Use of variable in Unix command line - r

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.

Answer 1

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)

Answer 2

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)
}