Emmanuel Paradis <Emmanuel.Paradis@...> writes:
>
> Hi Matt,
>
> This is because this accession number does not point to the sequence.
> For this particular one, you could use:
>
> seq1 <- read.GenBank("U00096.3")
>
> Best,
>
> Emmanuel
>
> Le 27/02/2014 01:35, Matt Curcio a écrit :
> > Greetings all,,
> > I received this error while using R version 2.15.1 and ape 3.0.11.
> > Error in FI[i]:LA[i] : NA/NaN argument
> >
> > I have tried several approaches:
> >
> > ref = "NC_000913.3"
> > seq1 = read.GenBank(ref)
> > Error in FI[i]:LA[i] : NA/NaN argument
> >
> > ref = read.csv(file="test2.csv", head=T)
> >
> > ref = str(ref)
> >
> > # Where test2.csv is in two rows
> >
> > 'data.frame': 1 obs. of 1 variable:
> > $ seq: Factor w/ 1 level "NC+AF8-000913": 1
> >
> > seq2 = read.GenBank(ref)
> > Error in FI[i]:LA[i] : NA/NaN argument
> >
> >
> > I was wondering if someone could lend a hand based on their own experience.
> >
> >
> >
>
>
Hi,
I do have similar problems.
I try downloading 1814 sequences from K. flaccidum.
I just try with two of them:
accessions = c("DF238762", "DF238763")
flaccidum_scaffolds <- read.GenBank(accessions)
# Error in FI[i]:LA[i] : NA/NaN argument
If I try out these accesions directly in the Browser at
http://www.ncbi.nlm.nih.gov/genbank/ ,
it works very well.
So, how do I infer the "correct" accessions to be used in read.GenBank?
Or, how do I come from "NC_000913.3" to "U00096.3" in the example above?
That doesn't seem straightforward ....
Thanks, Uwe
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