In Perl, IPC::Run [1], while a bit on the quirky side sometimes, can do that sort of thing.
use IPC::Run qw(run);
IPC::Run::run(["echo", "abc"], "|",
["tr", "a-z", "A-Z"], "|",
["cat"],
\$out);
print "out: $out";
will yield
out: ABC
Useless use of cat here just to make a point, of course.
It's easy to use Perl strings as input or output, or files, and there's also ways to interact with streams as they go along.
Generally speaking the slightly more verbose interaction with shell is made up for by the savings when you can use Perl directly to do something rather than spawn a shell process for something simple. (Shell composition can be powerful, yes, but on the other hand spawning a full process and setting up a pipe for things like "tr" or "wc" is often just silly.)
I also personally believe there's a win in the syntax; you may say "What? 'tr a-z A-Z' is way more convenient than '["tr", "a-z", "A-Z"]' but I say one of the biggest and most pervasive errors in shell is to incorrectly set up the arguments by having something interpolated in incorrectly. Having an unambiguous syntax for separating arguments has often made it much safer for me to write the code that has to use the shell. Used correctly it can even be made to work in the face of user-supplied input, something that should generally not be combined with any form of implicit argument separation. (Although bear in mind that "used correctly" encompasses more than just "separating the arguments correctly.")
I am also NOT claiming exclusivity; this is just the thing I know off the top of my head. I'm sure the other scripting languages have nice libraries, too. Though watch out for them being too nice. There's a bit of an impedance mismatch between shell and scripting language. Anything that smooths it over too well is probably either giving up critical features or introducing subtle bugs, which can become security bugs in the face of arbitrary user input.
[1]: http://search.cpan.org/~toddr/IPC-Run-0.96/lib/IPC/Run.pm