bionode-seq features as Atom.io plugin

bionode / bionode-seq

Module for DNA, RNA and protein sequences manipulation

MIT License

10 stars 5 forks source link

bionode-seq features as Atom.io plugin #4

Open ilevantis opened 7 years ago

ilevantis commented 7 years ago

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 commented 7 years ago

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 commented 7 years ago

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.