Thank you all - these suggestions have been very helpful! I've got it doing what I wanted know, and I appreciate the help!
Emily On Jan 27, 2013, at 1:18 PM, Rui Barradas <ruipbarra...@sapo.pt> wrote: > 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 <pda...@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@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@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. >> ______________________________________________ R-help@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.