Dear all,<br><br>here I come again for a problem with the query function. I still have some difficulties to obtain all the taxa names of my retrieve sequences.<br><br>Here is my code:<br><br>>query("seqsp","sp=eudicotyledons and K=rbcl")<br>
<div id=":yk">>TOTseq=sapply(seqsp$req, getSequence, as.string = TRUE)<br>>length(TOTseq)<br>30609<br>>TOTname=getName(seqsp)<br>>length(TOTname)<br>
30609<br>>query("sp","PS seqsp")<br>>namesp=getName(sp)<br>>length(namesp)<br>15831</div><br>As cou can see, the length of my namesp vector is much lower than the number of retrieved sequences and I do not understand why.<br>
Is someone can explain me why I can not retrieve all the taxa names associated with each sequence?<br><br>Many thanks in advance for your help,<br><br>Maxime<br><br><br><br><br><br><div class="gmail_quote">2012/5/31 Maxime Réjou-Méchain <span dir="ltr"><<a href="mailto:maxime.rejou@gmail.com" target="_blank">maxime.rejou@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">This is indeed a great solution,<br><br>Many Thanks!<br><br>Maxime<div><div><br><br><div class="gmail_quote">
2012/5/31 Leonor Palmeira <span dir="ltr"><<a href="mailto:mlpalmeira@ulg.ac.be" target="_blank">mlpalmeira@ulg.ac.be</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">-----BEGIN PGP SIGNED MESSAGE-----<br>
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Dear Maxime,<br>
<br>
what you could try is get all species that are in "genbank" by:<br>
<br>
query("seqsp","K=rbcl", virtual=T)<br>
<br>
and then project all these sequences to species:<br>
<br>
query("sp","PS seqsp")<br>
namesp=getName(sp)<br>
<br>
Once you have all the species names present in "genbank", you can make a<br>
condition on the iteration on 'Genustobefind', if you don't match a name<br>
in 'namesp', the query is not sent.<br>
<br>
Best,<br>
Leonor.<br>
<div><br>
On 31/05/12 15:33, Maxime Réjou-Méchain wrote:<br>
> Dear all,<br>
><br>
> I am currently using a loop with the function query to know which genera in<br>
> my list (n>2000 genera) have some sequences in genbank.<br>
><br>
> Here is the loop:<br>
><br>
> choosebank("genbank")<br>
> sequences=vector(mode="numeric",length=length(Genustobefind))<br>
> for (i in 1:length(Genustobefind)){<br>
> print(paste("Retrieving sequence ",Genustobefind[i]," i=",i,sep=""))<br>
> query1=paste("SP=",Genustobefind[i], " AND K=rbcl", sep="")<br>
> query("bb", query1,virtual=T)<br>
> sequences[i]=bb$nelem<br>
> }<br>
><br>
> The loop work well but a lot of genera block the query function. For<br>
> example, if I do<br>
><br>
> query("bb", "SP=Acanthodium AND K=rbcl",virtual=T)<br>
><br>
> The function run without stopping. I thus have to break the loop.<br>
><br>
> For information, if I submit manually the genera that block the query<br>
> function to genbank I obtain in the main cases:<br>
><br>
</div>> - The following term was not found in Nucleotide: Acanthodium.<br>
> - See the search<br>
> details<<a href="http://www.ncbi.nlm.nih.gov/nuccore/details?querykey=1" target="_blank">http://www.ncbi.nlm.nih.gov/nuccore/details?querykey=1</a>>.<br>
><br>
> - No items found.<br>
<div>><br>
> In fact all these genera are not present in Genbank. Have you any idea to<br>
> overcome this problem? I just want to have a value of zero for these genera<br>
> and to continue my loop.<br>
> Many thanks in advance for your help,<br>
><br>
> Maxime<br>
><br>
><br>
><br>
><br>
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<br>
- --<br>
Leonor Palmeira, PhD<br>
<br>
Phone: <a href="tel:%2B32%204%20366%2042%2069" value="+3243664269" target="_blank">+32 4 366 42 69</a><br>
Email: mlpalmeira AT ulg DOT ac DOT be<br>
<a href="http://sites.google.com/site/leonorpalmeira" target="_blank">http://sites.google.com/site/leonorpalmeira</a><br>
<br>
Immunology-Vaccinology, Bat. B43b<br>
Faculty of Veterinary Medicine<br>
Boulevard de Colonster, 20<br>
University of Liege, B-4000 Liege (Sart-Tilman)<br>
Belgium<br>
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</blockquote></div><br><br clear="all"><br></div></div><span><font color="#888888">-- <br>Maxime Réjou-Méchain<br>Laboratoire Evolution et Diversité Biologique UMR 5174<br>Centre National Recherche Scientifique/Université Paul Sabatier<br>
Bâtiment 4R1 31062 Toulouse<br>
France<br><a href="https://sites.google.com/site/maximerejoumechain/" target="_blank">Personal website</a><br><a href="tel:%2B33%20%280%29%205-61-55-85-81" value="+33561558581" target="_blank">+33 (0) 5-61-55-85-81</a><br>
<a href="mailto:maxime.rejou@gmail.com" target="_blank"></a><br>
</font></span></blockquote></div>