[Bioperl-l] Out of memory errors running Bio::ASN1::EntrezGene against latest Homo_sapiens.ags file

[Mauricio Herrera Cuadra]

Hi Susan,

Bio::ASN1::EntrezGene is not part of the BioPerl distribution, even 
though it shares the same namespace and is used by BP. Maybe you'd want 
to contact Mingyi Liu who is the author of the module. for more info 
take a look here:

http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene/

Regards,
Mauricio.

Susan Wilson wrote:
> Hi,
> 
> I downloaded the latest ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ 
> ASN_BINARY/Mammalia/Homo_sapiens.ags.gz and ran gene2xml on it to  
> generate Homo_sapiens.xml which is 5821420628 bytes.  I cannot parse  
> this file with Bio::ASN1::EntrezGene, even on a machine with 256GB of  
> memory.  I get a simple "Out of memory" output even with the  
> following code:
> 
> #!/usr/bin/perl
> use strict;
> use Bio::ASN1::EntrezGene;
>    my $parser = Bio::ASN1::EntrezGene->new('file' =>  
> "Homo_sapiens.xml");
>    while(my $result = $parser->next_seq)
>    {
>    }
> 
> 
> 
> Thanks.
> Susan
> 
> 
> 
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-- 
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Genética
Unidad de Morfofisiología y Función
Facultad de Estudios Superiores Iztacala, UNAM