[Bioperl-l] Bioperl parser for PolyPhred?

[Yee Man Chan]

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
>