[Bioperl-l] Bio::Root::Utilities.pm

Steve Chervitz sac at bioperl.org
Wed Feb 14 13:20:17 EST 2007


On 2/13/07, Chris Fields <cjfields at uiuc.edu> wrote:
>
>
> On Feb 13, 2007, at 5:00 PM, Steve Chervitz wrote:
>
> > I noticed that Bio::Root::Utilities was purged from bioperl-live
> > for the
> > 1.5.2 release, but I'd like us to consider adding it back. I agree
> > that the
> > other purged Root modules were ancient relics of the past, but
> > Bio::Root::
> > Utilities.pm still has signs of life (at least I still find
> > occasion to use
> > it, or refer to code in it).
> >
> > I know that it's not currently used by any other modules in
> > Bioperl, but
> > there are likely some legacy scripts out there that rely on it.
> > Probably
> > most of those scripts are ones I've written, but there have been
> > substantive
> > commits by others in the not-to-distant past (Dec 2005), so at
> > least some
> > folks besides myself are using it and may hesitate to upgrade their
> > bioperl
> > installation if it's absent.
> >
> > I'm all for avoiding bloat in the codebase and am eager to see
> > Bioperl be
> > more lean and mean, but I'd like to keep this module around. I'll
> > agree to
> > add some tests for it as well as clean some things up (e.g., use
> > Bio::Root::IO to get temp file name).
> >
> > Cheers,
> > Steve
> > --
> > Steve Chervitz
> > sac at bioperl.org
>
> I don't have a problem with adding it back, esp. if tests are added.
> Everything in Bio::Root* not tied to a module was yanked out when no
> one spoke up about cleaning up Bio::Root* modules:
>
> http://thread.gmane.org/gmane.comp.lang.perl.bio.general/12792/
> focus=12839
>
> Maybe others disagree?
>
> chris
>

Sorry I missed out on that thread. I had some trouble with my bioperl-l
email delivery getting disabled due to excessive bounces, and it took me a
while to catch it.

Bio::Root::Utilities is quite a grab bag of miscellaneous general functions
that are occasionally useful for perl scripting (e.g., determining
end-of-line characters, sending email, etc.). The code could definitely use
a review, and maybe an example script to advertise it. I can look into this,
and suggestions are welcome.

Steve


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