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

Susan Wilson smwilson at hpc.unm.edu
Fri Oct 12 13:45:41 EDT 2007


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:

use strict;
use Bio::ASN1::EntrezGene;
   my $parser = Bio::ASN1::EntrezGene->new('file' =>  
   while(my $result = $parser->next_seq)


More information about the Bioperl-l mailing list