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

Chris Fields cjfields at uiuc.edu
Thu Feb 15 16:50:54 EST 2007

On Feb 14, 2007, at 12:20 PM, Steve Chervitz wrote:

>> 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


I have added Root::Utilities back to CVS but I didn't know if I  
should add back the other related Root modules (didn't know what your  
future plans were for them).  Could the Bio::Root::Global and  
Bio::Root::Object stuff be consolidated into Bio::Root::Utilities or  
would that be too problematic?  None of the other Bio* modules  
currently use them.

Personally, I use Date::Manip for anything that requires date/time  
manipulation (updating seq records based on dates, for instance).   
Some of the other utilities could come in handy, though.  Don't know  
if that helps...


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