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Re^6: Searching array against hash

by BrowserUk (Pope)
on Aug 22, 2013 at 04:22 UTC ( #1050450=note: print w/ replies, xml ) Need Help??


in reply to Re^5: Searching array against hash
in thread Searching array against hash

You're not wrong, Bio::DB::Fasta is overkill for this specific purpose;

That was my point.

Also, it installs just fine on linux, where most of the users will be using it

Often only because that's their only choice if they want to use BIO::*. Which adds yet another barrier to many of them thinking of using Perl for their work.

I just don't see bashing a tool that has been helpful to bioinformaticists for something close to a decade.

Why does the Python toolset exist given the lead Perl had; and the greater performance Perl (simple, clean, basic, native Perl) has over native Python?

Perhaps because the PyGr consists of 54 files and 3MB; and installs easily wherever Python runs -- which includes Windows;

Rather than the 2,215 files and 43MB of BioPerl that only installs on *nix.

Perhaps if someone had been more (constructively) critical of the way the BioPerl project was going at an earlier stage; it might have favoured performance, ease-of-use and portability over monolithic architecture, Oh-OO fanatasism, and O'Woe engineering.

(IMO)BioPerl typifies what has gone wrong with Perl in the last decade. Gone the original, Unix principle of small, fast, dedicated tools that do one thing very well that can be combined to do many more things very well; in favour of a Java-esque monolith, consisting of layers upon layers; each contributing little value and lots of overhead; and nested so deep that it is impossible for the human brain to gain oversight of the whole; or even a clear, end-to-end view of any given end-use.

I'm in awe of the way BioPerl got started; but exasperated by where it has arrived; and troubled by where those who should be its natural user base are being driven as a result.


With the rise and rise of 'Social' network sites: 'Computers are making people easier to use everyday'
Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.
"Science is about questioning the status quo. Questioning authority".
In the absence of evidence, opinion is indistinguishable from prejudice.


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