I am looking for a way to automate with Python looking up sequence annotations from a GFF file (or a GBFF file) from genomes stored by NCBI.
I have a fasta file with kmers pulled from an NCBI genome. These kmers have coordinates such as the accession id, the contig id, and the start and end of the kmer. From that information, I would like a list of all annotations that cover or include that sequence as found in the GFF file. I would like to do it in Python.
I believe that BioPython has an experimental GFF file parser, but I do not know how to use it. It seems like there should be an easy way to do what I want with Python without having to write my own tool.