[Bioperl-l] Changes to Bio::SeqI broke Bio::Graphics

[Elia Stupka]

> We agree violently.  Everything is a feature and sequence is an attribute of 
> the feature.  BioPerl has it backward.

Same in GFD for that matter

Elia

> 
> Lincoln
> 
> On Tuesday 12 November 2002 04:01 pm, Matthew Pocock wrote:
> > Lincoln Stein wrote:
> > > This allows an
> > > entry to be a feature in a larger virtual sequence, such as a genome
> > > assembly.  I don't see why we persist in thinking in this flat-file EMBL
> > > entry way.
> > >
> > > Lincoln
> >
> > In BioJava we have a feature interface ComponentFeature with the two
> > important methods getComponentLocation() and getComponentSequence().
> > This indicates in an assembled sequence where you are to glue in bits of
> > other sequences. The ComponentFeatures location is where it is in the
> > assembly and the getComponentLocation is what region of
> > getComponentSeqeunce to insert there. This has many advantages over
> > making sequences features. Firstly, and most importantly, it allows us
> > to project a single sequence (or multiple portions of a single sequence)
> > into multiple assemblies (or different places in the same assembly). For
> > example, we can take the same clones and project them into multiple
> > versions of the human golden path. Translocations can trivialy be
> > represented by building one assembled sequence for the normal and
> > translocated chromosome, and the same underlying sequences can be used,
> > providing a benefit in both memory and integrity of the annotations. It
> > has many other benefits from the object modelling view of things,
> > allowing us to implement stuff via lazy proxies (portions of an assembly
> > don't need to be loaded untill you try to fetch data from them).
> >
> > I would caution against rolling the location of a sequene in a larger
> > assembly ino the sequence itself. At the very least, you are going to
> > need to publish a start and stop coordinate within the sequence that
> > gets projected. This whole line of modelling in our experience causes
> > problems rather than providing solutions.
> >
> > Matthew
> >
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> 

Elia

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