[Bioperl-l] Bio:Tools::Primer3, Bio::Seq::PrimedSeq, and Bio: :SeqFeature::Primer

[anthony.underwood at hpa.org.uk]

I do have File::Temp. I'm running on Sun Solaris 8 with perl 5.6.1. Any
suggestions from the community would be greatly appreciated.

Thanks,


Anthony

-----Original Message-----
From: redwards at utmem.edu [mailto:redwards at utmem.edu]
Sent: 04 April 2003 18:14
To: Anthony.Underwood at phls.org.uk
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] Bio:Tools::Primer3, Bio::Seq::PrimedSeq, and
Bio::SeqFeature::Primer


I am glad that the modules help.

The problem is weird because $tempfile and $temphandle are created by
Root::IO, so this shouldn't be the only module that fails. Do you have
File::Temp installed on your system? (try perldoc File::Temp). What system
are you running on?

It seems that Root::IO is returning the filename but not the filehandle, and
I am not sure why. 

Perhaps others can weigh in with suggestions?

Rob

On Friday 04 April 2003 10:13 am, anthony.underwood at hpa.org.uk wrote:
> Dear Rob,
>
> Thankyou very much for putting together the primer3 modules for bioperl.
> They really are extremely useful. However I've run into a problem with the
> Run/Primer3.pm module
>
> At line 341
>  print $temphandle join "\n", @{$self->{'primer3_input'}}, "=\n";
>
> This doesn't produce any data in the temporary file and none of the test
> scripts work due to primer3 failing  However if I replace it with the text
> below then all tests work.
>
>
>  open (INPUT, ">$tempfile");
>  print INPUT join "\n", @{$self->{'primer3_input'}}, "=\n";
>  close INPUT;
>
>
> Is this is a setup problem with my machine?
>
> Thanks for our help,
>
>
> Anthony
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