[Bioperl-l] primer3redux 0.09 add_targets is not there

[Anand Patel]

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.

Thanks,
Anand


On Mon, Aug 22, 2011 at 2:42 PM, Christopher Fields <cjfields1 at gmail.com> wrote:
> On Aug 22, 2011, at 2:25 PM, Anand Patel wrote:
>
>> I'm trying to get Primer3Redux to work, and am noticing some strange
>> things.  While I found and changed my parameters to the new primer3
>> 2.2.3 parameters, I still can't find add_targets.
>>
>> Assigning the parameters using set_parameters works for primer3redux,
>> add_targets is ?leftover? from primer3.
>>
>> So is this a doc/POD issue?
>
> I'm confused.  You are trying to use add_targets with the latest primer3, but it isn't there?  Or is the Primer3Redux wrapper missing this parameter?
>
> chris
>
>> Thanks,
>> Anand
>>
>> Anand C. Patel, MD MS
>> Washington University School of Medicine
>> acpatel at gmail.com
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>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>