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GNU Octave [0] is mostly compatible with MATLAB. GPLed and implemented in Fortran and C++, it's pretty much hack-able to your needs.

> MATLAB language is extremely awkward anytime you want to work with something that isn't a matrix.

From my limited experience, that's true but rarely of relevance. You can, and want to, use matrix operations all the way. Less bugs (simplier code), faster execution.

[0] http://www.gnu.org/software/octave/

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In my experience 90% of scientific data analysis work is: getting the data, cleaning it and transforming it into a form suitable for analysis. MATLAB fails miserably at these tasks.

> 90% of scientific data analysis work is: (...) and transforming it into a form suitable for analysis.

Is that infinite recursion or endless loop? Or is there an end to it, caused by quantum nature of work -- at some point the 90% becomes an undivisible unit? ;-)

((terribly sorry, couldn't help it))

At any rate, that sounds like you want to feed the input through a pipe of simple, programmable textual filters -- cue sed, awk etc. And then pipe into standard input of something -- I know Octave has standard input, MATLAB I wouldn't be so sure.

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