Prints the coordinates of all 5'UTR exons from a refGenefile. Based on https://www.biostars.org/p/10907/#10910
# gives the coordinates of all 5'UTR exons
awk '
BEGIN { OFS = "\t"; FS = "\t"} ;
{
# $7 is cdsStart
delete astarts;
delete aends;
split($10, astarts, /,/);
split($11, aends, /,/);
for(i=1; i <= length(astarts); i++){
if (! astarts[i]) continue
if ($4 == "+"){
if(astarts[i] > $7) break
if(aends[i] > $7) aends[i]=$7
print $3,astarts[i],aends[i],$2"_"i,length(astarts)-1,$4
}
else if ($4 == "-"){
if(aends[i] < $8) continue
if(astarts[i] < $8) astarts[i]=$8
print $3,astarts[i],aends[i],$2"_"i,length(astarts)-1,$4
}
}
}'