Feature Request: Proteomics Data

[linsalrob]

I have a feature request for Pharokka to add support for proteomics data that provides evidence that the gene predictions are real.

Our proteomic sequences are short peptides. I'd like to include a fasta file of peptide sequences as input to pharokka, and then end up with those annotated into the GenBank file with the /experimental= qualifier so that we retain a record of the evidence that this thing is real.

In addition, I'd like to request a ring to the beautiful plot to show where there are hits to proteomic sequences. I think it needs to highlight four cases:

• in-frame matches within the predicted ORF (ie. the gene caller has nailed it)?
• in-frame matches but upstream of the predicted start codon (ie. the gene caller has identified the wrong start site) (note those beyond the stop codon are upstream of the next ORF)
• out-of-frame matches shadowing a predicted ORF (ie the gene caller chose the wrong frame)?
• out-of-frame matches on the wrong strand (ie. the gene caller really messed up).