[Bioperl-l] use primer3 to design primers with multiple sequences

[Wiersma, Paul]

Hi Li,

The line "my $result = $primer3->run" is already in the code you submitted.  In the Bio::Tools::Primer3 module the author uses "$p3" for the object.  If you change your line to "my $p3 = $primer3->run" you should be able to run the examples below. Process the results for each sequence and output the results before looping to the next sequence.

>From Bio::Tools::Primer3.pm:

 # how many results were there?
 my $num=$p3->number_of_results;
 print "There were $num results\n";

 # get all the results
 my $all_results=$p3->all_results;
 print "ALL the results\n";
 foreach my $key (keys %{$all_results}) {print "$key\t${$all_results}{$key}\n"}

 # get specific results
 my $result1=$p3->primer_results(1);
 print "The first primer is\n";
 foreach my $key (keys %{$result1}) {print "$key\t${$result1}{$key}\n"}

Paul

Paul A. Wiersma
Agriculture and Agri-Food Canada/Agriculture et Agroalimentaire Canada
Summerland, BC
wiersmap at agr.gc.ca
 
 



-----Original Message-----
From: chen li [mailto:chen_li3 at yahoo.com] 
Sent: Monday, May 08, 2006 8:32 PM
To: Wiersma, Paul
Subject: Re: [Bioperl-l] use primer3 to design primers with multiple sequences

Hi Paul,

I read both documents. What I understand is that
Bio:Tools::Run:Primer3 is for designing primers and
Bio:Tools::Primer3 is for parsing the results. When I
read the documents I do not see this line
 $result = $primer3->run in Bio:Tools::Primer3. I
wonder how you get this infomration.

Thanks,

Li 

--- "Wiersma, Paul" <WiersmaP at agr.gc.ca> wrote:

> Hi Li,
> 
>  
> 
> When you execute $primer3->run with a
> Bio::Tools::Run::Primer3 object it
> opens -outfile=>"filename" for writing and then
> closes.  That's why
> putting it in a loop will overwrite your output file
> each time so you
> only see the last one.  I suppose you could read in
> each output file
> before looping to the next seq and append it to
> another file.
> 
>  
> 
> If you're doing a fair bit of work with this module
> it would be worth
> looking at the Bio::Tools::Primer3 module.  The
> statement $result =
> $primer3->run produces a Bio::Tools::Primer3 object
> which has all the
> methods you need for customizing your output.
> 
>  
> 
> Paul
> 
>  
> 
> Paul A. Wiersma
> Agriculture and Agri-Food Canada/Agriculture et
> Agroalimentaire Canada
> Summerland, BC
> 
> wiersmap at agr.gc.ca
> 
>  
> 
>  
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 


__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com