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Question: (Closed) How to write a GO Annotation File (GAF) in R
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gravatar for lukeholman
6 days ago by
lukeholman0
lukeholman0 wrote:

Hi there,

I recently got some help on here downloading an OrgDB using the AnnotationHub package for R. I'd like to transform the GO annotations into a slim version, for example using the command line tool Map2Slim https://github.com/owlcollab/owltools/wiki/Map2Slim. R makes it very easy to download the annotation SQL database, but to use Map2Slim I need to save the GO annotations in the GAF file format. I've done some Googling, and it seems like there is not yet any ready-made R function to do this (or indeed, in any language). For example, in this thread, someone asks for help with the same task, and the answer is "meh, just figure out the specific requirements of the format and write a script" https://www.biostars.org/p/129057/

Is there seriously no tool (in R, bash, or whatever) for producing a GAF, taking the standard SQL format as input? Yes, I could probably write a ton of SQL queries and make the GAF myself (it has a mere 11 essential columns that must be entered in a specific way... http://geneontology.org/page/go-annotation-file-format-20), but this feels like a problem that probably already has been solved.

Alternatively, is it possible to download a GAF for a named species, from NCBI or wherever? Then one could directly pipe it into Map2Slim, instead of having to get the OrgDB first.

Cheers,

Luke

 

 

ADD COMMENTlink modified 6 days ago • written 6 days ago by lukeholman0

Hello lukeholman!

We believe that this post does not fit the main topic of this site.

This question isn't about any Bioconductor package. You might ask on Biostars.org.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink written 6 days ago by James W. MacDonald47k

Well, it's relevant in the sense that there is very likely to be a BioConductor package for making GO slims, and one for saving GO databases in the standard file format, but yeah, close the question if you like.

ADD REPLYlink written 2 days ago by lukeholman0
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