[Bioperl-l] Bio::Tools

[Rob Edwards]

Hi all,

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 
others) suggested.

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).

2. Use
Bio::Tools::Analysis
Bio::Tools::Analysis::Nucleotide
Bio::Tools::Analysis::Protein

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 
SeqStats)

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.

Rob