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biocore / qurro

Visualize differentially ranked features (taxa, metabolites, ...) and their log-ratios across samples
https://biocore.github.io/qurro
BSD 3-Clause "New" or "Revised" License
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Replace "exact separated text fragment(s)" with "exact text fragment(s) separated by semicolons" #196

Open fedarko opened 5 years ago

fedarko commented 5 years ago

This will let us deal with taxonomy strings that include spaces (e.g. k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Oceanospirillales; f__Halomonadaceae; g__Candidatus Portiera; s__), because those apparently exist. Huh.

This will also make things clearer for users IMO (taking care of this would be sufficient for #123, I think).

fedarko commented 5 years ago

SO a problem with only caring about semicolons is that you have problems with the abc; def pattern you see in some taxonomy strings -- you won't get a match for def, since textToRankArray("abc; def") will give you ["abc", " def"].

I guess we could trim each element produced by textToRankArray(), but dang, this is going to be a pain to address.