[Bioperl-l] primer3redux 0.09 add_targets is not there

Frank Schwach fs5 at sanger.ac.uk
Tue Aug 30 05:45:46 EDT 2011


Yes, I still have the primer3redux doc on my TODO list. Sorry, haven't
had the time to do this lately but will loook into this as soon as I
can.
Frank


On Mon, 2011-08-22 at 15:10 -0500, Chris Fields wrote:
> 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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