[Biojava-l] Fasta & EMBL feature table parsing

Matthew Pocock mrp@sanger.ac.uk
Mon, 27 Nov 2000 17:20:21 +0000

Keith James wrote:

> >>>>> "Matthew" == Matthew Pocock <mrp@sanger.ac.uk> writes:
> I think we call fuzzy locations something different e.g.
> FT   fuzzy_3p        complement(130.140..2780)
> FT   fuzzy_both      123.130..789.796
> Thankfully, I have some Perl classes to deal with these and I'm going
> to ignore them.
> The < and > fuzziness is more important for us because they signify
> e.g. that there is more of the feature on an adjacent cosmid, or
> perhaps just 'beware incomplete CDS'. We sometimes use this to
> reconstitute bacterial genes across cosmid overlaps.
> Support for these would be great.

I have just checked in org.biojava.bio.symbol.FuzzyLocation which deals with
< and > locations (getMinFuzzy & getMaxFuzzy are the two properties). I
don't know how to handle the interval case (x.y rather than x..y) so I
intend to duck that untill absolutely necisary.

In an earlier post, there was a request for 'between' locations - I still
can't see how to do that cleanly, so I haven't added it yet.


> Keith
> --
> -= Keith James - kdj@sanger.ac.uk - http://www.sanger.ac.uk/Users/kdj =-
> The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA