I seek guidance re: best approach to integrate the emboss freak command for protein analysis into Geneious.
freak "Generates residue/base frequency table" which is output as a per-residue score ranging from 0 to 1.
I would like to display results as graph, similar to amino acid change, or GC content.
In addition to the sequence, parameters to freak include -step, -window, and, -letters. I am happy to hardcode these values into command line if doing so allows me to use your "Wrapper PlugIn" capability. Indeed, I have tried to do just this, however, there seems to be no plugin type that will consume freak's results, however reformatted.
I contrived to reformat freak's output as a .qual file thinking that might "just work", having read https://support.geneious.com/hc/en-us/community/posts/218314028-Wrapper-plugin-question which discusses a similarly capability, but for GFF features.
Possibly more contemporary would be to reformat it as a .wig file (for proteins).
I see the opensource coiled-coils code, but I don't think I'm ready to take this on at this point as I really only have sparse reading knowledge of java.
Hillarly Miller advised a pose such questions here when I asked a similar question about integrating plaac as a protein analysis tool. https://support.geneious.com/hc/en-us/requests/23345 .
If I manage to integrate freak, I may then turn back to plaac, whose results might best be thought of as a multiple per-residue named vectors (arranged as matrix), each of which could generate a graph (if the name is user selected via checkbox).
All direction, suggestions, code fragments, or other legs up are very welcome before I continue on this endevour.