[Bioperl-l] Proposed improvement to to Bio::Tools::Run::Primer3Redux

Ma, Man Chun John manchunjohn-ma at uiowa.edu
Mon Jan 24 17:44:53 UTC 2011


Attached are my proposed diff for some changes for Bio::Tools::Run::Primer3Redux to more fully implement the new features of Primer3 version 2.x.x:

1. Adding support for the commond-line argument p3_settings_file that has been available for all 2.x.x versions, and
2. Adding support for the "Sequence" tag SEQUENCE_PRIMER_PAIR_OK_REGION_LIST, a new function in version 2.2.3

Although I have used this module quite heavily in my projects and it appeared to run well, I'm not sure if there are bugs--not to say I have yet understand how to write /t scripts, so I wonder if someone would like to test this up.


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