[Bioperl-l] Trace files and trace points

[Lincoln Stein]

Great work!

Lincoln
On Wednesday 10 July 2002 08:00 pm, Aaron J Mackey wrote:
> I have absolutely no use for trace data (peak height and peak indices and
> all that jazz), but I'm sure others who do have a list of "usual
> operations" they expect to be able to do (Chad's scf module already
> provides a useful baseline to start out with).  Like the PrimaryQual
> object, these would need to be tightly bound to their underlying sequence
> (and altering the sequence itself should be a runtime error, IMHO).
>
> I'm going to punt on this until someone begs for it at BOSC; it'll be
> trivial to add to the read/write routines (since the io_lib is doing all
> the grunt work) when we have a place to put the data.
>
> -Aaron
>
> P.S. Thanks to Robson de Souza, I now have some abi files, and SeqIO::abi
> works (again, for input only - no output).  Still looking for these
> mysterious 'ALF' format files ...
>
> On Wed, 10 Jul 2002, Jason Stajich wrote:
> > Way cool stuff Aaron.  I think this will be very very useful.  I like the
> > idea of Seq::Trace object.  When you get to thinking about building one,
> > can you send out a list of methods you think it would need - this is
> > mostly for my edification about how one might want to design a trace
> > object.
> >
> > -jason
> >
> > On Wed, 10 Jul 2002, Aaron J Mackey wrote:
> > > So the other large chunk of data in a trace file besides the quality
> > > values are the trace point data.  Chad's scf.pm module is storing them
> > > in the io object (not in the Seq object itself) (which of course makes
> > > writing an SCF file with peak info a bit difficult - maybe I've
> > > misunderstood something there).  Regardless, do we want to just trash
> > > this info for now, put it in a data field of the seq object, or make a
> > > Seq::Trace object to hold them (and potentially do interesting stuff
> > > with it?) ... we don't have to answer this immediately, but until we
> > > do, 'ctf' format output won't work (as it requires trace info).
> > >
> > > And, I've found that the io_lib routines don't write 'abi' or 'alf'
> > > (multi-seq abi format) formats (and also no 'ctf' unless trace info is
> > > available, as I said above).  Everything else is ready to go, just
> > > putting finishing touches on make test (100 tests!) and whatnot.
> > >
> > > -Aaron

-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
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