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

[chen li]

Thanks Paul it REALLY works.

I have other questions:
1) When I run the script I use this line on the
command prompt

perl primer.pl >test

When I check the default output file(temp.out) used by
the script I only see the information about the last
sequence which is different from what is in the test
file. In test file I can get all the information for
all the sequences.

2)Is it possible directly to use Bio::Tools:: Primer3
to print out selective information such as the primer
sequence and the size of PCR product?  Or do I have
parse the file by myself?

After I get all these information I would like to post
the script for bacth-designing PCR primers.


Thanks,

Li 



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

> 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
> > 
> 
> 
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