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

[Chris Fields]

John,

If you want you can submit a patch to address this.  The current Primer3Redux implementation is experimental (parameter work for the wrapper may be , but the API won't necessarily change much.  Though, it certainly isn't fixed in place, hence it being in bioperl-dev ;>

I'm a little unsure what you mean with #2 below.  If primer3 in now in v2 final (no longer alpha), yes we can change that.  Otherwise I'm not sure I want to make the default an alpha version.

chris

On Apr 13, 2010, at 8:54 PM, Ma, Man Chun John wrote:

> 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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