[Seqinr-forum] Seqinr

[Jean Lobry]

Hi Tiago,

not sure what you want to do, but did you try this:

where.is.this.acc("KU497555")

Best,

JLO

Le 19/07/2017 à 20:59, Jean Lobry a écrit :
> Hi Tiago,
> 
> I'm unable to reproduce the behaviour you reported.
> Copy/pasting your code works fine for me:
> 
>  > access <- "KU497555"
>  >
>  >  message("Running: ", access, ".")
> Running: KU497555.
>  >
>  >  ############################
>  >  # Loads
>  >  ############################
>  >  require("seqinr")
>  >
>  > ############################
>  > # Load the sequence from access number
>  > ############################
>  >
>  > banks <- choosebank()
>  > i <- 1
>  > choosebank(banks[i])
>  > repeat{seqraw = tryCatch(query("seqtambonis", paste("AC=", access, 
> sep="")),
> +                             error=function(...) NULL); if 
> (!is.null(seqraw)) break
> +     closebank()
> +     closeAllConnections()
> +     i <- i + 1
> +     choosebank(banks[i])
> + }
>  > seqraw <- getSequence(seqraw$req[[1]])
>  > closebank()
> 
> 
> Here is my session info :
> 
>  > sessionInfo()
> R version 3.4.1 (2017-06-30)
> Platform: x86_64-apple-darwin15.6.0 (64-bit)
> Running under: macOS Sierra 10.12.5
> 
> Matrix products: default
> BLAS: 
> /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
> LAPACK: 
> /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
> 
> locale:
> [1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] seqinr_3.4-0
> 
> loaded via a namespace (and not attached):
> [1] compiler_3.4.1 tools_3.4.1    ade4_1.7-6
> 
> 
> You should perhaps update and try again. Let us
> know if it doesn't work for you.
> 
> Best,
> 
> JLO
> 
> Le 19/07/2017 à 20:21, Tiago Tambonis a écrit :
>> access <- "KU497555"
>>
>>   message("Running: ", access, ".")
>>
>>   ############################
>>   # Loads
>>   ############################
>>   require("seqinr")
>>
>> ############################
>> # Load the sequence from access number
>> ############################
>>
>> banks <- choosebank()
>> i <- 1
>> choosebank(banks[i])
>> repeat{seqraw = tryCatch(query("seqtambonis", paste("AC=", access, 
>> sep="")),
>>                              error=function(...) NULL); if 
>> (!is.null(seqraw)) break
>>      closebank()
>>      closeAllConnections()
>>      i <- i + 1
>>      choosebank(banks[i])
>> }
>> seqraw <- getSequence(seqraw$req[[1]])
>> closebank()
> 
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