nickjd / storf-reporter Goto Github PK

This is a valuable tool for enhancing gene annotations. I do have one suggestion: Bakta provides its output in the form of individual directories for each genome, each containing GFF and other files. It might be more user-friendly if StORF-Reporter could directly utilize the Bakta output without requiring users to create a new directory specifically for the GFF files when supplementing multiple Prokka/Bakta outputs.

Hello! Thanks for making such helpful and exciting tool!

I am interested in trying to gain the amino acid sequences for my StORFs, but am having trouble understanding the correct way to produce this output. I was attempting to use the -aa flag to produce the sequences, however, I do not see any additional files or sequences within the .gff file that is being produced. Below is how I am running the tool:

StORF-Reporter -anno Feature_Types Multiple_Genomes -p MARINE_MAGS -aa True

The path contains the fast files and gff files for each MAG of interest. Any help or advice for what I may be missing for how to fix this step would be greatly appreciated! Hopefully there is just some piece of the puzzle I am missing?

It's great to see such a great tool, I realized in my own case that if I use a Bakta folder, the fna file needs to be the same as the folder name. For example if my folder is set to Ecoli_23_BAKTA, StORF will only look for Ecoli_23_BAKTA.fna, when in fact the contents of my folder is Ecoli_23.fna. So would it be possible to add an option to cope with this situation.