[Bioperl-l] ABI file parsing

[Lincoln Stein]

I don't think that we should namespace via graphics file format,
because it should someday be possible to have the same layout module
produce GD, SVG and postscript output (it's really a matter of
encouraging the ensembl folk to turn their GD/SVG/PS/WBMP wrapper into
a CPAN module).  I would prefer a namespace based on what the layout
module is trying to draw:

       Bio::Graphics::FeatureMap
       Bio::Graphics::Chromatogram
       Bio::Graphics::Pedigree

etc

Lincoln

Heikki Lehvaslaiho writes:
 > Malay,
 > 
 > I tried to have a look at the your modules at CPAN, but could not find them
 > there yet.  Could  you consider submitting your code into BioPerl instead? 
 > If you have generic SGV code ready I am sure we can come up with other uses
 > of it.
 > 
 > In more general terms:
 > 
 > We have a separate bioperl-gui CVS repository which gives you a cmplete TK
 > based user interface. Lincold has already committed code using GD to draw
 > genome pictures. Jason has written Pedigree modules, again using GD, to draw
 > family pedigrees.
 > SGV is getting more and attractive choice of graphics and now you have
 > written code to draw the cromatograms.
 > 
 > In my opinion we should have a namespace for generating Bio related
 > graphics, e.g.:
 > 
 > Bio::Graphics
 > Bio::Graphics::GD
 > Bio::Graphics::SGV
 > ...
 > 
 > If these different graphics formats objects end up using same objects, the
 > interfaces would be e.g Bio::Graphics::ChromosomeI
 > 
 > There should be standards for calling these drawing modules and so on...
 > 
 > 
 > 	-Heikki
 > 
 > 
 > 
 > Malay wrote:
 > > 
 > > I could not wait and I am not sure whether my effort
 > > was in vain(read reinventing the wheel) or not but I
 > > have written ABI.pm which can parse an ABI file. It
 > > can give the sequence and raw traces.
 > > 
 > > By the way, the module was written for my BioSVG set
 > > of modules and BioSVG now can generate chromatograms
 > > in SVG format. "BioSVG::ABI" uses ABI.pm to extract
 > > the ABI traces to draw the cromatograms.
 > > 
 > > Both these modules will be available from CPAN.
 > > 
 > > Regards,
 > > 
 > > Malay
 > > 
 > > --- Peter Kos <kos@rite.or.jp> wrote:
 > > > Hi,
 > > >
 > > > > Before I go ahead and write a module, has anyone
 > > > > written a module for parsing ABI chromatogram
 > > > file?
 > > > Once I was considering that but ABI somehow refused
 > > > to give me the specification.
 > > > Now I use a stone-age solution, so I would be
 > > > interested
 > > > if you have/find something better.
 > > >
 > > > Be aware, however, that phred usually provides a
 > > > better
 > > > base-calling, so you might want to pass your ABI
 > > > files
 > > > through phred first, if it is OK at your site. And
 > > > phred
 > > > can write scf files which have been already dealt
 > > > with in
 > > > Bioperl, if I am right.
 > > >
 > > > Good luck
 > > > Peter
 > > >
 > > 
 > > __________________________________________________
 > > Do You Yahoo!?
 > > Yahoo! Health - your guide to health and wellness
 > > http://health.yahoo.com
 > > _______________________________________________
 > > Bioperl-l mailing list
 > > Bioperl-l@bioperl.org
 > > http://bioperl.org/mailman/listinfo/bioperl-l
 > 
 > -- 
 > ______ _/      _/_____________________________________________________
 >       _/      _/                      http://www.ebi.ac.uk/mutations/
 >      _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
 >     _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
 >    _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
 >   _/  _/  _/  Cambs. CB10 1SD, United Kingdom
 >      _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
 > ___ _/_/_/_/_/________________________________________________________
 > _______________________________________________
 > Bioperl-l mailing list
 > Bioperl-l@bioperl.org
 > http://bioperl.org/mailman/listinfo/bioperl-l

-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
Positions available at my lab: see http://stein.cshl.org/#hire
========================================================================