[Bioperl-l] What is the relationship between primer3 module and run-primer3 module?

[Jason Stajich]

Bio::Tools::Run::XXX modules are for running applications...

On May 10, 2006, at 8:27 PM, chen li wrote:

> First thank you all for replying my previous post
> about primer3.
>
> But now I am a little confused even after I read the
> documents: What is the relationship between these two
> modules? What is correct/standard way to use them to
> do the batch-primer design? What I do is that I use
> Bio::Tools::Run::Primer3 to design primers. Based on
> Dr. Roy Chaudhuri's information I can set the
> parameters using the following syntax:
>
> $primer3->add_targets(PRIMER_PRODUCT_SIZE_RANGE=>'490-510');
>
> Based on Paul A. Wiersma's explanation I can also
> print out part of the primer results(because I don't
> need all the information). But there is a little
> trouble: PRIMER_SEQUENCE_ID can't be accessed using
> this method. And Paul points out that
> "PRIMER_SEQUENCE_ID and SEQUENCE are not part of the
> individual
> results but only end up by default with
> $results->primer_results(0)".  So it seems there is no
> way to get around this problem using
> Bio::Tools::Run::Primer3. And others suggest using
> Bio::Tools::Primer3 to parse the results. So is true
> that Bio::Tools::Run::Primer3 is for primer design and
> Bio::Tools::Primer3 is for parsing the results from
> Bio::Tools::Run::Primer3? But what I find is that I
> get almost all the results (except PRIMER_SEQUENCE_ID
> and SEQUENCE ) without providing a line code
>
> use Bio::Tools::Primer3
>
> in the script.  How to explain this? Is it because the
> following line code?
>
> my $result=$primer3->run;
>
> The last question: which line code is used to invoke
> program primer3.exe? How does Perl script call the
> primer3.exe?
>
> Once again thank you all very much,
>
> Li
>
>
>
>
>
>
>
>
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--
Jason Stajich
Duke University
http://www.duke.edu/~jes12