[Seqinr-forum] Problem with query when species are not in Genbank

[Leonor Palmeira]

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Dear Maxime,

what you could try is get all species that are in "genbank" by:

query("seqsp","K=rbcl", virtual=T)

and then project all these sequences to species:

query("sp","PS seqsp")
namesp=getName(sp)

Once you have all the species names present in "genbank", you can make a
condition on the iteration on 'Genustobefind', if you don't match a name
in 'namesp', the query is not sent.

Best,
Leonor.

On 31/05/12 15:33, Maxime Réjou-Méchain wrote:
> Dear all,
> 
> I am currently using a loop with the function query to know which genera in
> my list (n>2000 genera) have some sequences in genbank.
> 
> Here is the loop:
> 
> choosebank("genbank")
> sequences=vector(mode="numeric",length=length(Genustobefind))
> for (i in 1:length(Genustobefind)){
> print(paste("Retrieving sequence ",Genustobefind[i]," i=",i,sep=""))
> query1=paste("SP=",Genustobefind[i], " AND K=rbcl", sep="")
> query("bb", query1,virtual=T)
> sequences[i]=bb$nelem
> }
> 
> The loop work well but a lot of genera block the query function. For
> example, if I do
> 
> query("bb", "SP=Acanthodium AND K=rbcl",virtual=T)
> 
> The function run without stopping. I thus have to break the loop.
> 
> For information, if I submit manually the genera that block the query
> function to genbank I obtain in the main cases:
> 
>    - The following term was not found in Nucleotide: Acanthodium.
>    - See the search
> details<http://www.ncbi.nlm.nih.gov/nuccore/details?querykey=1>.
> 
>    - No items found.
> 
> In fact all these genera are not present in Genbank. Have you any idea to
> overcome this problem? I just want to have a value of zero for these genera
> and to continue my loop.
> Many thanks in advance for your help,
> 
> Maxime
> 
> 
> 
> 
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- -- 
Leonor Palmeira, PhD

Phone: +32 4 366 42 69
Email: mlpalmeira AT ulg DOT ac DOT be
http://sites.google.com/site/leonorpalmeira

Immunology-Vaccinology, Bat. B43b
Faculty of Veterinary Medicine
Boulevard de Colonster, 20
University of Liege, B-4000 Liege (Sart-Tilman)
Belgium
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