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

[Cui, Wenwu (NIH/NCI) [F]]

1. Bio::Tools::Primer3 is already included in Bio::Tools::Run::Primer3 module so that you can parse the result file.
 
2. There is a bug in Bio::Toos::Primer3.pm line 264 as I mentioned. Once fixed, it can output PRIMER_SEQUENCE_ID
 
3. primer3.exe is called in the Bio::Tools::Run::Primer3  "run" function, please read the function definition.



________________________________

From: chen li [mailto:chen_li3 at yahoo.com]
Sent: Wed 5/10/2006 8:27 PM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] What is the relationship between primer3 module andrun-primer3 module?



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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