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

Hilmar Lapp lapp@gnf.org
Wed, 24 Jan 2001 16:36:29 -0800

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 ...

> to make sure we are really getting everything to work, but the test in
> t/SeqIO  test.genbank in genbank.out seem to work for most things except
> the  variation feature type which uses the operator 'replace'.  We'll have
> to define that in the FTHelper model, I didn't plan for it.

I'm not sure the 'replace' operator is still standard (i.e., allowed).
I seem to recall that it is no longer among the allowed operators, so
you might wish to double-check on NCBI's feature table grammar

Hilmar Lapp                            email: lapp@gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757