A lightweight python toolkit for common manipulations on GFF3 files. Inspired by seqkit (but clearly not as well written)
Alternatively, you might take a look at things like the AGAT suite: https://agat.readthedocs.io/en/latest/why_agat.html
usage: gffkit.py <command> [<args>]
The commands are:
grep Filter GFF3 features based on regular expressions.
sort **Not implemented.** Use genometools (https://github.com/genometools/genometools) with 'gt gff3 -tidy -sort -retainids'
rc Update the extent of GFF3 features to their reverse complement
offset Shift GFF3 features by a constant offset
restart For circular references, reset the GFF3 record break (see https://github.com/shenwei356/seqkit) 'seqkit restart' for the analogous operation on FASTA files.
subgff get features within a specific subregion
add_ids Add ID lines to features that lack it
augustus_gtf_to_gff3 Convert augustus gtf format to GFF3
add_name_to_fasta Looks up the Name attribute from GFF3 & adds it to a fasta record