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I kind of wonder if modern FORTRAN would be the right option... Or pushing towards something like Oberon or a Pascal dialect.



I actually got to the end and said "never heard of Fortran?".

Modern Fortran would be a good option; 'right' is a different matter. Certainly, Fortran 2003/2008/2018 are expressive languages (way more than F77), has an extensive ecosystem with good integration with C, has compilers that generate very fast code, handles parallel computations and SIMD and first-class language features, is already well established in the STEM world, etc., etc.

The biggest downside of Fortran is it's called 'Fortran' and so many people are unwilling to believe it's changed since the 70s.


Where does one go to learn modern Fortran? Is there a particular book or reference source that's recommended? What's the tooling like?


Fortran Wiki is an OK place to start: http://fortranwiki.org/fortran/show/HomePage

There are quite a number of books. I recently got this one that is pretty good: https://www.amazon.com/Modern-Fortran-Explained-Incorporatin...

One note, Fortran 2018 compliance in the compilers is still evolving, so not all features are in all compilers yet. Fortran 95/2003 support should be solid and most all have all of 2008 in.


checkout https://fortran-lang.org/ for help and hints on Fortran.


Biologists are text-mungers extraordinaire so I don't think Fortran will ever be right for them


Treating sequences as strings of characters is a peculiarity, but it really isn't much like text. The operations you would expect to perform on text like uppercase, lowercase, tokenize at word boundaries, etc. are irrelevant. The operations that you perform on sequences like reverse, reverse complement, align, edit distance are separate. No reason why FORTRAN couldn't do great for that.


My first ever professional program was a source code formatter (for Jovial language) written in Fortran (77 I think). Writing a parser in Fortran (early 80's) is an exercise I am glad I never had to repeat.


IIRC, modern versions of 'FORTRAN' dropped the all caps name. So Fortran 90+ is standard now and implies modern fortran version.


Modern Fortran does a vastly better job on text than classical Fortran, but you have a very good point.


I was in the lab when Ham Smith wrote a sequence search program in FORTRAN about 7 years ago.


Pl/1 ?


It is the right option for anything numerical and array-based. Any super-cool array-based feature that people see in MATLAB and Python was inherited from Fortran 90. Yes, that is true. Sadly, modern Fortran is treated quite unfairly within the field of computer science and engineering because of people's lack of knowledge of modern Fortran, which reminds me of the famous quote: "People hate each other because they do not know each other, and they do not want to know each other, because they hate each other".




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