[Bioperl-l] Tools::Run::Primer3Redux

[Ma, Man Chun John]

Hi,

This is the first time I write about development here and I hope I have
noticed most things.

It was until today I noticed the existence of Tools::Run::Primer3Redux
(which means the searching function needs improvement), and I already
have some code implementing the -p3_settings_file parameter-- however,
before I start rounding up, testing and commit, I see some problems we
have to discuss:

1. Should we implement the -io_version flag in primer3 2.X? Although it
does not seem difficult to implement, the major issue is we only do
sanity checks at set_parameters. Should the user change io_version after
settings parameters, the wrong kind of parameters may be fed to the
program.

2. Because I also do version check for p3_settings_file implementation
already, would it be better if we keep a permanent (program) version 2
flag in place? It'd be handy if we decided to re-implement $verbose, as
it will certainly trigger -echo_settings_file in p3_2.

Cheers,

John Ma
Kwitek Lab
Department of Internal Medicine
University of Iowa
Iowa City, Iowa, USA
 

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