[Bioperl-l] Bio::PopGen

Jason Stajich jason at cgt.duhs.duke.edu
Thu Mar 18 14:13:12 EST 2004

Rich -
Looks great.

The ped info is incorporated into the bioperl-pedigree cvs module where I
have father/mother/sibling information as well as a ped parser.  Since the
types of analyses are different for related individuals than for
unrelated populations.

If you send me your changes I can see about incorporating them - but you
may want to look at the bioperl-pedigree dist first as well.


On Thu, 18 Mar 2004, rich wrote:

> Hi,
> 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
> csv.pm):
> 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)
> cheers
> Rich
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Jason Stajich
Duke University
jason at cgt.mc.duke.edu

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