Question: New functions to
gravatar for Csaba Ortutay
20 months ago by
Csaba Ortutay0 wrote:


I use package to access data in my projects. One thing I miss often is to convert easily UniProt taxon names to scientific species names, like ECOLX to Escherichia coli, or HUMAN to Homo sapiens. Manual conversion is a no-go for larger projects (I do often phylogenetics with dozens of such conversions).

I have written three new functions to assist this:

taxname2species() # ECOLX -> Escherichia coli

taxname2taxid() # ECOLX -> 562

taxname2domain() # ECOLX -> B

These works also in vector context, e.g.

> taxname2species(c("HUMAN","YEAST","PIG","ABIBR","ECOLX"))
[1] "Homo sapiens"             "Saccharomyces cerevisiae" "Sus scrofa"              
[4] "Abies bracteata"          "Escherichia coli"        

The code is in pastebin:

I would like to add this code to the package, but I could not figure out how to do that for the documentation. I do not want to create a new package, as it is clearly in the domain of

I would appreciate any advice on this. (I have some experience with git, no svn.)

Thank you,


ADD COMMENTlink modified 20 months ago by Valerie Obenchain ♦♦ 6.5k • written 20 months ago by Csaba Ortutay0
gravatar for Valerie Obenchain
20 months ago by
Valerie Obenchain ♦♦ 6.5k
United States
Valerie Obenchain ♦♦ 6.5k wrote:

Hi Csaba,

These look like useful helper functions. If you put together a patch (code, man page and unit tests) I can add this to Please make sure passes R CMD build and check with your new additions. Let me know ( when it's ready.


ADD COMMENTlink written 20 months ago by Valerie Obenchain ♦♦ 6.5k

Thanks, I will work on a patch, and I will contact you when it is ready. Csaba

ADD REPLYlink written 20 months ago by Csaba Ortutay0
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