[Bioperl-l] Question for Bio::SeqIO::scf.pm

[Hilmar Lapp]

Kwon Tae-Joon wrote:
> 
> 
> Nowadays, I made a perl code to treat the SCF files,
> not only the sequence info, but also the quality and sample info.
> 
> 
> Please let me know how can I contribute to bioperl with my SCF.pm module..
> 

Kwon,

I'm not sure who is maintaining the SCF module in BioPerl, and I must
admit that I'm even not familiar with the SCF format and its contents.
Having the quality values (do these express some sort of confidence for
each base call?) is certainly very useful.

In fact, I did this for Phred-produced quality files some time ago, and
my quick hack was to derive a class from Bio::Seq that knows about
quality values and handles these properly for calls to $seq->truncate()
and $seq->revcom(). I can commit this to the BioPerl development tree if
there are no better suggestions.

Maybe James can comment on this, too, and maybe you could post what you
have done so far, and we'll see how it fits in.

	Hilmar

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Hilmar Lapp                                email: hlapp@gmx.net
NFI Vienna, IFD/Bioinformatics             phone: +43 1 86634 631
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