db=$1
tmp=remove.me.temp.dir

rm -rf $tmp
mkdir $tmp
hgsql $db -Ne "select transcript from knownCanonical" | awk '{print $1, 2}' > $tmp/knownCanon.txt
hgsql $db -Ne "select * from knownToTag" | grep basic |  sed 's/basic/1/' > $tmp/knownTag.txt
hgsql $db -Ne "select kgId,transcriptClass from knownAttrs where transcriptClass='pseudo'" |  sed 's/pseudo/4/' > $tmp/knownAttrs.txt
sort $tmp/knownCanon.txt $tmp/knownTag.txt $tmp/knownAttrs.txt | awk '{if ($1 != last) {print last, sum; sum=$2; last=$1}  else {sum += $2; }} END {print last, sum}' | tail -n +2  > $tmp/knownScore.txt
hgsql $db -Ne "select * from kgColor" > $tmp/colors.txt
hgsql $db -Ne "select * from knownGene" | sort -k2,2 -k4,4n > $tmp/knownGene.txt
hgsql $db -Ne "select kgId, geneSymbol, spID from kgXref" > $tmp/geneNames.txt
hgsql $db -Ne "select * from knownCds" > $tmp/knownCds.txt
genePredToBigGenePred -cds=$tmp/knownCds.txt -score=$tmp/knownScore.txt  -colors=$tmp/colors.txt -geneNames=$tmp/geneNames.txt  -known $tmp/knownGene.txt  $tmp/knownGene.bgpInput
bedToBigBed -type=bed12+8 -tab -as=$HOME/kent/src/hg/lib/bigGenePred.as $tmp/knownGene.bgpInput /cluster/data/$db/chrom.sizes $db.knownGene.bb
rm -rf $tmp
