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

Mingyi Liu mingyi.liu at gpc-biotech.com
Fri Oct 12 15:06:25 EDT 2007


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


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