You can grab all the possible values for intron and exon with your regex and then split them up.
Consider replacing your intron/exon elsif blocks with this:
#new intron elsif block
elsif(/\s+\/intron="(.+)"\n/) {
foreach $item (split('\;',$1)) {
print OUT "Intron\t $item\n";
}
}
I replaced all the *s with +s, from my understanding this is more efficient, but I'm no regex guru :) The regex puts everything between the "double quotes" in $1
This will print out, based on your input data:
Intron 1-48
Intron 334-385
Now that they are separated, you can do whatever you want with them.
Ryan
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