[Bioperl-l] ABI file parsing

[Heikki Lehvaslaiho]

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
> >
> 
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-- 
______ _/      _/_____________________________________________________
      _/      _/                      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
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