[BioRuby] Parse big PDB use up all memory

[Yen-Ju Chen]

Thank you for the hint for retrieve only header.

I am using the default Ruby on Mac OS X 10.5.
Here is the output of 'ruby -v'

ruby 1.8.6 (2007-06-07 patchlevel 36) [universal-darwin9.0]

And bioruby is 1.1.0 from gems.

I will test it on Linux and see.

Yen-Ju

On Dec 12, 2007 7:49 PM, Alex Gutteridge <alexg at kuicr.kyoto-u.ac.jp> wrote:
> Hi,
>
> Could you give some more details on what system and ruby/bioruby
> version you are running? The same script uses less than 20MB on my
> machine (ruby 1.8.6 / bioruby 1.1.0 / ubuntu linux), which doesn't
> seem so bad. Also 1w6k is biggish, but there are certainly bigger PDB
> files out there so if you're having trouble with this one then others
> will certainly be a problem.
>
> In answer to your second question, yes you should be able to just
> extract the header (everything up to the ATOM records). But if you're
> really running out of memory just parsing that file then I suspect you
> have deeper issues. Anyway, the sample below works for me for parsing
> the header from 1w6k:
>
> require 'bio'
>
> serv = Bio::Fetch.new
> entry = serv.fetch('pdb','1w6k')
>
> header = ''
> entry.each do |l|
>    break if l.match(/^ATOM/)
>    header << l
> end
>
> pdb = Bio::PDB.new(header)
> p pdb.accession
>
>
> On 13 Dec 2007, at 10:54, Yen-Ju Chen wrote:
>
> > This is what I did:
> >
> > require 'bio'
> > serv = Bio::Fetch.new()
> > entry = serv.fetch('pdb', '1w6k')
> > pdb = Bio::PDB.new(entry)
> >
> > The last step use up all memory and quit.
> > The pdb file is quite big and I only need the information from header.
> > Is it possible to do something like this ?
> >
> > pdb = Bio::PDB.new(entry[0-40000])
> >
> > Thanx for the help
> > _______________________________________________
> > BioRuby mailing list
> > BioRuby at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioruby
> >
>
> Alex Gutteridge
>
> Bioinformatics Center
> Kyoto University
>
>
>