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bionode-seq features as Atom.io plugin #4

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ilevantis opened this Issue Feb 22, 2017 · 2 comments

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@ilevantis

ilevantis commented Feb 22, 2017

It would be useful to have some of the bionode-seq features in Atom for playing with DNA, RNA, AA sequences in much the same way as https://packagecontrol.io/packages/BioPythonUtils for Sublime Text.

I think some useful features would be:

  • reverse complement selected DNA/RNA sequence
  • translate selected DNA/RNA sequence (using standard genetic code)
  • backtranslate AA sequence to DNA/RNA
  • sequence search that ignores newlines and space characters and optionally also looks for reverse complement
@thejmazz

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thejmazz commented Feb 22, 2017

Ooooh neat idea!

I'm actually working on a (neo)Vim plugin for MSA atm, heres ClustalW vs Muscle on some blasted homologs for AT3G27350 from A. thaliana:

Wouldn't mind separating out common pieces so an Atom one can be made as well.

Planning on adding bionode integration later - probably send buffer as stdout into a bionode tool's stdin or something, read back output.

I guess your suggesting Atom because it is JS based, so shouldn't be too hard to wire up some functions.

@ilevantis

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ilevantis commented Feb 22, 2017

I guess your suggesting Atom because it is JS based, so shouldn't be too hard to wire up some functions.

Yes, that was my thinking.

Your neoVim plugin looks really cool, though I'm not sure how useful I would find MSAs in a text editor but the more bio plugins for Atom, the better IMO.

@bmpvieira bmpvieira added this to Backlog in Bionode Project Board Mar 29, 2017

@bmpvieira bmpvieira added the feature label Mar 29, 2017

@bmpvieira bmpvieira added the mozsprint label Apr 24, 2017

@bmpvieira bmpvieira referenced this issue May 24, 2017

Closed

Mozilla's Global Sprint (June 1st and 2nd 2017) #44

7 of 17 tasks complete
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