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

[Mingyi Liu]

BTW, here's the syntax in one of my messages last year about how to 
convert the compressed binary ASN format NCBI provides to the text ASN 
format my module (or Stefan's SeqIO::entrezgene) expects (the -x switch 
does the trick, overwriting the default option to produce XML output):

my $parser = Bio::ASN1::EntrezGene->new('file' => "gene2xml -i Homo_sapiens.ags.gz -c -x -b | "); # Homo_sapiens.ags.gz is the gzipped binary file directly downloaded from NCBI

Same syntax should be used when you're using SeqIO (thus SeqIO::entrezgene).

BTW, text ASN is both smaller and faster to parse than XML format.

Best,

Mingyi