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

Smithies, Russell Russell.Smithies at agresearch.co.nz
Tue Jan 6 15:36:27 EST 2009


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
> _______________________________________________
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