[Bioperl-l] bp_genbank2gff.pl bug

Scott Cain scott at scottcain.net
Wed Nov 9 15:48:07 EST 2011


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 Something like "bp_genbank2gff is obsolete and will be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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