bioperl/bioperl-run

Bio::Tools::Run::Primer3 has not updated for Primer3 versions 2 and above

cjfields opened this issue · 3 comments

cjfields commented

Author Name: John MC (John MC)
Original Redmine Issue: 3056, https://redmine.open-bio.org/issues/3056
Original Date: 2010-04-12
Original Assignee: Bioperl Guts

Bio::Tools::Run::Primer3 relies on the list of Primer3 1.X arguments hardcoded at $self->@PRIMER3_PARAMS for sanity check in add_targets.

However, primer3 versions 2.X, released from December 2008, uses a totally different set of arguments, many of them absent from @PRIMER3_PARAMS. As a result, if these new arguments were invoked at add_targets, such arguments would be patently ignored, per line 367 of primer3.pm.

Of course, experienced users can invoke $self->{’no_param_checks’}=1 to bypass the sanity check, but this is not something known to newcomers.

There’re three possible ways to solve the problem:

  1. Expand @PRIMER3_PARAMS to include the 2.X arguments;
  2. Remove line 367 of primer3.pm such that “invalid” arguments will be warned but will continued be processed nonetheless, or
  3. Encode a setter for no_param_checks.
cjfields commented

Original Redmine Comment
Author Name: Chris Fields
Original Date: 2010-04-12T16:42:50Z

Won’t fix. We have an experimental Primer3 reimplementation in bioperl-dev that you are welcome to try, called Bio::Tools::Primer3Redux (it has a different API, hence the name).

You can checkout the latest code using svn. I’ll leave this open in the meantime, as it still needs tests.

cjfields commented

Original Redmine Comment
Author Name: Chris Fields
Original Date: 2010-07-30T01:09:04Z

Addendum : code is now in GitHub.

(In reply to comment #1)

Won’t fix. We have an experimental Primer3 reimplementation in bioperl-dev
that you are welcome to try, called Bio::Tools::Primer3Redux (it has a
different API, hence the name).

You can checkout the latest code using svn. I’ll leave this open in the
meantime, as it still needs tests.

cjfields commented

Original Redmine Comment
Author Name: Chris Fields
Original Date: 2010-10-11T14:14:39Z

Code is here:

http://github.com/cjfields/Bio-Tools-Primer3Redux

This should work for any of the 1.6.x release series. Tests and docs included. I’ll release it to CPAN after a bit of discussion on list.