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

[Abhishek Pratap]

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> 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] On Behalf Of Abhishek Pratap
> > Sent: Tuesday, 6 January 2009 6:43 p.m.
> > To: 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/
> >
> > Chair
> > RSG-Worldwide
> > ISCB-Student Council
> > http://iscbsc.org/rsg
> >
> > www.bioinfosolutions.com
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
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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/

Chair
RSG-Worldwide
ISCB-Student Council
http://iscbsc.org/rsg

www.bioinfosolutions.com