[Bioperl-l] Thoughts on Bio::Tools::Glimmer

Chris Fields cjfields at uiuc.edu
Thu Apr 12 14:11:33 EDT 2007

Agreed; anyone can suggest code enhancements and bug fixes and submit  
patches for these:


You'll see a long list of unimplemented enhancement requests in  
Bugzilla.  These are the ones where no patch is given; you'll find  
that very few are willing to go through the effort to work on them  
unless there is something in it for them!  Enhancement requests that  
come with patches and tests tend to get committed fairly rapidly  
(sometimes within hours).


On Apr 12, 2007, at 12:26 PM, Mark Johnson wrote:

>     I'd call that a buggy regexp.  Sounds like a good (but minimal)
> fix.  Torsten, I don't have cvs write access, I think you do, can you
> fix that up?  Andrew, can you file that as a bug:
> http://bugzilla.bioperl.org/
>     Everything else sounds like enhancements.  I'm not necessarily
> opposed, but a little discussion is probably in order before putting
> any tickets in for any of that.  Also, I'm not sure when I'll be able
> to spare some time to work on the module.  It was easy to justify
> spending time from my day job getting the module up to where is now,
> as I needed a BioPerl-ish glimmer2/glimmer3 parser.  It's working
> quite well for my purposes.  Again, I'm not opposed to further
> enhancements, but If I'm going to work on any of them, they'll have to
> fit into everything else I'm doing and it could be a while.  However,
> there's no reason somebody else can't do what I did.  Discuss the
> changes here, work out a plan, implement it, send along the diff(s)
> attached to a bug in bugzilla.  Next thing you know, your changes are
> in cvs.  8)
> On 4/11/07, Torsten Seemann  
> <torsten.seemann at infotech.monash.edu.au> wrote:
>> Andrew,
>>>                 # Glimmer 3.X prediction
>>>                 (/\w+(\d+)\s+       # orf (numeric portion)
>>> ...isn't picking up more than the last digit in the orf-number.  Not
>>> sure if that's intentional.  A sample of the feature output using -
>>>> gff_string shows up as ...
>> I think that regexp should be \w+?(\d+)
>> ie. the \w+ should be non-greedy, otherwise it will swallow up all  
>> but
>> one of the following \d+ (as \d is a subset of \w)
>> I've CC:ed this to Mark Johnson who made the recent changes to  
>> this module.
>> Thanks for your feedback,
>> --Torsten Seemann

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