[Bioperl-l] primer3redux 0.09 add_targets is not there

Chris Fields cjfields at illinois.edu
Mon Aug 22 16:10:25 EDT 2011


On Aug 22, 2011, at 2:52 PM, Anand Patel wrote:

> my $primer3 = Bio::Tools::Run::Primer3Redux->new(-outfile =>
> "temp.out", -path => "/usr/bin/primer3_core");
> 
> If I use this:
> $primer3->add_targets(
> 	'PRIMER_OPT_TM'=>$PRIMER_OPT_TM,'PRIMER_MIN_TM'=>$PRIMER_MIN_TM,
> 'PRIMER_MAX_TM'=>$PRIMER_MAX_TM,
> 'PRIMER_PAIR_MAX_DIFF_TM'=>$PRIMER_MAX_DIFF_TM,
> 	'PRIMER_MAX_SIZE'=>$PRIMER_MAX_SIZE,'PRIMER_OPT_SIZE'=>$PRIMER_OPT_SIZE,
> 'PRIMER_MIN_SIZE'=>$PRIMER_MIN_SIZE,
> 	'PRIMER_MAX_GC'=>$PRIMER_MAX_GC,
> 'PRIMER_OPT_GC_PERCENT'=>$PRIMER_OPT_GC_PERCENT,
> 'PRIMER_MIN_GC'=>$PRIMER_MIN_GC,
> 	'SEQUENCE_TARGET'=>$TARGET, 'PRIMER_PRODUCT_SIZE_RANGE'
> =>$PRIMER_PRODUCT_SIZE_RANGE);
> 
> I get:
> Can't locate object method "add_targets" via package
> "Bio::Tools::Run::Primer3Redux" at p3ra.pl line 31, <GEN0> line 1.
> 
> On the other hand, if I change that line to:
> $primer3->set_parameters(
> 	'PRIMER_OPT_TM'=>$PRIMER_OPT_TM,'PRIMER_MIN_TM'=>$PRIMER_MIN_TM,
> 'PRIMER_MAX_TM'=>$PRIMER_MAX_TM,
> 'PRIMER_PAIR_MAX_DIFF_TM'=>$PRIMER_MAX_DIFF_TM,
> 	'PRIMER_MAX_SIZE'=>$PRIMER_MAX_SIZE,'PRIMER_OPT_SIZE'=>$PRIMER_OPT_SIZE,
> 'PRIMER_MIN_SIZE'=>$PRIMER_MIN_SIZE,
> 	'PRIMER_MAX_GC'=>$PRIMER_MAX_GC,
> 'PRIMER_OPT_GC_PERCENT'=>$PRIMER_OPT_GC_PERCENT,
> 'PRIMER_MIN_GC'=>$PRIMER_MIN_GC,
> 	'SEQUENCE_TARGET'=>$TARGET, 'PRIMER_PRODUCT_SIZE_RANGE'
> =>$PRIMER_PRODUCT_SIZE_RANGE);
> 
> It works.  When I looked at the source code for Primer3Redux, I
> couldn't find add_targets, but set_parameters looked like it might
> work, so I used that instead, and it worked.
> 
> But I see over in the github that there are other issues with the
> documentation (how primer3redux's result object is now 3 deep rather
> than 2 deep).  Not sure if this is in that category or not.

That is true; documentation was to be updated but that hasn't happened yet (haven't had the free time to work specifically on this, and I think fschwach was to work on some HOWTO documentation).  I do plan on an update in the next few weeks to address the various Issues on github, if you can file this as well it would help.

I have to go back and look at the history of add_targets() reative to primer3 bioperl code, but I don't think this was part of the commit history of Bio::Tools::Run::Primer3Redux (maybe for the old version, Bio::Tools::Run::Primer3), so that is probably cruft left over from the update.  Would be easy enough to alias it for convenience...

chris

> Thanks,
> Anand
...


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