[Bioperl-l] How complete is the bioperl-pedigree?

Ma, Man Chun John manchunjohn-ma at uiowa.edu
Wed Mar 7 17:07:50 EST 2012

Hi all,

I tried to use bio-pedigree to output some genotype files to PED files for Haploview. While the script itself was easy to write, I have to wonder--how complete is bioperl-pedigree? What I have found up to this point included:

1. There's no Pedigree::Genotype classes when it should (if it's based on PopGen);
2. Nearly all methods in Pedigree::GroupI were never implemented, even there're other methods that would call them (PedIO classes).
3. Probably because of (2), adding a Pedigree::Group object into Pedigree::Pedigree object does not import the Group's markers.
4. I used Pedigree::PedIO::linkage, and there are even syntax errors in it (Line 281: there are one more sprintf FORMAT than LIST).

PopGen modules in core did not appear to be able to output to pedigree files like this. Are there any alternatives that I can use? PED files are complicated enough that even I know how to code for it, I don't really feel like coding for that.

Thanks for you guys!


John MC Ma
Graduate Assistant
Kwitek Lab
Department of Pharmacology
3125E MERF
375 Newton Road
Iowa City IA 52242

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