[adegenet-forum] Loading fasta files

[Jombart, Thibaut]

Cheers Fede.

OK so the problem is clear. 'system.file' is only used to access files in the R installation. 
I used it in the example because the example file is distributed with the package.

Try:
##
goldenberry <- fasta2genlight("np_join.fasta", chunk=10)
##

with "np_join.fasta" in your working directory.

Cheers

Thibaut


________________________________________
From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Felix Enciso [fenciso13 at gmail.com]
Sent: 09 July 2012 21:03
To: adegenet-forum at lists.r-forge.r-project.org
Subject: [adegenet-forum] Loading fasta files

Hi,

I'm new using adegenet. I have a multifasta file aligned and I'm trying to load it using fasta2genlight but I get this error:

Error en if (!ext %in% c("FASTA", "FA", "FAS")) warning("wrong file extension - '.fasta', '.fa' or '.fas' expected"),

I really appreciate if some one can help me.

Thanks

Felix

Felix Eugenio Enciso-Rodriguez MSc.
Research Assistant
Plant Molecular Genetics Laboratory
Biotechnology and Bioindustry Center (CBB)
Colombian Corporation for Agricultural Research (CORPOICA)
Colombia
Phone: 57-1-4227300 Ext:1427


________________________________________
From: Federico Calboli [f.calboli at imperial.ac.uk]
Sent: 10 July 2012 18:31
To: Jombart, Thibaut
Cc: adegenet-forum at lists.r-forge.r-project.org
Subject: Fwd: [adegenet-forum] Loading fasta files

Theebs, we had more info (below)

F

PS next time reply to the list

Begin forwarded message:

From: Felix Enciso <fenciso13 at gmail.com<mailto:fenciso13 at gmail.com>>
Subject: Re: [adegenet-forum] Loading fasta files
Date: 9 July 2012 21:24:21 GMT+01:00
To: Federico Calboli <f.calboli at imperial.ac.uk<mailto:f.calboli at imperial.ac.uk>>

Hi,

My file name is np_join.fasta, and the command line is:

> sample1 <- system.file("files/np_join.fasta",package="adegenet")
> goldenberry <- fasta2genlight(sample1, chunk=10)

Thanks,

Felix


On Mon, Jul 9, 2012 at 3:18 PM, Federico Calboli <f.calboli at imperial.ac.uk<mailto:f.calboli at imperial.ac.uk>> wrote:
what is the name of the file you are trying to load, what *exact* command are you using?

F


On 9 Jul 2012, at 21:03, Felix Enciso wrote:

> Hi,
>
> I'm new using adegenet. I have a multifasta file aligned and I'm trying to load it using fasta2genlight but I get this error:
>
> Error en if (!ext %in% c("FASTA", "FA", "FAS")) warning("wrong file extension - '.fasta', '.fa' or '.fas' expected"),
>
> I really appreciate if some one can help me.
>
> Thanks
>
> Felix
>
> Felix Eugenio Enciso-Rodriguez MSc.
> Research Assistant
> Plant Molecular Genetics Laboratory
> Biotechnology and Bioindustry Center (CBB)
> Colombian Corporation for Agricultural Research (CORPOICA)
> Colombia
> Phone: 57-1-4227300 Ext:1427<tel:57-1-4227300%20Ext%3A1427>
>
> _______________________________________________
> adegenet-forum mailing list
> adegenet-forum at lists.r-forge.r-project.org<mailto:adegenet-forum at lists.r-forge.r-project.org>
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum

--
Federico C. F. Calboli
Neuroepidemiology and Ageing Research
Imperial College, St. Mary's Campus
Norfolk Place, London W2 1PG

Tel +44 (0)20 75941602<tel:%2B44%20%280%2920%2075941602>   Fax +44 (0)20 75943193<tel:%2B44%20%280%2920%2075943193>

f.calboli [.a.t] imperial.ac.uk<http://imperial.ac.uk/>
f.calboli [.a.t] gmail.com<http://gmail.com/>




--
Felix Eugenio Enciso-Rodriguez MSc.
Investigador Asistente
Laboratorio de Genética Molecular Vegetal
Centro de Biotecnología y Bioindustria (CBB)
Corporación Colombiana de Investigación Agropecuaria
Telefono: 57-1-4227300 Ext:1427

Felix Eugenio Enciso-Rodriguez MSc.
Research Assistant
Plant Molecular Genetics Laboratory
Biotechnology and Bioindustry Center (CBB)
Colombian Corporation for Agricultural Research (CORPOICA)
Colombia
Phone: 57-1-4227300 Ext:1427


--
Federico C. F. Calboli
Neuroepidemiology and Ageing Research
Imperial College, St. Mary's Campus
Norfolk Place, London W2 1PG

Tel +44 (0)20 75941602   Fax +44 (0)20 75943193

f.calboli [.a.t] imperial.ac.uk<http://imperial.ac.uk>
f.calboli [.a.t] gmail.com<http://gmail.com>