Use of variable in Unix command line

Question

I'm trying to make life a little bit easier for myself but it is not working yet. What I'm trying to do is the following:

NOTE: I'm running R in the unix server, since the rest of my script is in R. That's why there is system(" ")

system("TRAIT=some_trait")

system("grep var.resid.anim rep_model_$TRAIT.out > res_var_anim_$TRAIT'.xout'",wait=T)

When I run the exact same thing in putty (without system(" ") of course), then the right file is read and right output is created. The script also works when I just remove the variable that I created. However, I need to do this many times, so a variable is very convenient for me, but I can't get it to work.

Vaja · Accepted Answer · 2021-02-17 11:05:00Z

2

This code prints nothing on the console.

system("xxx=foo")
system("echo $xxx")

But the following does.

system("xxx=foo; echo $xxx")

The system forgets your variable definition as soon as you finish one call for "system".

In your case, how about trying:

system("TRAIT=some_trait; grep var.resid.anim rep_model_$TRAIT.out > res_var_anim_$TRAIT'.xout'",wait=T)

edited Feb 17, 2021 at 11:05

Vaja

311 silver badge9 bronze badges

answered Sep 30, 2016 at 14:37

Kota Mori

6,7621 gold badge25 silver badges28 bronze badges

Sign up to request clarification or add additional context in comments.

Comments

hrbrmstr · Accepted Answer · 2016-09-30 15:08:55Z

You can keep this all in R:

grep_trait <- function(search_for, in_trait, out_trait=in_trait) {
  l <- readLines(sprintf("rep_model_%s.out", in_trait))
  l <- grep(search_for, l, value=TRUE) %>% 
  writeLines(l, sprintf("res_var_anim_%s.xout", out_trait))
}

grep_trait("var.resid.anim", "haptoglobin")

If there's a concern that the files are read into memory first (i.e. if they are huge files), then:

grep_trait <- function(search_for, in_trait, out_trait=in_trait) {
  fin <- file(sprintf("rep_model_%s.out", in_trait), "r")
  fout <- file(sprintf("res_var_anim_%s.xout", out_trait), "w")
  repeat {
    l <- readLines(fin, 1)
    if (length(l) == 0) break;
    if (grepl(search_for, l)[1]) writeLines(l, fout)
  }
  close(fin)
  close(fout)
}

Collectives™ on Stack Overflow

Use of variable in Unix command line

2 Answers 2

Comments

Comments

Your Answer

Hot Network Questions

Collectives™ on Stack Overflow

2 Answers 2

Comments

Comments

Your Answer

Sign up or log in

Post as a guest

Related