[Bioperl-l] Truncate sequence with features

Roy Chaudhuri roy at colibase.bham.ac.uk
Thu Jun 8 12:31:10 EDT 2006

Hi all.

I've been playing around with a subroutine to truncate a sequence and 
adjust the coordinates of any features that overlap the specified 
region- something that according to the comments in 
Bio::Location::Simple has been abortively worked on in the past.

I've submitted the subroutine as an enhancement in Bugzilla. It's a bit 
hacky but works for what I needed it for. However I'm a bit unsure on 
the best way to deal with split locations where one of the sublocations 
is entirely outside the truncated region. My current method results in 
locations like:
join(1..500, >1000..>1000)

which is quite ugly and possibly invalid, but kind of makes sense. Does 
anyone know what would be the correct behaviour for this situation?

Dr. Roy Chaudhuri
Bioinformatics Research Fellow
Division of Immunity and Infection
University of Birmingham, U.K.


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