4 ms·

While some people tend to say Perl was chosen by the young bioinformatics community because of it's excel in text processing, I think Perl was just the go-to sc

by ktpsns 8y ago

While some people tend to say Perl was chosen by the young bioinformatics community because of it's excel in text processing, I think Perl was just the go-to scripting language in the late 90s. In my field (numerical relativity), Perl was also the go-to language in the early days. People then moved on to Python because of the numpy/scipy ecosystem which allowed to combine Perl-like scripts with Matlab/Fortran like post processing. Today, everything is Python. Python2 :-P

dalke 8y ago
Perl was being used in bioinformatics in the early 1990s - definitely before the "late 90s". Perl was becoming the go-to language in Unix fields in early 1990s, and bioinformatics comes out of that Unix tradition. (See also my comment at https://news.ycombinator.com/item?id=11381917 https://news.ycombinator.com/item?id=11381917 .) There's no reason to guess which factors contributed to Perl's uptake in the young bioinformatics community. Text processing is only one of six reasons Lincoln Stein listed in 1996 in "How Perl Saved the Human Genome Project". See https://web.stanford.edu/class/gene211/handouts/How_Perl_HGP.html https://web.stanford.edu/class/gene211/handouts/How_Perl_HGP...
- collyw 8y ago
  I switched to Python in 2011 (basically because Django was a lot easier to get into as web framework, better docs and because too many ways to do things made Catalyst confusing for a beginner). Perl was starting to loose ground by then, but was still pretty popular. My guess is around a third of bioinformaticans were using it as the goto language at that point. Its a pity, I miss Perl and still pull it out for quick scripts that involve manipulating the filesystem as its got so much better syntactic sugar for that sort of thing. And using regexes in Python is such a chore in comparison. I always need to look up the docs, whereas I remember how to use them in Perl despite hardly using the language in 8 years
  - dalke 8y ago
    You might enjoy, in a "never try this in practice" sort of way, some code I did to make a working Python variant, which compiled to Python byte code, and supported Perl-like pattern match syntax, like: # get_function_names.py for line in open("python_yacc.py"): if line =~ m/def (?P<name>\w+) *(?P<args>$.*$) *:/: print repr($1), repr($args) See http://dalkescientific.com/Python/python4ply-tutorial.html http://dalkescientific.com/Python/python4ply-tutorial.html . It got appreciative hisses when I did a lightning talk about it at a PyCon. FWIW, I co-founded Biopython back in 1999.

by ktpsns 8y ago

dalke 8y ago

Perl was being used in bioinformatics in the early 1990s - definitely before the "late 90s". Perl was becoming the go-to language in Unix fields in early 1990s, and bioinformatics comes out of that Unix tradition. (See also my comment at https://news.ycombinator.com/item?id=11381917 https://news.ycombinator.com/item?id=11381917 .) There's no reason to guess which factors contributed to Perl's uptake in the young bioinformatics community. Text processing is only one of six reasons Lincoln Stein listed in 1996 in "How Perl Saved the Human Genome Project". See https://web.stanford.edu/class/gene211/handouts/How_Perl_HGP.html https://web.stanford.edu/class/gene211/handouts/How_Perl_HGP...

collyw 8y ago
I switched to Python in 2011 (basically because Django was a lot easier to get into as web framework, better docs and because too many ways to do things made Catalyst confusing for a beginner). Perl was starting to loose ground by then, but was still pretty popular. My guess is around a third of bioinformaticans were using it as the goto language at that point. Its a pity, I miss Perl and still pull it out for quick scripts that involve manipulating the filesystem as its got so much better syntactic sugar for that sort of thing. And using regexes in Python is such a chore in comparison. I always need to look up the docs, whereas I remember how to use them in Perl despite hardly using the language in 8 years
- dalke 8y ago
  You might enjoy, in a "never try this in practice" sort of way, some code I did to make a working Python variant, which compiled to Python byte code, and supported Perl-like pattern match syntax, like: # get_function_names.py for line in open("python_yacc.py"): if line =~ m/def (?P<name>\w+) *(?P<args>$.*$) *:/: print repr($1), repr($args) See http://dalkescientific.com/Python/python4ply-tutorial.html http://dalkescientific.com/Python/python4ply-tutorial.html . It got appreciative hisses when I did a lightning talk about it at a PyCon. FWIW, I co-founded Biopython back in 1999.