[Bioperl-l] Bio::Location::Fuzzy, Bio::Location::Split

[Ewan Birney]

On Thu, 25 Jan 2001, Jason Stajich wrote:

> On Wed, 24 Jan 2001, Hilmar Lapp wrote:
> 
> > Jason Stajich wrote:
> > > 
> > > I'd just like to reiterate - beware bioperl-live is development code.
> > > 
> > > I added these handlers for Fuzzy and Split features.  I decided to create
> > > methods start_fuzzy,end_fuzzy for Bio::Location::Fuzzy to handle whether
> > > or not we saw the <, > descriptors.  I probably need some more test cases
> > 
> > I may have missed the obvious solution, but how are we going to
> > distinguish 'unknown start/end' and 'somewhere in between'? That is,
> > '<150' meaning 'before position 150', making it non-obvious how to
> > return a minimal start, and '120.130' meaning it's between two known
> > positions. Will I have to test fuzzy_start() before I'm allowed to
> > safely call min_start()? (no, I don't want to suggest exceptions ...
> > :O)
> 
> Hmm, perhaps I was confused.  I thought Split Location would deal with
> min_start/max_end.  I believe fuzzy can have 3 qualities, a fuzzy start
> (<150..100) a fuzzy end (90..<100) and fuzzy 'range' (1.12) [for lack of a
> better word, suggestions welcome]. All 3 can be present in the same
> location so they have to be independent operators.   When you call
> start, it will return what it thinks is the start but you'll have to
> test to see if the range or the start is fuzzy ($loc->range_fuzzy ||
> $loc->start_fuzzy).  Perhaps that is too tedious?  I'd rather not throw an
> exception here, but can be persuaded.    

In my experience it is crucial to treat
join((<10..100),(200..300),(400..500>)) as a class of SplitLocation, not
as a class of FuzzyFeature.

The above syntax is the most used "fuzziness" and nearly everyone discards
the leading and trailing '<' '>' as it means "partial gene" with the
coordinates interpreted in a hard way.




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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
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