[Bioperl-l] Genetic Analysis Modules

[Steve Mathias]

Hello Bioperlers,

I've noted several postings on the list over the last few months on genetic 
maps, pedigrees, populations, genotypes, phenotypes, etc. - basically, things 
I consider to fall into the realm of genetic analysis.  So I thought it might 
be of interest to some in the group to know that I have written a series of 
modules related to genetic analysis.  The distribution of Genetics modules, 
aka GenPerl, is available in the CPAN directory SLMATH, or you can find it by 
doing a CPAN search on 'Genetics'.

There's some documentation with the distribution outlining the functionality 
and how to use it.  Briefly there are a series of Perl classes implementing a 
full genetic analysis object model.  Then there are a set of modules 
implementing an API for managing persistence of the data in a relational 
database (currently only MySQL is supported), and for performing analysis on 
genotype/phenotype data.  The former is basically a wrapper around DBI.  The 
latter includes functionality for writing linkage format files and running 
linkage analysis software (E.g. Genehunter).  There is some other analysis 
functionality, but it is mostly just stuff that I've played around with at 
one time or another.

The Genetics modules are not structured in a very "bioperl" way.  However, if 
there is interest in including this kind of functionality in bioperl, I'd be 
willing to volunteer to do this.  If so, I'd be interested in hearing 
comments on where/how you all think it would be best to do this.  Obviously, 
this would be a post 1.0 thing, but let me know what you think.

	-Steve
-- 
Stephen L. Mathias
smathias1@qwest.net