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Perl has really fallen out of favor in bioinformatics. I inherited a bunch of Perl scripts that have been running basically for over 10 years. The input data

Perl has really fallen out of favor in bioinformatics. I inherited a bunch of Perl scripts that have been running basically for over 10 years. The input data is the same so they keep working. I’m not great at Perl and I do find them hard to read. While I get the goals I’m not super happy to have these scripts end up on the continuous upgrade as the language changes path. The goals seem good. A language needs users, and fewer and fewer are using it lately. Error messages can be obtuse, the package system while powerful is confusing.. Out cluster upgraded the os a couple years ago. Once you figure out how to a missing Perl library installed everything kept working. (The cpan installation story isn’t easy for a novice). the fact that it hasn’t changed much is kind of nice compared to some other language where a lot of scripts needed a fair amount of touch up when the language had a lot of breaking changes.

ktpsns 6y ago
The same is true in many other data science branches (such as physics). Perl was the perfect glue language in the 90s but then got more and more replaced by python. I think one reason for that is Numpy/Pylab, which makes python a perfect replacement for proprietary Matlab codes. All at once, scientists can write most of their codes in a single language/software ecosystem which also feels relatively close to mathematical notation, at least you can write equations similarly readable as in (modern) Fortran. The perl sigils really got out of fashion.
valarauko 6y ago
Similar story here - during my PhD my lab worked mostly in perl & C, but for my purposes R was a better fit. Some years down the line, I grew frustrated & moved to python, where I've been ever since. In my postdoc lab we're mostly leaning R, though a few of us are on python. I suspect newer members will be mostly python.
attractivechaos 6y ago
> compared to some other language where a lot of scripts needed a fair amount of touch up when the language had a lot of breaking changes. Python, I am looking at you!

ktpsns 6y ago

The same is true in many other data science branches (such as physics). Perl was the perfect glue language in the 90s but then got more and more replaced by python. I think one reason for that is Numpy/Pylab, which makes python a perfect replacement for proprietary Matlab codes. All at once, scientists can write most of their codes in a single language/software ecosystem which also feels relatively close to mathematical notation, at least you can write equations similarly readable as in (modern) Fortran. The perl sigils really got out of fashion.

valarauko 6y ago

Similar story here - during my PhD my lab worked mostly in perl & C, but for my purposes R was a better fit. Some years down the line, I grew frustrated & moved to python, where I've been ever since. In my postdoc lab we're mostly leaning R, though a few of us are on python. I suspect newer members will be mostly python.

attractivechaos 6y ago

> compared to some other language where a lot of scripts needed a fair amount of touch up when the language had a lot of breaking changes. Python, I am looking at you!