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

[Smithies, Russell]

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
=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================