[Bioperl-l] Possible memory leak in Bio::SeqFeature::Gene::GeneStructure?

[Stefan Kirov]

Oops, actually Bio::SeqFeature::Gene::Transcript::parent does not allow 
as it is undef.... Either should be fixed ot DESTROY needs to directly 
undef $transcript->{parent}.

Hilmar Lapp wrote:

> Those modules probably can use some serious review. If there is a 
> cycle then Jason should be on the right path with overriding DESTROY, 
> but first one would need to know where the cycle is. I don't recall 
> one being there on purpose ...
>
> Sorry to not be of more help ...
>
>     -hilmar
>
> On Tuesday, March 29, 2005, at 01:14  PM, Stefan Kirov wrote:
>
>> I am working on the Entrezgene parser and tried to use 
>> Bio::SeqFeature::Gene::GeneStructure to describe NC/NT to NM and NP 
>> relationships. I am pretty much done with the parser (based on Mingyi 
>> Liu low lovel parser), but once I tried to parse a whole file (Homo 
>> sapiens) I ran out of memory. I think the problem might be 
>> Bio::SeqFeature::Gene::GeneStructure::add_Transcript.
>> Here is the code which I used to simulate the problem and the 
>> resulting report file. It seams adding Bio::SeqFeature::Gene::Exon to 
>> Bio::SeqFeature::Gene::Transcript do not contribute to the problem.
>> Any suggestions?
>> Stefan
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>> 6620    6650
>> use Bio::SeqFeature::Gene::Exon;
>> use Bio::SeqFeature::Gene::Transcript;
>> use Bio::SeqFeature::Gene::GeneStructure;
>> use strict;
>> use Devel::Cycle;
>>
>> my ($prevmem,$growth,$first);
>> for my $k (1..100) {
>> open (FREE, "free -m|");
>> my $buf=<FREE>;
>> my $buf=<FREE>;
>> my ($x1,$x2,$mem,$x3)=split(/\s+/,$buf,4);
>> if ($prevmem) {
>>     $growth+= $mem-$prevmem;
>>     print "Simulation $k\t$growth","MB\n";
>> }
>> else { $first=$mem;}
>> $prevmem=$mem;
>> for my $i (1..20) {
>> my $gstruct=new Bio::SeqFeature::Gene::GeneStructure;
>> for my $n (0..3) {
>> my $transcript=new 
>> Bio::SeqFeature::Gene::Transcript(-primary=>'memleak'.$n,
>>                                           
>> -start=>1,-end=>2000,-strand=>, -desc=>'test for memmory leaks');
>>
>>
>> foreach my $e (1.10) {
>>     my $exonobj=new 
>> Bio::SeqFeature::Gene::Exon(-start=>$e*10,-end=>$e*10+9,-strand=>1);
>>     $transcript->add_exon($exonobj);
>> }
>> $gstruct->add_transcript($transcript);
>> }
>> }
>> }
>> print 
>> "$first\t$prevmem\n";_______________________________________________
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>

-- 
Stefan Kirov, Ph.D.
University of Tennessee/Oak Ridge National Laboratory
5700 bldg, PO BOX 2008 MS6164
Oak Ridge TN 37831-6164
USA
tel +865 576 5120
fax +865-576-5332
e-mail: skirov at utk.edu
sao at ornl.gov

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And all these things are swept aside"