[Bioperl-l] phrap ace format parser?

[Jason Stajich]

We can parse in rudimentary Ace files with Bio::SeqIO using
Bio::SeqIO::ace but it doesn't read quality or anything other than raw
sequence right now.  However now that quality data can be handling with
Bio::Seq::PrimaryQual I think we should be able to adapt the ace parser to
do this - Brian perhaps this is where your routines could go?  The current
Bio::SeqIO::qual pulls the data from scf files I believe.  Chad correct me
if I'm missing something.

On Fri, 26 Jul 2002, Brian Desany wrote:

>
> >Does any know whether there is bioperl module to parse from or
> >to  phrap
> >ace output file? BTW, does anyone know the documentation of
> >this ace format?
>
> Documentation can be found at http://www.phrap.org, it's part of the consed
> documentation.
>
> I have cobbled together a module that parses Ace files, but it's not
> "bioperl-compliant" yet, in that coding style isn't up to snuff and there's
> site-specific code in it.
>
> I can send it to you off-list if you like, or you can wait until I get
> around to bioperl-ifying it (I don't have a timeframe for that).
>
> -Brian.
> --------------------------------------------
> Brian A. Desany, Ph.D.
> Dictyostelium Genome Sequencing Project
> Baylor College of Medicine
> bdesany@bcm.tmc.edu
> (713)798-5639
> http://www.dictygenome.org
> --------------------------------------------
>
>
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-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu