gffread
GFF/GTF parsing utility providing format conversions, region filtering, FASTA sequence extraction and more.
Use gffread -h to check the usage options.
Compiling this program from source requires my other code library, GCLib. It can be done like this:
cd /some/build/dir
git clone https://github.com/gpertea/gclib
git clone https://github.com/gpertea/gffread
cd gffread
make release
This should build the gffread binary in the current directory.