4 ms·

I love this article but i've always thought it should be about how unix pipes and streaming text files saves the human genome project.

tyingq 5y ago
They do make several points farther down the page about Perl specifically, including: "Perl is remarkably good for slicing, dicing, twisting, wringing, smoothing, summarizing and otherwise mangling text. Although the biological sciences do involve a good deal of numeric analysis now, most of the primary data is still text." Which seems fair. Perl is very good at that sort of thing.
- micro_cam 5y ago
  Perl was the tool for the job at the time no doubt. But the streaming pattern still applies no matter what language you use and really should be emphasized. (I worked in bio as we were moving away from Perl)
  - mst 5y ago
    Thing is, for simple to medium complexity streaming stuff the sed -> awk -> perl progression is still entirely valid. I don't honestly think it's a bad thing on the science side that python's won for -programs- simply because maintainable perl at scale requires focus and discipline that is frankly energy the average scientist would be far better of expending elsewhere, but even if it's only really in commercial settings where large scale perl is still worthwhile it definitely still has its place in pipelines.
throwanem 5y ago
That's fair, but on the other hand, those aren't going anywhere for decades yet at least, and it's been a long time since Perl was much of anything to the industry at large beyond a punchline. We can let it have a moment in the sun.
- mst 5y ago
  Speaking as somebody who does consultancy and commercial support around the perl ecosystem the number of people who completely fail to realise how much revenue it's still generating for how many companies is part depressing, part hilarious. Then again, Java, PHP etc. programmers seem to have the same experience on a regular basis, and these days the naysayers seem to have come for Rails as well. Programming is, as ever, a pop culture, and given our tendency towards self deprecatory humour as a community the worst part of the whole thing for us a lot of the time is that 99% of the people criticising/insulting perl are so bad at it.
AceJohnny2 5y ago
I once got excited explaining this new thing I discovered about Process Substitution [1] to my bioinformatics friend, and they patiently explained to me that yes, this was the basics of all their work. [1] https://wiki.bash-hackers.org/syntax/expansion/proc_subst https://wiki.bash-hackers.org/syntax/expansion/proc_subst

tyingq 5y ago

They do make several points farther down the page about Perl specifically, including: "Perl is remarkably good for slicing, dicing, twisting, wringing, smoothing, summarizing and otherwise mangling text. Although the biological sciences do involve a good deal of numeric analysis now, most of the primary data is still text." Which seems fair. Perl is very good at that sort of thing.

micro_cam 5y ago
Perl was the tool for the job at the time no doubt. But the streaming pattern still applies no matter what language you use and really should be emphasized. (I worked in bio as we were moving away from Perl)
- mst 5y ago
  Thing is, for simple to medium complexity streaming stuff the sed -> awk -> perl progression is still entirely valid. I don't honestly think it's a bad thing on the science side that python's won for -programs- simply because maintainable perl at scale requires focus and discipline that is frankly energy the average scientist would be far better of expending elsewhere, but even if it's only really in commercial settings where large scale perl is still worthwhile it definitely still has its place in pipelines.

throwanem 5y ago

That's fair, but on the other hand, those aren't going anywhere for decades yet at least, and it's been a long time since Perl was much of anything to the industry at large beyond a punchline. We can let it have a moment in the sun.

mst 5y ago
Speaking as somebody who does consultancy and commercial support around the perl ecosystem the number of people who completely fail to realise how much revenue it's still generating for how many companies is part depressing, part hilarious. Then again, Java, PHP etc. programmers seem to have the same experience on a regular basis, and these days the naysayers seem to have come for Rails as well. Programming is, as ever, a pop culture, and given our tendency towards self deprecatory humour as a community the worst part of the whole thing for us a lot of the time is that 99% of the people criticising/insulting perl are so bad at it.

AceJohnny2 5y ago

I once got excited explaining this new thing I discovered about Process Substitution [1] to my bioinformatics friend, and they patiently explained to me that yes, this was the basics of all their work. [1] https://wiki.bash-hackers.org/syntax/expansion/proc_subst https://wiki.bash-hackers.org/syntax/expansion/proc_subst