$db.ncbiRefSeqPredicted.bigGp
   bigBedInfo \$db.ncbiRefSeqPredicted.bb | egrep "^itemCount:|^basesCovered:" \\
     | sed -e 's/,//g' > \$db.ncbiRefSeqPredicted.stats.txt
   LC_NUMERIC=en_US /usr/bin/printf "# ncbiRefSeqPredicted %s %'d %s %'d\\n" `cat \$db.ncbiRefSeqPredicted.stats.txt` | xargs echo
   ~/kent/src/hg/utils/automation/gpToIx.pl process/\$db.predicted.gp \\
     | sort -u > \$db.ncbiRefSeqPredicted.ix.txt
   ixIxx \$db.ncbiRefSeqPredicted.ix.txt \$db.ncbiRefSeqPredicted.ix{,x}
   rm -f \$db.ncbiRefSeqPredicted.ix.txt
 fi
 
 ### all other annotations, not necessarily genes
 if [ -s "process/\$db.other.bb" ]; then