[Bioperl-l] Primer 3: MSG: Can't open RESULTS

[Greg Wilson]

Ok, I think I figured this out. The following line (***)  needs to be 
added to Bio/Tools/Run/Primer3.pm:

356 # make a temporary file and print the instructions to it.
357 my ($temphandle, $tempfile)=$self->io->tempfile;
358 print $temphandle join "\n", @{$self->{'primer3_input'}}, "=\n";
359 open (RESULTS, "$executable < $tempfile|") || $self->throw("Can't 
open RESULTS");
*** close $temphandle ||  $self->throw("Can't close TEMPFILE");

The temporary file never gets closed so the file descriptors just pile 
up until the overall script ends. This will clean them up as soon as we 
do not need them any more.

Not sure who needs to do the actual patching of the module in CVS though.

Greg


Gregory Drake Wilson wrote:
> I am resurrecting a question posted last June (archived here
> http://bioperl.org/pipermail/bioperl-l/2004-June/016255.html) regarding
> bioperl's usage of Primer3 because the issue continues to plague me. All
> of my implementations die reliably after a fixed number of attempts at
> generating primers with this error:
> 
> ------------- EXCEPTION  -------------
> MSG: Can't open RESULTS
> STACK Bio::Tools::Run::Primer3::run
> /usr/lib/perl5/vendor_perl/5.8.2/Bio/Tools/Run/Primer3.pm:360
> STACK toplevel ./primer_maker.pl:128
> 
> --------------------------------------
> 
> The offending line (360) is:
>   open (RESULTS, "$executable < $tempfile|") || $self->throw("Can't open
> RESULTS");
> 
> As the old thread suggests it is probably a numer of open files issue.
> 
> 
>>lsof -c pri +Lr
> 
> returns an ever increasing amount of entries like:
>  primer_ma 28830 gdw1  425u   REG    3,6     1140     0  807353
> /tmp/twdZa7turz (deleted)
> primer_ba 28830 drakos7  426u   REG    3,6     1170     0  807354
> /tmp/QDJv6Mb8iV (deleted)
> 
> Does anyone know a way to make sure those file descriptors are cleaned up
> after each primer generation?
> 
> Greg
> 
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