[Bioperl-l] BioPerl and quality files

Clarke, Wayne ClarkeW at AGR.GC.CA
Thu Jun 29 11:01:52 EDT 2006

Thanks Chris, 

I don't know how I didn't come up with this before. Can I use
Bio::SeqIO::qual as follows?

my $in = Bio::SeqIO->new(-file => $qual_file , -format => 'qual');

Cheers, Wayne

-----Original Message-----
From: Chris Fields [mailto:cjfields at uiuc.edu] 
Sent: Thursday, June 29, 2006 8:55 AM
To: Clarke, Wayne; bioperl-l at lists.open-bio.org
Subject: RE: [Bioperl-l] BioPerl and quality files

> Recently I was working on a project which required some manipulation
> Quality files. I may be wrong in this, but I don't believe that there
> 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
> 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
> and contribute my limited amount. Any comments would be appreciated,
> don't be afraid to tell me this is a lost cause. I realize that
> 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
> working with.

Here's a list I dredged up when looking for Bio::Seq::Quality in
which is the sequence implementation for sequences with quality data
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
> summer student. I have some limited experience with writing perl
> 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
> appreciate it.

Always can use an extra hand!


> Cheers, Wayne
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