[Seqinr-forum] Seqinr

[Jean Lobry]

Dear Ran,

are you sure about your AC=NC001477, I've no google it for.

Best,

JLO

Le 07/08/2017 à 21:08, Ran Wei a écrit :
> 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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