[Bioperl-l] phrap ace format parser?

[Andreas Matern]

For now, why not just use:  Bio::Tools::Alignment::Consed ?

Brian Desany wrote:
> I agree Jason, it has been on my to-do list for a while. I'll keep you
> posted on progress - now that we're talking about this again it'll get done
> faster :)
> 
> 
>>-----Original Message-----
>>From: Jason Stajich [mailto:jason@cgt.mc.duke.edu]
>>Sent: Friday, July 26, 2002 11:36 AM
>>To: Brian Desany
>>Cc: 'Lu, Hong'; bioperl-l@bioperl.org
>>Subject: RE: [Bioperl-l] phrap ace format parser?
>>
>>
>>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
>>>--------------------------------------------
>>>
>>>
>>>_______________________________________________
>>>Bioperl-l mailing list
>>>Bioperl-l@bioperl.org
>>>http://bioperl.org/mailman/listinfo/bioperl-l
>>>
>>
>>--
>>Jason Stajich
>>Duke University
>>jason at cgt.mc.duke.edu
>>
>>
> 
> 
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-- 
--------------
Andreas Matern
Bioinformatician
Bioinformatics - Research and Development
Lion Bioscience Research Inc.
141 Portland Street, 10th floor
Cambridge, MA 02139  USA
Phone: 617-245-5483
Fax: 617-245-5499
amatern@lbri.lionbioscience.com
www.lionbioscience.com