[Bioperl-l] bp_genbank2gff.pl bug

Fields, Christopher J cjfields at illinois.edu
Wed Nov 9 16:59:48 EST 2011


Works for me, it's a standard deprecation policy.  The only caveat is that the next 'release' of the code would be when the related code is split out into it's own distribution (which will require it's own versioning).

chris

On Nov 9, 2011, at 2:48 PM, Scott Cain wrote:

> Hi Carnë,
> 
> You are absolutely correct; that is the right way to do it.  I'll add that right now (and if the original posts fix is an easy one, I'll fix that too :-)
> 
> Scott
> 
> 
> 2011/11/9 Carnë Draug <carandraug+dev at gmail.com>
> On 9 November 2011 18:43, Scott Cain <scott at scottcain.net> wrote:
> > Hi Chris,
> >
> > Actually, removing it from the distribution (but letting it remain in the
> > code repository) is not a bad idea.  I can't really think of a down side.
> >
> > Scott
> 
> Hi
> 
> can I suggest instead to simply make the script issue a warning right
> at the start? Something like "bp_genbank2gff is obsolete and will be
> removed from a future version of bioerl; please use bp_genbank2gff3
> instead". You could leave it there for the next 2 releases and then
> finally remove it. This would have 2 advantages:
> 
> 1) people that have been using it will immediately know what to use as
> replacement (instead of coming and ask in the mailing list)?
> 2) people who use it but don't know anything about the subject,
> someone told them to "just press this button" or "just type this in
> the terminal", won't have suddenly a broken system and will have time
> to find someone that will make it work again.
> 
> That's what's done in GNU octave and I think it works good there.
> Carnë
> 
> 
> 
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research




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