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

[Maxime Réjou-Méchain]

This is indeed a great solution,

Many Thanks!

Maxime

2012/5/31 Leonor Palmeira <mlpalmeira at ulg.ac.be>

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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
> >
> >
> >
> >
> > _______________________________________________
> > Seqinr-forum mailing list
> > Seqinr-forum at lists.r-forge.r-project.org
> >
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/seqinr-forum
>
> - --
> 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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-- 
Maxime Réjou-Méchain
Laboratoire Evolution et Diversité Biologique UMR 5174
Centre National Recherche Scientifique/Université Paul Sabatier
Bâtiment 4R1 31062 Toulouse
France
Personal website <https://sites.google.com/site/maximerejoumechain/>
+33 (0) 5-61-55-85-81
<maxime.rejou at gmail.com>
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