[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
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
Department of Pharmacology
375 Newton Road
Iowa City IA 52242
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