Piping a file list for another shell command

Being a student again takes a longer while than I expected to get used to, which gives me a long hiatus in my posting, but also puts me in a different and stimulating environment.

This post was inspired by a question from my colleague, who want to first find some file entries and then merge them into a file, so the initial attempt was:

# There are 6 files in my example directory
> ls
1.txt  2.txt  3.txt  a.txt  b.txt  c.txt

# Let's say we are looking for only those with lower case alphabetical names
> find . -regex "./[a-z].txt"

After getting the list of file names , it might be tempting to pipe this result to cat and then to a text file like:

find . -regex “./[a-z].txt" | cat > "merged.txt"

But this is only giving you the list of file names in merged.txt because it is actually ./c.txt\n./b.txt\n./a.txt (\n is the new-line character) being piped to cat. Though cat does try to find a file matching this name, there is obviously none in this directory, and cat has no other choice but printing the string it receives as it is.

I am bad at terminal commands, so the first thing I came up with was to use awk to send the file names one by one to cat with system(), which makes a system call in awk scripts.

# Awk will pass each file name to the system call (cat $0)
# and *append* it to a file because now the results are processed separately and will overwrite each other if we use > instead of >>

find . -regex “./[a-z].txt" | awk '{system("cat " $0 " >> 'merged.txt'")}'

This worked, but the use of awk seemed like an overkill.

I later noticed xargs, which takes standard input, splits it by blanks or new lines and sends the resulting list to a command. This looked like exactly the thing I wanted.

Indeed, find . -regex “./[a-z].txt" | xargs cat >> "merged.txt" does exactly the same thing in a more elegant way. Additionally, xargs is of course more versatile than that.

  • If you get a file containing the list, it can read from file directly (xargs -s). from file directly (xargs -s).
  • If you are unsure what xargs is going to do, -p turns it interactive, and it prints the command that is elicited by xargs and asks whether you want to run it. xargs and asks whether you want to run it.
  • If you just want to know what command xargs elicits, -t prints the command (to stderr) before it is actually running without asking. running without asking.
PhD Student

A graduate student interested in developmental biology, neurobiology and bioinformatics.