hlapp at gmx.net
Tue Sep 19 20:21:30 UTC 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
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):
> Glimmer 3.X ( bacteria, archaea, and viruses):
> GlimmerHMM ( eukaryotes ):
> GlimmerM ( eukaryotes ):
> 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:
> 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?
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
: Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net :
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