[Bioperl-l] Re: [Root-l] new Bioperl bug tracking system

[Lars G. T. Jorgensen]

Jason Stajich <jason@cgt.mc.duke.edu> writes:

> > I just think it's a bit strange that I have to change my Sequence
> > object depending on my input size. It was the thing that confused me
> > the most when starting to use bioperl was the inheritens tree of a
> > sequence.
> >
> 
> You're more than welcome to propose a fix and we'll incorporate it.  It
> has to do with Bio::Seq implementation assuming you can fit all of the
> sequence into memory as a string.  This doesn't work for large sequences.
> If you want to create an object which can dynamically tell that it is
> taking up too much memory and then revert to a separate implementation
> which manages the sequence as a disk file we would glady see it
> implemented.  If this is something you need I urge you to write it or at
> least start it and see if others can help.
> 
> > But most of my problems might be caused by my lack of
> > insight into biology jargon...
> >
> Ask questions and we can try and help answer them.

Ok, whats a "live" sequence and what is a "rich" sequence. Is the
latter just a sequence taken from a database?

> > >
> > > ...confused...
> > >
> > >
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> > > Bioperl-l@bioperl.org
> > > http://bioperl.org/mailman/listinfo/bioperl-l
> > >
> > >
> >
> >

-- 
Mvh|Regards, Lars
System administrator     | Student 
Bioinformatics Centre    | Department of Computer Science  
University of Copenhagen | University of Copenhagen
http://www.binf.ku.dk    | http://www.diku.dk
When's the last time you used duct tape on a duct? -- Larry Wall