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

Hilmar Lapp hlapp at gmx.net
Tue Sep 19 16:21:30 EDT 2006


If the differences aren't too big, or if you there is only specific  
sections for which you need to branch based on version, then handling  
all in a single module would be more cohesive and simpler for the user.

For example, Bio::Tools::GFF supports different flavors of GFF all in  
one module; you specify the one you want as a named parameter to the  
constructor.

	-hilmar

On Sep 19, 2006, at 11:33 AM, Mark Johnson wrote:

>     The initial checkin comments (circa '03) for Bio::Tools::Glimmer
> describe it as a 'GlimmerM 3.0' parser.  The POD says '...a module for
> parsing Glimmer predictions (currently GlimmerM
> 3.0 is all that has been tested)...'.  However, the latest version of
> GlimmerM looks to be 2.5.1 (ftp://ftp.tigr.org/pub/software/GlimmerM),
> and there are multiple versions/flavors of Glimmer besides GlimmerM:
>
> Glimmer 2.X ( bacteria, archaea, and viruses):
>     http://www.cbcb.umd.edu/software/glimmer/glimmer2.jun01.shtml
> Glimmer 3.X ( bacteria, archaea, and viruses):
>     http://www.cbcb.umd.edu/software/glimmer/
> GlimmerHMM ( eukaryotes ):
>     http://www.cbcb.umd.edu/software/GlimmerHMM/
> GlimmerM ( eukaryotes ):
>     http://www.cbcb.umd.edu/software/glimmerm/index.shtml
>     http://www.tigr.org/software/glimmerm/
>
>     I suspect Bio::Tools::Glimmer only parses GlimmerM, *maybe*
> GlimmerHMM, but not Glimmer 2.X or Glimmer 3.X.
>     People do seem to be confused, see Michael Watson's post to
> bioperl-l on 10/18/2004:
> http://bioperl.org/pipermail/bioperl-l/2004-October/017112.html.
>     It seems that Glimmer is really more of a 'family' of programs.
> Should there be one module that tries to parse all the different
> output formats, or should there be Bio::Tools::Glimmer2,
> Bio::Tools::Glimmer3, Bio::Tools::GlimmerHMM, Bio::Tools::GlimmerM?
> I'm presently leaning towards the latter, and would not be opposed to
> working on Glimmer2 and Glimmer3 myself, as I'm going to need them.
>     Comments, suggestions, opposition, rotten fruit?
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-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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