[Seqinr-forum] Prepgetannot and getAnnot - a doubt

[Simon Penel]

Dear Federico,
sorry for the delay in answering.
It seems there is a problem with theses functions at the server level, 
thanks for pointing this.
I will try to fix this bug as  soon as possible.
All the best,
Simon



Le 10/06/15 14:29, Fede a écrit :
> I'm trying to get some specific annotations using seqinr. I recently 
> started using R and also, too seqinr. So, the question is: I want to 
> get some specific fields of the annotations section using first 
> prepgetannot and then getAnnots. I tell you what i'm doing:
>
> First (until here no problem)
> s <- choosebank("genbank")
> cavia <- query("cavia", "TID=10140 AND O=mitochondrion", socket = 
> s$socket)
>
> At this moment I can use getAnnots to get some annotations of cavia 
> like getAnnots(cavia$req[1:2]) but my intention is for example to 
> filter this and get only the definition or the organism.
>
> I suppose that i could do this with the prepgetannot function but, 
> really, honestly I don't know how to do that. My first idea was using 
> prepgetannot and then getAnnots but this don't seems to work out. This 
> is what I do.
>
> prepgetannots(what = "OR", setfor = c("scan", "getannots"), socket = 
> s$socket, verbose = FALSE)
>
> And then use the getAnnots() function like before but I get the same 
> result, that is, the complete annotation with all the fields. 
> Obviously I'm doing something wrong but I cant realize what's my 
> mistake. Thanks, and sorry for my english, this is my first time 
> posting a question here. If you want I can post the output of the 
> annotations but is simply the entire annotations of the accesions that 
> I request
>
> Thanks!!
>
> Federico
>
>
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-- 
Simon Penel
Laboratoire de Biometrie et Biologie Evolutive
Bat 711 - CNRS UMR 5558 - Universite Lyon 1
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