[Bioperl-l] Primer3.pm problems.

[Jason Stajich]

On Wed, 21 Apr 2004, Rob Edwards wrote:

>
> On Apr 19, 2004, at 9:29 AM, john herbert wrote:
>
> > Hello Bioperlers
> > I have been trying to use the BioPerl-run Primer3.pm module to run
> > primer3. In doing so I think I have found 2 bugs that prevent it from
> > working properly (I hope this is the right place to ask this).
>
> This is exactly the right place to ask this question
>
> >
> > The line
> > my $executable = $self->{'program_dir'}.$self->{'program'};
> > I think should be
> > my $executable = $self->{'program_dir'}.$self->{'program_name'};
> > otherwise the primer3 executable is never found using the -path option
> > in a call to the constructor
> > my $primer3 =
> > Bio::Tools::Run::Primer3->new(-path=>'/usr/mbin/primer3_core',-
> > seq=>$seq,
> > -outfile=>"temp.out");

and rob - I think you want to call $self->program_dir and $self->program
so they can overriden as well - that's why I set up the Base Class to have
these methods.

>
> Looking at the code it appears that I have used either program or
> program_name to mean the same things at various times. I will check
> through the whole thing and correct all of them. Totally my mistake!
>
>
> >
> > The second is beyond my ability in BioPerl. basically the line
> > my ($temphandle, $tempfile)=$self->io->tempfile;
> >
> > The temporary file never has any data in it. If you add the line
> > `cat $tempfile`; following the line
> > print $temphandle join "\n", @{$self->{'primer3_input'}}, "=\n";
> > The tempfile is empty but the variable @{$self->{'primer3_input'}} does
> > contain data.
> >
> > I proved this by putting a crude temporary fix in with the lines
> > $tempfile = "/tmp/primer3_temp_file.$$";
> >  open(FH,">$tempfile") or die;
> >  print FH join "\n", @{$self->{'primer3_input'}}, "=\n";
> >  close FH;
>
> Part of this is also because I lack a detailed knowledge of the bioperl
> IO structure as witnessed by the next lines:
>
>    # I can't figure out how to use either of these to write the results
> out.
>    # neither work, what am I doing wrong or missing in the docs?
>
>    #  $self->{output}=$self->_initialize_io(-file=>$self->{'outfile'});
>    #  $self->{output}=$self->io;
>
>    # OK, for now, I will just do it myself, because I need this to check
> the parser :)
>    open (OUT, ">".$self->{'_outfilename'}) || $self->throw("Can't open
> ".$self->{'_outfilename'}." for writing");
>
> I'll try and figure this out while I am looking through program and
> program_name, but if anyone has a suggestion about the IO approach I'd
> be glad to hear it.
>
> Rob
>
>
>
> > Then everything works fine.
> >
> > I hope it is ok to point these out and please correct me if I am
> > missing something.
> >
> > Kind regards,
> >
> > John.
> >
> >
> >
> >
> >
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>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu