[Bioperl-l] BioPerl and quality files

Chris Fields cjfields at uiuc.edu
Thu Jun 29 10:55:16 EDT 2006

> Recently I was working on a project which required some manipulation of
> Quality files. I may be wrong in this, but I don't believe that there is
> a Quality format for Bio:SeqIO. If there is, someone could point me in
> the right direction as I could write a much nicer script then what I
> currently have, if not I was wondering if anyone here has any use for
> such a thing. I am pretty new to developing but would be willing to give
> it a shot, as I feel that for all the use I get out of BioPerl with no
> thanks to anyone who spent time on writing something I used, I could try
> and contribute my limited amount. Any comments would be appreciated, and
> don't be afraid to tell me this is a lost cause. I realize that quality
> files tend to be less important than FASTA sequence files. I will give
> you a little information on me so that you know what to expect/what I am
> working with.

Here's a list I dredged up when looking for Bio::Seq::Quality in BioPerl,
which is the sequence implementation for sequences with quality data and/or
trace values:

Instances: 2    Module : Bio::Assembly::Contig
Instances: 2    Module : Bio::Assembly::IO::ace
Instances: 1    Module : Bio::Assembly::Singlet
Instances: 1    Module : Bio::Index::Fastq
Instances: 2    Module : Bio::Seq::Meta::Array
Instances: 1    Module : Bio::Seq::MetaI
Instances: 8    Module : Bio::Seq::Quality
Instances: 1    Module : Bio::Seq::SeqWithQuality
Instances: 6    Module : Bio::Seq::SequenceTrace
Instances: 1    Module : Bio::Seq::TraceI
Instances: 2    Module : Bio::SeqIO::abi
Instances: 2    Module : Bio::SeqIO::ctf
Instances: 2    Module : Bio::SeqIO::exp
Instances: 10   Module : Bio::SeqIO::fastq
Instances: 5    Module : Bio::SeqIO::phd
Instances: 5    Module : Bio::SeqIO::qual
Instances: 3    Module : Bio::SeqIO::raw
Instances: 13   Module : Bio::SeqIO::scf
Instances: 2    Module : Bio::SeqIO::ztr

Does that help?

> I am a fourth year bioinformatics student, and am currently working as a
> summer student. I have some limited experience with writing perl modules
> and test scripts. Mostly I write perl to do specific jobs, that I or
> someone else has come up with to fill some immediate need of the
> company. I am interested in most things bioinformatics/computer
> sci/biology and am hoping to do Graduate studies when I finish my
> degree.
> Well that's enough for now, if you have any comments/suggestions I would
> appreciate it.

Always can use an extra hand!


> Cheers, Wayne
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