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