join, a little python script, a little perl script, R, grep, etc.

There are many ways to do this. What have you tried that didn't work?

If you want to write a header, you could use a variety of tools, such as awk, echo and others.

For example, to add the tab-delimited header A \t B \t C to foo.txt:

$ awk 'BEGIN{print "A\tB\tC"} {print $0;}' foo.txt > foo-with-header.txt

Or via echo:

$ echo -e "A\tB\tC" | cat - foo.txt > foo-with-header.txt

Lots of ways to do this.