Re: [R-sig-phylo] ape package gives 'Error in FI[i]:LA[i] : NA/NaN argument'

[Uwe Menzel]

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 - R-sig-phylo@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/

Re: [R-sig-phylo] ape package gives 'Error in FI[i]:LA[i] : NA/NaN argument'

[Emmanuel Paradis]

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.





___
R-sig-phylo mailing list - R-sig-phylo@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/

[R-sig-phylo] ape package gives 'Error in FI[i]:LA[i] : NA/NaN argument'

[Matt Curcio]

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.



-- 
Thank You,

Matt Curcio
Bioinformatics Dept.
Worcester Polytechnic Institute
Worcester, MA, USA
M: 401-316-5358
E: matt.curcio...@gmail.com

[[alternative HTML version deleted]]

___
R-sig-phylo mailing list - R-sig-phylo@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/