[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?

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

http://xbase.bham.ac.uk


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