[adegenet-forum] adegenet not recognizing file extensions

[Jombart, Thibaut]

Hi Ella,

It looks like the path to your file is incorrect  - can you double-check?

Cheers
Thibaut

________________________________
From: bowlese at gmail.com [bowlese at gmail.com] on behalf of Ella Bowles [ebowles at ucalgary.ca]
Sent: 28 September 2015 18:56
To: Jombart, Thibaut
Subject: Re: [adegenet-forum] adegenet not recognizing file extensions

Hi Thibaut,

I'm now using the line (all in one line)
data <- read.structure("C:/Users/Ella Bowles/Desktop/batch_1_8c9.str", n.ind = 186, n.loc = 4099, onerowperind = FALSE, col.lab = 1, col.pop = 2, col.others = NULL, row.marknames = 2, NA.char = "0", ask = TRUE)

for the attached dataset

and I'm still getting the error
Which other optional columns should be read (press 'return' when done)? 1:

 Converting data from a STRUCTURE .stru file to a genind object...

Error in file(file, "r") : cannot open the connection
In addition: Warning message:
In file(file, "r") :
  cannot open file 'C:/Users/Ella Bowles/Desktop/batch_1_8c9.str': No such file or directory

Can you see what may be wrong?

​Thank you for your time,
Ella​


On Fri, Sep 25, 2015 at 7:16 PM, Ella Bowles <ebowles at ucalgary.ca<mailto:ebowles at ucalgary.ca>> wrote:
Hi Thibaut,

I'm now using the line (all in one line)
data <- read.structure("C:/Users/Ella Bowles/Desktop/batch_1_8c9.str", n.ind = 186, n.loc = 4099, onerowperind = FALSE, col.lab = 1, col.pop = 2, col.others = NULL, row.marknames = 2, NA.char = "0", ask = TRUE)

for the attached dataset

and I'm still getting the error
Which other optional columns should be read (press 'return' when done)? 1:

 Converting data from a STRUCTURE .stru file to a genind object...

Error in file(file, "r") : cannot open the connection
In addition: Warning message:
In file(file, "r") :
  cannot open file 'C:/Users/Ella Bowles/Desktop/batch_1_8c9.str': No such file or directory

Can you see what may be wrong?

With thanks,
Ella


On Fri, Sep 25, 2015 at 11:54 AM, Ella Bowles <ebowles at ucalgary.ca<mailto:ebowles at ucalgary.ca>> wrote:
thank you!

On Fri, Sep 25, 2015 at 9:10 AM, Jombart, Thibaut <t.jombart at imperial.ac.uk<mailto:t.jombart at imperial.ac.uk>> wrote:
Hi there,

please check the forum archives, this has been answered several times. I think I even mention it in the tutorial. You need to remove 'system.file' and just indicate the path to your file.

Cheers
Thibaut


==============================
Dr Thibaut Jombart
MRC Centre for Outbreak Analysis and Modelling
Department of Infectious Disease Epidemiology
Imperial College - School of Public Health
Norfolk Place, London W2 1PG, UK
Tel. : 0044 (0)20 7594 3658
http://sites.google.com/site/thibautjombart/
http://sites.google.com/site/therepiproject/
http://adegenet.r-forge.r-project.org/
Twitter: @thibautjombart


________________________________
From: adegenet-forum-bounces at lists.r-forge.r-project.org<mailto:adegenet-forum-bounces at lists.r-forge.r-project.org> [adegenet-forum-bounces at lists.r-forge.r-project.org<mailto:adegenet-forum-bounces at lists.r-forge.r-project.org>] on behalf of Ella Bowles [ebowles at ucalgary.ca<mailto:ebowles at ucalgary.ca>]
Sent: 24 September 2015 20:07
To: adegenet-forum at lists.r-forge.r-project.org<mailto:adegenet-forum at lists.r-forge.r-project.org>
Subject: [adegenet-forum] adegenet not recognizing file extensions

Hello,

I'm trying to read files into adegenet and convert to genind objects, but am getting an error. After I have correctly specified/set the directory that the files are in I have used the line

data <- read.genetix(system.file("8c9.gtx", package = "adegenet"))

for many different permutations of filetype. These include read.genepop for genepop files, read.structure for structure filies. I keep getting the error

 Converting data from GENETIX to a genind object...
Error in if (toupper(.readExt(file)) != "GTX") stop("File extension .gtx expected") :
  argument is of length zero

The thing that I can see as the possible issue is that my files originally had different extensions (from the populations program of stacks). They were previously ".genepop" and ".strucuture", and I changed them manually to the ".gen" and ".stru" suffixes. Can you see a way around this?

With thanks,
Ella

--
Ella Bowles
PhD Candidate
Biological Sciences
University of Calgary

e-mail: ebowles at ucalgary.ca<mailto:ebowles at ucalgary.ca>, bowlese at gmail.com<mailto:bowlese at gmail.com>
website: http://ellabowlesphd.wordpress.com/



--
Ella Bowles
PhD Candidate
Biological Sciences
University of Calgary

e-mail: ebowles at ucalgary.ca<mailto:ebowles at ucalgary.ca>, bowlese at gmail.com<mailto:bowlese at gmail.com>
website: http://ellabowlesphd.wordpress.com/



--
Ella Bowles
PhD Candidate
Biological Sciences
University of Calgary

e-mail: ebowles at ucalgary.ca<mailto:ebowles at ucalgary.ca>, bowlese at gmail.com<mailto:bowlese at gmail.com>
website: http://ellabowlesphd.wordpress.com/



--
Ella Bowles
PhD Candidate
Biological Sciences
University of Calgary

e-mail: ebowles at ucalgary.ca<mailto:ebowles at ucalgary.ca>, bowlese at gmail.com<mailto:bowlese at gmail.com>
website: http://ellabowlesphd.wordpress.com/
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