gff_parser

Python parser to add external gene calls and functional annotation from Prokka or IMG to Anvi'o.
Uses Python3 and gffutils package (https://github.com/daler/gffutils).
Install gffutils using conda: conda install -c bioconda gffutils

Annotate your genome/metagenome with Prokka or download annotations from the IMG database. Use the script to get two files needed for external gene calls and annotations for Anvi'o.
With the --source flag you can specify where the annotations are coming from.

gff_parser.py GFF3_file --gene-calls gene_calls.txt --annotation gene_annot.txt
--source Prokka

This might or might not work for your files. But I hope it works for you too.

But at least you can try it out with the test files provided in the test folder (Thanks to Andrew Morris).

PROKKA annotations:

python gff_parser.py test/PROKKA.gff --gene-calls Prokka_gene_calls.txt --annotation Prokka_annotation.txt --process-all --source Prokka

IMG annotations:

python gff_parser.py test/IMG.gff --gene-calls IMG_gene_calls.txt --annotation IMG_annotation.txt --process-all --source IMG