[Bioperl-l] Bioperl parser for PolyPhred?

[Jason Stajich]

Yee Man -

AFAIK no one has written one so you will probably have to roll your own.

We would be delighted to have you contribute it to Bioperl.

You might also look at PolyBayes as another potential automated SNP
calling system that Gabor Marth, Ian Korf and others worked on which uses
phred/phrap as part of the system.
 http://www.genome.wustl.edu/groups/informatics/software/polybayes/

-jason

On Mon, 8 Dec 2003, Yee Man Chan wrote:

> Thanks for your reply, Chris. I am aware of this phrap module. However, it
> only parses phred output but not polyphred output. Phred is a base calling
> program whereas PolyPhred is a SNP identification program. They are quite
> different in terms of purposes. However, they do share very similar
> structure in terms of output. If there is not such a module, maybe I can
> write one and contribute it back to bioperl.
>
> Regards,
> Yee Man
>
> On Mon, 8 Dec 2003, Christopher Milton wrote:
>
> > Yee,
> > --- Yee Man Chan <ymc at paxil.stanford.edu> wrote:
> > > Hi people
> > >
> > > 	My boss asked me to parse output generated by SNP identification
> > > program called PolyPhred (http://droog.mbt.washington.edu/PolyPhred.html).
> > > Is there a parser already in bioperl that can save me the pain of writing
> > > one?
> >
> > I use Search.CPAN.org to check for (Bio)Perl modules:
> > http://search.cpan.org/
> >
> > http://search.cpan.org/search?query=phred&mode=all
> > searching for "phred" got me
> > http://search.cpan.org/~birney/bioperl-1.2.3/Bio/Assembly/IO/phrap.pm
> >
> > which is part of the standard BioPerl distribution.
> >
> > Chris Milton
> >
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu