[Seqinr-forum] Seqinr

[Ran Wei]

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



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