create a bed12 file from a ucsc database.

canonical.sh

ORG=$1
mysql --user=genome --host=genome-mysql.cse.ucsc.edu -NA -D $ORG -e \
"select K.chrom,chromStart,chromEnd,X.geneSymbol,G.exonCount,strand from knownCanonical as K, kgXref as X, knownGene as G where 
     X.kgId=K.transcript and G.name=X.kgID;"

ucsc-bed12.sh

ORG=$1
mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D $ORG -P 3306   -e "select chrom,txStart,txEnd,K.name,X.geneSymbol,strand,exonStarts,exonEnds from knownGene as K,kgXref as X where  X.kgId=K.name;" > tmp.notbed

grep -v txStart tmp.notbed | awk '
        BEGIN { OFS = "\t"; FS = "\t"} ;
            {
                delete astarts;
                delete aends;
                split($7, astarts, /,/);
                split($8, aends, /,/);
                starts=""
                sizes=""
                exonCount=0
                for(i=1; i <= length(astarts); i++){
                    if (! astarts[i]) continue
                    sizes=sizes""(aends[i] - astarts[i])","
                    starts=starts""(astarts[i] = astarts[i] - $2)","
                    exonCount=exonCount + 1
                }
                print $1,$2,$3,$5","$4,1,$6,$2,$3,"0",exonCount,sizes,starts
            }' | sort -k1,1 -k2,2n > knownGene.$ORG.bed12

for refGene, this looks like:

mysql -D $org -e "SELECT chrom,txStart,txEnd,name2,strand,exonStarts,exonEnds from refGene;" | awk 'BEGIN{ OFS="\t" }(NR > 1){ 
                delete astarts;
                delete aends;
                split($6, astarts, /,/);
                split($7, aends, /,/);
                starts=""
                sizes=""
                exonCount=0
                for(i=0; i < length(astarts); i++){
                    if (! astarts[i]) continue
                    sizes=sizes""(aends[i] - astarts[i])","
                    starts=starts""(astarts[i] = astarts[i] - $2)","
                    exonCount=exonCount + 1
                }
                print $1,$2,$3,$4,1,$5,$2,$3,"0",exonCount,sizes,starts
}' | sort -k 1,1 -k 2,2n > refGene.$org.bed12