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

Steve Chervitz sac at bioperl.org
Tue Feb 13 18:00:46 EST 2007

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).

Steve Chervitz
sac at bioperl.org

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