[Seqinr-forum] Seqinr

[Ran Wei]

Dear Simon,


Thank you for your reply. I will continue my work according to your suggestion. I hope all the partitions can be indexed in the future.


Best regards and have a good weekend,

Ran Wei

________________________________
From: PENEL SIMON <Simon.Penel at univ-lyon1.fr>
Sent: Thursday, August 10, 2017 8:15:20 AM
To: Ran Wei; seqinr-forum at lists.r-forge.r-project.org
Cc: LOBRY RAYMOND
Subject: RE: [Seqinr-forum] Seqinr

Dear Ran Wei,

the problem is related to the fact that there are refseq "partitions" for different type of data, as you can see on the ftp which is  where we get the data for indexing  acnuc databases

ftp://ftp.ncbi.nlm.nih.gov/refseq/release/


We do not index all these partitions, but maybe we should do it in the future (not before October however).

The current  acnuc database called RefSeq contains  RNA refseq sequence.



However you can access to your RefSeq sequence in Genbank, when  the sequence derives from Genbank.


There must be several ways to do it but for your  example:


https://www.ncbi.nlm.nih.gov/nuccore/NC_001477<https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fnuccore%2FNC_001477&data=02%7C01%7Cweira%40njms.rutgers.edu%7C5bbb52afbc424537694908d4dfe97b7b%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C636379641272858926&sdata=jLL08vryNYuUrw3XlM7cUdsfrdyOF6fXwIMUXubnZME%3D&reserved=0>



you can find  in the COMMENTS fields  the accession number of the Genbank sequence : U88536

https://www.ncbi.nlm.nih.gov/nuccore/U88536<https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fnuccore%2FU88536&data=02%7C01%7Cweira%40njms.rutgers.edu%7C5bbb52afbc424537694908d4dfe97b7b%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C636379641272858926&sdata=RyacQbiDzojlO9chGiebDpx9KRtUo%2BheRiqj1DXYTAA%3D&reserved=0>



with seqinr:


> choosebank("genbank")

> lambda <- query("lambda","AC=U88536")

>myseq <-getSequence(lambda)



Note: be carefull that you should give the same name to the list in the query and to the results of the query


I think there are cross reference files between Genbank and Refseq, you may find some information here
ftp://ftp.ncbi.nlm.nih.gov/genomes/README_assembly_summary.txt

I hope this help a little

all the best


Simon



________________________________
De : seqinr-forum-bounces at lists.r-forge.r-project.org <seqinr-forum-bounces at lists.r-forge.r-project.org> de la part de Ran Wei <weira at njms.rutgers.edu>
Envoyé : lundi 7 août 2017 21:08
À : seqinr-forum at lists.r-forge.r-project.org
Objet : [Seqinr-forum] Seqinr

Hello all,

I am new to seqinr. Today I was trying to connect to the genbank database and send queries. It worked well for some sequences:

> choosebank("genbank")
> query("lambda","AC=CP001252")
> mylambda <- get("lambda",env=.seqinrEnv)
> attributes(mylambda)
$names
[1] "call"     "name"     "nelem"    "typelist" "req"      "socket"

$class
[1] "qaw"

However, for a set of other sequences an error was thrown:

> query("dengue1", "AC=NC001477")
Error in query("dengue1", "AC=NC001477") :
  invalid request:"unknown accession number at (^): \"AC

And not only accession number, using other parameters also incurs error:

> query('naturepaper', 'R=Nature/460/352')
Error in query("naturepaper", "R=Nature/460/352") :
  invalid request:"unknown reference at (^): \"R

In addition, I also found that not all databases could be loaded:

> choosebank("refseqViruses")
Error in acnucopen(bank, socket) :
  Database with name -->refseqViruses<-- is not known by server.

Could anyone let me know how should I fix these problems? Version of this seqinr package is 3.3-6, running under 64-bit R in Win10 system.

Thank you and best regards,
Ran Wei



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/seqinr-forum/attachments/20170811/5a3b4f5c/attachment.html>