[Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl

Tue Jan 6 22:49:42 UTC 2009

Sounds like a good plan but I wouldn't know where to start. 
That level of Perlyness is a bit beyond me  :-(

--Russell

> -----Original Message-----
> From: Chris Fields [mailto:cjfields at illinois.edu]
> Sent: Wednesday, 7 January 2009 11:13 a.m.
> To: Smithies, Russell
> Cc: 'Abhishek Pratap'; 'bioperl-l at lists.open-bio.org'
> Subject: Re: [Bioperl-l] Parser: Ace file (Sequence Assembly) in
> Bioperl
> 
> How about re-implementing Bio::Assembly classes so they simply map to
> Bio::DB::SeqFeature::Store (or similar) methods?  Scaffold could just
> be a wrapper around a Bio::DB::SeqFeature::Store (which can be BDB/
> mysql/postgresql/memory) and return Contigs.
> 
> Similarly, the IO classes could probably act as specialized
> Bio::DB::SeqFeature::Store::Loade classes for the database and just
> return the Scaffold instance.
> 
> chris
> 
> On Jan 6, 2009, at 3:31 PM, Smithies, Russell wrote:
> 
> > I agree with the need for a faster parser.
> > Although the current version does a great job, it is slow and memory
> > intensive as it loads everything into Bio::Assembly::Scaffold
> > objects composed of Bio::Assembly::Contig objects.
> > I'm not sure exactly what the best solution would be, perhaps a new
> > constructor with a named contig would simplify things?
> >
> >    $io = new Bio::Assembly::IO(-file=>"454_assy.ace",-format=>"ace");
> >
> >    $contig = $io->next_assembly_with_contig(-contig=>"Contig000100")-
> > >select_contig;
> >
> > Or do we even need a next_assembly method?
> > Can there be more than one assembly in an .ace file?
> >
> > --Russell
> >
> >
> >
> > From: Abhishek Pratap [mailto:abhishek.vit at gmail.com]
> > Sent: Wednesday, 7 January 2009 10:07 a.m.
> > To: Chris Fields
> > Cc: Smithies, Russell; bioperl-l at lists.open-bio.org
> > Subject: Re: [Bioperl-l] Parser: Ace file (Sequence Assembly) in
> > Bioperl
> >
> > Ok .. Sure in case we do write something which eventually I will
> > have to :)  I will fwd it.
> >
> > @Russel:
> >
> > I feel to get info for specific the current method is very slow as
> > it tries to store the info for all contigs into memory. Such info
> > could be memory intensive specially with the next gen data coming
> > from 454 sequencers. I think we should grep to the contig/s of
> > itnerest and then create a record for it. Please correct me if I am
> > wrong.
> >
> > Thanks,
> > -Abhi
> > On Tue, Jan 6, 2009 at 3:52 PM, Chris Fields
> <cjfields at illinois.edu<mailto:cjfields at illinois.edu
> > >> wrote:
> > Not at this time (write_assembly is not implemented).  If you come
> > up with code to do so let us know (patches are always welcome).
> >
> > chris
> >
> >
> > On Jan 6, 2009, at 2:43 PM, Abhishek Pratap wrote:
> > Thanks that helped.
> >
> > Any method to write Ace files ?
> >
> > Thanks,
> > -Abhi
> >
> > On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell <
> >
> Russell.Smithies at agresearch.co.nz<mailto:Russell.Smithies at agresearch.co
> .nz
> > >> wrote:
> > Here's how I've been doing it:
> >
> >
> > my $infile = "454Contigs.ace";
> > my $parser = new Bio::Assembly::IO(-file   => $infile ,-format =>
> > "ace") or
> > die $!;
> > my $assembly = $parser->next_assembly;
> >
> > # to work with a named contig
> > my @wanted_id = ("Contig100");
> > my ($contig) = $assembly->select_contigs(@wanted_id) or die $!;
> >
> > #get the consensus
> > my $consensus = $contig->get_consensus_sequence();
> >
> > #get the consensus qualities
> > my @quality_values  = @{$contig->get_consensus_quality()->qual()};
> >
> > hope this helps,
> >
> > Russell
> >
> > -----Original Message-----
> > From: bioperl-l-bounces at lists.open-bio.org<mailto:bioperl-l-
> bounces at lists.open-bio.org
> > > [mailto:bioperl-l-<mailto:bioperl-l->
> > bounces at lists.open-bio.org<mailto:bounces at lists.open-bio.org>] On
> > Behalf Of Abhishek Pratap
> > Sent: Tuesday, 6 January 2009 6:43 p.m.
> > To: bioperl-l at lists.open-bio.org<mailto:bioperl-l at lists.open-bio.org>
> > Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl
> >
> > Hi All
> >
> > I am looking for some code to parse the ACE file format. I have big
> > ACE
> > files which I would like to trim based on the user defined Contig
> name
> > and
> > specific region and write out the output to another fresh ACE file.
> >
> > For now I am trying to tweak Bio::Assembly::IO; but it is kind of
> > slow.
> > Any
> > other alternative or suggestions.
> >
> > Thanks All,
> > -Abhi
> >
> >
> >
> >
> >
> >
> >
> >
> > --
> > -----------------------------
> > Abhishek Pratap
> > Bioinformatics Software Engineer
> > Institute for Genome Sciences
> > School of Medicine, Univ of Maryland
> > 801, W. Baltimore Street, Baltimore, MD 21209
> > Ph: (+1)-410-706-2296
> > www.igs.umaryland.edu/<http://www.igs.umaryland.edu/>
> >
> > Chair
> > RSG-Worldwide
> > ISCB-Student Council
> > http://iscbsc.org/rsg
> >
> > www.bioinfosolutions.com<http://www.bioinfosolutions.com>
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> > --
> > -----------------------------
> > Abhishek Pratap
> > Bioinformatics Software Engineer
> > Institute for Genome Sciences
> > School of Medicine, Univ of Maryland
> > 801, W. Baltimore Street, Baltimore, MD 21209
> > Ph: (+1)-410-706-2296
> > www.igs.umaryland.edu/<http://www.igs.umaryland.edu/>
> >
> > Chair
> > RSG-Worldwide
> > ISCB-Student Council
> > http://iscbsc.org/rsg
> >
> > www.bioinfosolutions.com<http://www.bioinfosolutions.com>
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> >
> > --
> > -----------------------------
> > Abhishek Pratap
> > Bioinformatics Software Engineer
> > Institute for Genome Sciences
> > School of Medicine, Univ of Maryland
> > 801, W. Baltimore Street, Baltimore, MD 21209
> > Ph: (+1)-410-706-2296
> > www.igs.umaryland.edu/<http://www.igs.umaryland.edu/>
> >
> > Chair
> > RSG-Worldwide
> > ISCB-Student Council
> > http://iscbsc.org/rsg
> >
> > www.bioinfosolutions.com<http://www.bioinfosolutions.com>
> >
> > =
> >
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