Hi Uwe,
read.GanBank has problems reading scaffolds. You may use a modified
version on GitHub:
https://github.com/emmanuelparadis/read.GenBank.FASTA
You can source it directly into R:
source("https://raw.githubusercontent.com/emmanuelparadis/read.GenBank.FASTA/master/read.GenBank.FASTA.R";
Best,
Emmanuel
Le 10/09/2015 16:49, Uwe Menzel a écrit :
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
_______________________________________________
R-sig-phylo mailing list - [email protected]
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/[email protected]/
_______________________________________________
R-sig-phylo mailing list - [email protected]
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/[email protected]/
