Finding a one line solution to pass variable arguments to an R script

Question

I have two principal data files (datafile1 and datafile2) that are split by chromosome, so I have a number of files that look like this:

datafile1_chr1.txt
datafile1_chr2.txt
datafile1_chr3.txt

datafile2_chr1.txt
datafile2_chr2.txt
datafile2_chr3.txt

I'm trying to write a bit of Bash code that can identify the two datafiles from the same chromosome and run an R script using those two files as variables.

What I have at the moment is very verbose:

Rscript --vanilla matchdata.R datafile1_chr1.txt datafile2_chr1.txt
Rscript --vanilla matchdata.R datafile1_chr2.txt datafile2_chr2.txt
Rscript --vanilla matchdata.R datafile1_chr3.txt datafile2_chr3.txt

Could someone suggest a one line solution for this? I am not sure how I could encorporate variables to help me here.

muru · Accepted Answer · 2016-03-08 14:24:32Z

2

A simple loop should be enough:

for i in {1..3}
do
    Rscript --vanilla matchdata.R datafile1_chr${i}.txt datafile2_chr${i}.txt
done

Or, in one line:

for i in {1..3}; do Rscript --vanilla matchdata.R datafile{1,2}_chr${i}.txt; done

Note the second use of brace expansion ({1,2}) - that should expand datafile{1,2}_chr${i}.txt into datafile1_chr${i}.txt datafile2_chr${i}.txt.

answered Mar 8, 2016 at 14:24

muru

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