[Bioperl-l] Primer3 help

Chris Fields cjfields at illinois.edu
Fri Mar 6 14:51:45 EST 2009


You need bioperl-run:

http://search.cpan.org/~cjfields/BioPerl-run-1.6.1/

chris

On Mar 6, 2009, at 11:00 AM, Paolo Pavan wrote:

> Hi all,
> Is the first time I need to use Primer3 with bioperl and I was  
> trying to
> investigate the API. I found the snip of code below but it reports  
> to me:
> Can't locate Bio/Tools/Run/Primer3.pm in @INC (@INC contains:
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi
> /usr/lib64/perl5/site_perl/5.8.7/x86_64-linux-thread-multi
> /usr/lib64/perl5/site_perl/5.8.6/x86_64-linux-thread-multi
> /usr/lib64/perl5/site_perl/5.8.5/x86_64-linux-thread-multi
> /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl/5.8.7
> /usr/lib/perl5/site_perl/5.8.6 /usr/lib/perl5/site_perl/5.8.5
> /usr/lib/perl5/site_perl
> /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi
> /usr/lib64/perl5/vendor_perl/5.8.7/x86_64-linux-thread-multi
> /usr/lib64/perl5/vendor_perl/5.8.6/x86_64-linux-thread-multi
> /usr/lib64/perl5/vendor_perl/5.8.5/x86_64-linux-thread-multi
> /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl/5.8.7
> /usr/lib/perl5/vendor_perl/5.8.6 /usr/lib/perl5/vendor_perl/5.8.5
> /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux- 
> thread-multi
> /usr/lib/perl5/5.8.8 .) at primers.3.pl line 8.
> BEGIN failed--compilation aborted at primers.3.pl line 8.
>
> In fact the file:
> /usr/lib/perl5/site_perl/5.8.8/Bio/Tools/Run/Primer3.pm
> does not exist in my system.
>
> My bioperl's instalation dir is /usr/lib/perl5/site_perl/5.8.8/Bio  
> that is
> in the path and the bioperl distribution is 1.6.
> Do I haven't understood how to use Primer3 or is a distribution  
> problem?
>
> Thank you in advance,
> Paolo
>
>
>
> # The easiest way to use this is probably either, (i), get the
> # output from Bio::Tools::Run::Primer3, Bio::Tools::Primer3, or
> # Bio::Tools::PCRSimulation:
>
> # For example, start with a fasta file
> use Bio::SeqIO;
> use Bio::Tools::Run::Primer3;
>
> my $file = shift || die "need a file to read";
> my $seqin = Bio::SeqIO->new(-file => $file);
> my $seq = $seqin->next_seq;
>
> # use primer3 to design some primers
> my $primer3run = Bio::Tools::Run::Primer3->new(-seq => $seq);
> $primer3run -> run; # run it with the default parameters
>
> # create a file to write the results to
> my $seqout = Bio::SeqIO->new(-file => ">primed_sequence.gbk",
>   -format => 'genbank');
>
> # now just get all the results and write them out.
> while (my $results = $primer3run->next_primer) {
> $seqout->write_seq($results->annotated_seq);
> }
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