interface with EMBOSS freak command

Cook, Malcolm

• January 17, 2018 19:56

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.

Thanks!

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  Matthew Cheung

  • January 18, 2018 03:37

  Hi Malcolm,

  The only way to add a graph to Geneious will be to write a plugin.  Unfortunately as you have discovered you cannot do this via the wrapper plugin system.

  You're probably best to start with the ExampleSequenceGraphPlugin in our development kit.  I see you made a post asking about getting things running in Eclipse, so it looks like you may have already started exploring the devkit.

  You mention you only have sparse knowledge of Java.  Do you have any Object Orientated programming experience?  If you do then it shouldn't be too difficult to get a plugin working.

  You'll need to replace the Scorer in the example with your own that runs freak and extracts the value.  You'll need to use the Execution class to run a command line program.

  
  Cheers,
  Matthew

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