[Bioperl-l] SeqIO out of memory

[Brian Osborne]

Bioperl-l,
Check out this one-liner, where the input file is rscu.gbff, a
Genbank-formatted file with 111,220 entries. The fasta file that's made
contains only 42,451 entries. Is "Out of memory" the expected result for an
input file this size?

~/data/refseq>perl -e 'use Bio::SeqIO; $in =
Bio::SeqIO->new(-file=>"rscu.gbff",
-format=>"genbank"); open MYOUT,">rscu.fa"; while ( $seq =
in->next_seq ){ print
 MYOUT ">" . $seq->accession_number . "\n" . $seq->seq . "\n"; }'

Out of memory during "large" request for 33558528 bytes, total sbrk() is
3822837
76 bytes at /usr/lib/perl5/site_perl/5.8.0/Bio/Seq/RichSeq.pm line 114,
<GEN0> l
ine 6433958.

Brian O.