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

[Jason Stajich]

> 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.

> >
> > ...confused...
> >
> >
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> >
> >
>
>

-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu