[Bioperl-l] primer parameters using primer3

[Jason Stajich]

I'm not really familiar with the module more  than what the  
documentation says so did you try and use the add_targets method to  
add arguments instead?  I had thought the AUTOLOAD method took care  
of access to the cmd line arguments as it does for the other Run  
modules but I am not really sure.  Perhaps folks on the list who use  
this module can provide better advice.

-jason
On May 7, 2006, at 9:18 PM, chen li wrote:

> Hi Jason,
>
> I add the line code
> $primer3->primer_product_size_range("490-510");
>  to my script. But it doesn't work nor primer3
> complains it.
>
> Li
>
> --- Jason Stajich <jason.stajich at duke.edu> wrote:
>
>> I put up some info on the wiki (and I encourage
>> other people to do
>> the same!)
>>
> http://bioperl.org/wiki/Module:Bio::Tools::Run::Primer3
>>
>> Set the command line parameters by just calling a
>> function of the
>> name of the parameter.  To get a list of the
>> available options, this
>> perl code will report it to you:
>>
>> # what are the arguments, and what do they mean?
>>    my $args = $primer3->arguments;
>>
>>    print "ARGUMENT\tMEANING\n";
>>    foreach my $key (keys %{$args}) {print "$key\t",
>> $$args{$key}, "\n"}
>>
>> The info for PRODUCT_SIZE_RANGE is:
>>    (size range list, default 100-300) space
>> separated list of product
>> sizes eg <a>-<b> <x>-<y>
>>
>> I believe you can set the PCR product size with
>>    $primer3->primer_product_size_range("490-510");
>>
>> -jason
>> On May 7, 2006, at 3:34 AM, chen li wrote:
>>
>>> Hi all,
>>>
>>> I use Bio::Tools::Run::Primer3 to design PCR
>> primers.
>>> I want to change some default values, for example,
>> to
>>> increase the PCR product size to 490-510 bp
>> instead of
>>> using the default value of 100-300 bp. What should
>> I
>>> do ?
>>>
>>>
>>> Thanks,
>>>
>>> Li
>>>
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>> --
>> Jason Stajich
>> Duke University
>> http://www.duke.edu/~jes12
>>
>>
>>
>
>
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--
Jason Stajich
Duke University
http://www.duke.edu/~jes12