[Bioperl-guts-l] [Bug 3056] New: Bio::Tools::Run::Primer3 has not updated for Primer3 versions 2 and above

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=3056

           Summary: Bio::Tools::Run::Primer3 has not updated for Primer3
                    versions 2 and above
           Product: BioPerl
           Version: main-trunk
          Platform: All
        OS/Version: Windows XP
            Status: NEW
          Severity: normal
          Priority: P2
         Component: bioperl-run
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: manchunjohn-ma at uiowa.edu


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.


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