redwards at utmem.edu
Mon Jun 23 21:15:28 EDT 2003
As others have pointed out Bio::Tools is a real mess of modules and it is
hard to know what is there.
I propose the following changes based in part on what Hilmar and Heikki (and
1. Move all the parsers out of Bio::Tools. It seems to make (more?) sense to
put these in a separate directory, e.g. Bio::Tools::Parsers, and perhaps
distribute them with Bio::Tools::Run instead of core. There are at least 35
parsers. It seems that if you don't have the Run modules you are unlikely to
use the parsers (I know this isn't always true if you have run the app
without using bioperl, but it is an approximation).
The last one is currently in the cvs but has a wrapper for NetPhos that
should be in Bio::Tools::Run
In that case, several modules could be moved out of Tools such as:
ECnumber.pm -> Analysis/Protein
Gel.pm -> Analysis/Nucleotide
OddCodes.pm -> Analysis/Protein
SeqStats.pm -> Analysis
SeqWords.pm -> Analysis
SiRNA.pm -> Analysis/Nucleotide
Sigcleave.pm -> Analysis/Protein
pICalculator.pm -> Analysis/Protein (but I think this should be part of
3. Aren't the blast parsers being folded into SearchIO, in which case they
could be moved to the attic at somepoint?
This is quite drastic and would probably break a few things, but I think it
would make Bio::Tools a lot cleaner and clearer in the long run.
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