[Bioperl-l] primer3redux 0.09 add_targets is not there

Chris Fields cjfields at illinois.edu
Tue Aug 30 09:54:19 EDT 2011


S'okay, we're all a bit busy :P

chris

On Aug 30, 2011, at 4:45 AM, Frank Schwach wrote:

> 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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> 
> 
> 
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