[Bioperl-l] ABI file parsing
Wed, 1 May 2002 23:20:09 -0400
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:
Heikki Lehvaslaiho writes:
> 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.:
> 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...
> 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 <email@example.com> 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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