[Bioperl-l] Bio::PopGen

rich dobbo at thevillas.eclipse.co.uk
Thu Mar 18 12:43:33 EST 2004


i've been using a number of modules under Bio::PopGen.

I have extended and added to suit my needs. I was
wondering whether the modules/changes might be worth
adding to the distro?

Basically I have,

1) created two new Bio::PopGen::IO modules (based on

Bio::PopGen::IO::ped.pm - takes ped format data (incl
family, member, parentage, gender, affeted status).

This module also has the option to look at family
structure and create missing parents.This is required
for using TRANSMIT

Bio::PopGen::IO::phase.pm - deals with PHASE format data

(I am also creating a Bio::PopGen::IO::hapmap.pm mod
that deals with hapmap data)

2) I have changed Bio::PopGen::IO::csv.pm (and included
within Bio::PopGen::IO::ped.pm) the ability to accept
data where the field delim is the same as the allele delim
(doesn't affect Bio::PopGen::IO::phase.pm)

3)In order to deal with the ped format I extended
Bio::PopGen::Individual.pm so that an individual object
 will take ped data (fam id, member id,mother, father,
sex, affected status)


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