[Bioperl-l] SeqIO out of memory

[Ewan Birney]

On Fri, 28 Feb 2003, Brian Osborne wrote:

> 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?
>

Probably means we have an introduced a cycle. Bugger it. (grrrr. Perl's
memory management)


- which version are you using?

- is there anything weird about the last entry that is printed/used?

- can you replicate it with a smaller file?




> ~/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.
>
>
>
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