[Bioperl-l] Parsing fuzzy locations

Keith James kdj@sanger.ac.uk
15 Dec 2000 12:54:10 +0000

I have some code which does this, including an EMBL parser and generic
feature object which supports fuzzies. This aspect of parsing hasn't
been heavily tested and there are odd things it won't cope with

e.g. I discovered a couple of days ago that it balked at locations like


which cropped up in an E. coli EMBL entry. I'm in the process of
fixing that now.

I've also got some preliminary support for reverse-complementing and
sub-sequencing sequences with such features attached. Due to lack of
free time I've had to put aside plans to incorporate this into
Bioperl, but the Bio:PSU package and method documentation can be
obtained from





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