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Weeks-UNC / RNAvigate

Very flexible tools for plotting and analyzing all kinds of RNA structure data
MIT License
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lowercase format not kept for bases in varna files #9

Closed scottallen877 closed 1 year ago

scottallen877 commented 2 years ago

We have some varna files with a mix of lowercase/uppercase bases to indicate intron versus exon sequences. When we upload the secondary structures to RNAvigate, all of the bases are plotted as uppercase. Is there a way to preserve the lowercase/uppercase sensitivity in the secondary structure plot? Or can this be edited within RNAvigate itself?

Psirving commented 2 years ago

I will add support to preserve lowercase lettering in the future. For now, you can manually set the sequence: my_sample.data["ss"].sequence="augcAUGCaugc" Note: lowercase lettering will not play well with coloring by sequence identity or using Leonitis-Westoff base-pairing conventions.

You might also play around with using color or annotations to highlight these regions in addition to sequence.