[Biopython-dev] Pathway module

[Tarjei Mikkelsen]

I've committed the following modules to the CVS tree:

Bio.Pathway
Bio.KEGG.Map
Bio.MetaTool.Input

Together they form my first (and rather rudimentary) attempt at creating 
classes for representing and working with metabolic and signalling pathways.

Bio.Pathway contains classes for representing collections of biochemical 
reactions of the type A + B <-> C (Reaction/System), and classes for 
representing explicit networks of arbitrary interactions 
(Interaction/Network).

Bio.KEGG.Map contains a parser for reading a KEGG metabolic pathway map into 
Reaction/System objects.

Bio.MetaTool.Input contains a function for converting a System object into a 
string that can be used as input tothe MetaTool program.

Sample usage can be deduced from the correponding test files.

This is very much a prototype so I welcome anyone interested to have a look 
and poke at it (and rip it apart). I don't recommend that it is included in 
the actual Biopython distribution until it is a bit more fleshed out and 
tested, but I'll leave that up to whoever makes those decisions.

thanks,

Tarjei Mikkelsen
tarjei at genome.wi.mit.edu

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