[BioRuby] Parse big PDB use up all memory

[Yen-Ju Chen]

I did a quick test and found the problem is that I ran it in irb.
If I run it in script, like 'ruby test.rb', then it works fine.

Yen-Ju

On Dec 12, 2007 8:50 PM, Yen-Ju Chen <yjchenx at gmail.com> wrote:
> 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
> >
> >
> >
>