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

Jason Stajich jason@chg.mc.duke.edu
Wed, 24 Jan 2001 18:44:06 -0500 (EST)

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 now we saw the <, > descriptors.  I probably need some more test cases
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.

So the checked in code will screw up the variation features, but
everything else seems to work.  I'd like to do a better job detecting the
feature location type from [.., ., ^] and use that to describe the
Location object better, but we have the case of '<' and '>' which are
technically fuzzy so I'm not sure how I really want to store these types
of locations.  Anyways, I'm not being very clear, so have a look, I know
there are areas of improvement, you too can help us make this a robust


Jason Stajich
Center for Human Genetics
Duke University Medical Center