[Bioperl-l] phrap ace format parser?

[Brian Desany]

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
>> --------------------------------------------
>>
>>
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>
>--
>Jason Stajich
>Duke University
>jason at cgt.mc.duke.edu
>
>