e22f12e30ffc45d4b6657aeca878a22eeb239edd
braney
  Thu Jul 2 16:05:42 2020 -0700
add gencode transcript details to hgGene

diff --git src/hg/makeDb/doc/ucscGenes/hg38.gencodeV35.sh src/hg/makeDb/doc/ucscGenes/hg38.gencodeV35.sh
index 48d114a..9548366 100644
--- src/hg/makeDb/doc/ucscGenes/hg38.gencodeV35.sh
+++ src/hg/makeDb/doc/ucscGenes/hg38.gencodeV35.sh
@@ -136,30 +136,39 @@
 hgsql -e "select geneSymbol from malacards" --skip-column-names $db | sort > malacardExists.txt
 join malacardExists.txt  geneSymbolToKgId.txt | awk 'BEGIN {OFS="\t"} {print $2, $1}' > knownToMalacard.txt
 hgLoadSqlTab -notOnServer $tempDb  knownToMalacards $kent/src/hg/lib/knownTo.sql  knownToMalacard.txt
 
 twoBitToFa -noMask /cluster/data/$db/$db.2bit -bed=ucscGenes.bed stdout | faFilter -uniq stdin  ucscGenes.fa
 hgPepPred $tempDb generic knownGeneMrna ucscGenes.fa
 
 
 hgMapToGene -tempDb=$tempDb $db gnfAtlas2 knownGene knownToGnfAtlas2 '-type=bed 12'
 hgMapToGene -tempDb=$tempDb $db affyU133 knownGene knownToU133
 hgMapToGene -tempDb=$tempDb $db affyU95 knownGene knownToU95
 
 hgsql $tempDb -Ne "create view all_mrna as select * from $db.all_mrna"
 hgsql $tempDb -Ne "create view ensGene as select * from $db.ensGene"
 hgsql $tempDb -Ne "create view gtexGene as select * from $db.gtexGene"
+hgsql $tempDb -Ne "create view gencodeAnnotV35 as select * from $db.gencodeAnnotV35"
+hgsql $tempDb -Ne "create view gencodeAttrsV35 as select * from $db.gencodeAttrsV35"
+hgsql $tempDb -Ne "create view gencodeGeneSourceV35 as select * from $db.gencodeGeneSourceV35"
+hgsql $tempDb -Ne "create view gencodeTranscriptSourceV35 as select * from $db.gencodeTranscriptSourceV35"
+hgsql $tempDb -Ne "create view gencodeToPdbV35 as select * from $db.gencodeToPdbV35"
+hgsql $tempDb -Ne "create view gencodeToPubMedV35 as select * from $db.gencodeToPubMedV35"
+hgsql $tempDb -Ne "create view gencodeToRefSeqV35 as select * from $db.gencodeToRefSeqV35"
+hgsql $tempDb -Ne "create view gencodeTagV35 as select * from $db.gencodeTagV35"
+hgsql $tempDb -Ne "create view gencodeTranscriptSupportV35 as select * from $db.gencodeTranscriptSupportV35"
 
 bioCycDir=/hive/data/outside/bioCyc/190905/download/humancyc/21.0/data
 mkdir $dir/bioCyc
 cd $dir/bioCyc
 
 grep -E -v "^#" $bioCycDir/genes.col  > genes.tab  
 grep -E -v "^#" $bioCycDir/pathways.col  | awk -F'\t' '{if (140 == NF) { printf "%s\t\t\n", $0; } else { print $0}}' > pathways.tab
 
 kgBioCyc1 -noEnsembl genes.tab pathways.tab $tempDb bioCycPathway.tab bioCycMapDesc.tab  
 hgLoadSqlTab $tempDb bioCycPathway ~/kent/src/hg/lib/bioCycPathway.sql ./bioCycPathway.tab
 hgLoadSqlTab $tempDb bioCycMapDesc ~/kent/src/hg/lib/bioCycMapDesc.sql ./bioCycMapDesc.tab
 
 mkdir -p $dir/kegg
 cd $dir/kegg