[R] scan not working

[Rui Barradas]

Hello,

Try the following. Create a file called test.R with these instructions:

cmd <- commandArgs(TRUE)
if(any(grepl("--ext", cmd))){
	suffix <- cmd[grep("--ext", cmd)]
	suffix <- unlist(strsplit(suffix, ":"))[2]
	fl <- paste0("test_", suffix, ".txt") # underscore included
}else{
	fl <- "test.txt"
}
write(cmd, file = fl)

# Call like this
#$ Rscript test.R other --options --ext:cro


This creates a file test_cro.txt with the command line options written 
to it. You can adapt this R script to your needs.
Instead of 'suf', I've used option '--ext' for 'extension'. Change to 
fit your taste.


Hope this helps,

Rui Barradas

Em 27-01-2013 17:27, Emily Sessa escreveu:
> Hello all (again),
>
> I received a very helpful answer to this question, and would like to pose one more:
>
> Right now I have this script, which is being called from the command line, writing output to two generically named files ("pvalues" and "qvalues") that are named in the script using the line:
>
> write(pvalues, file="pvalues", ncol=1)
> write(adjusted, file="qvalues", ncol=1)
>
> However, ideally I would like those two files to have something appended to their names that make them separate from one another, so I can identify which input they went with and so they won't write over each other when I script this into a Perl pipeline that will process many input files, which is my ultimate goal. I know how to do this in Perl, but not R... is there some way I can add another argument on the command line that will get passed to the R.script, like a simple letter code (e.g. "cro"), and then have it append that to the output file names, so they are, for example: "qvalues_cro" and "pvalues_cro"?
>
> Thank you very much,
> Emily
>
> On Jan 27, 2013, at 4:34 AM, peter dalgaard <pdalgd at gmail.com> wrote:
>
>>
>> On Jan 27, 2013, at 08:33 , Emily Sessa wrote:
>>
>>> Hi all,
>>>
>>> I am trying to use the scan function in an R script that I am calling from the command line on a Mac; at the shell prompt I type:
>>>
>>> $ Rscript get_q_values.R LRT_codeml_output
>>>
>>> in the hope that LRT_codeml_output will get passed to the get_q_values R script. The first line of that script is:
>>>
>>> chidata <- scan(file="")
>>>
>>> which, as I understand how scan works, will read the contents of the file from the command line into the object chidata. I did this a few times and it worked like a charm. And then, it stopped working. Now, every time I try to do this, I get "Read 0 items" as the next line in the terminal window, and the output produced by the script is empty, because it's apparently no longer reading anything in. I don't think I changed anything in the script; it just stopped being able to execute the scan function. Does anyone have any idea how to fix this?? I did not have anything else in that scan line when it was working before. I've updated R and restarted my computer in the hope that it would help, but it hasn't. Any help would be much appreciated.
>>
>> I don't see how that would ever work. The 2nd and further args to Rscript are passed to R and accesible via commandArgs(). There's no way that scan() can know what the arguments are. It might work with
>>
>> Rscript get_q_values.R < LRT_codeml_output
>>
>> though. Or you need to arrange explicitly for scan(file=commandArgs(TRUE)[1]).
>>
>>>
>>> -ES
>>> ______________________________________________
>>> R-help at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>
>
> 	[[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>