Bioawk is a great project started by Heng Li some years ago. The aim was to take the awk source code and modify it slightly for use with common biological formats and adding in some new functions. Heng’s original doesn’t accept too many pull requests so to add in some features, I maintain my own fork that has a few improvements.
Long ago I added in a translate function and recently I added in a function that will take the attribute string from a GFF file and turn it into an awk array. It was possible to split the GFF attribute string in awk itself as the following awk code demonstrates
function gffattr(attr, array){
# split the attribute string into key value pairs
split(attr, a, ";")
for (i in a) {
# now split out the key and value
split(a[i], b, "=")
for (j in b) {
array[j] = b[j]
}
}
}
but this is a bit clunky and not suited for the kind of one-liner processing that awk excels at. So now with the latest update of my bioawk fork this function is built-in. If you want to filter a GFF on some attribute you can now do something like the following
bioawk -c gff '{gffattr($attribute, a); if(a["some_attr"] == "some_value") print}'
The base awk source code has been getting a lot more love recently and my fork has so far merged in all of the upstream updates so there are a few new bug fixes in there.
Bioawk used to ignore the output field separator when printing the whole record – this is no longer the case in my fork.