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

[Greg Wilson]

Ok, I see that CVS revision 1.4 back in Jul 2004 has the change.

I have bioperl-run 1.4 installed (and bioperl 1.5). This may just be a 
linux distro issue that I need to sort out.

Sorry for not checking CVS first.

Greg


Jason Stajich wrote:
> What version of bioperl-run are you on - this looks to already be  fixed 
> in CVS.
> 
> -jason
> On May 12, 2005, at 11:11 AM, Greg Wilson wrote:
> 
>> 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
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