[Bioperl-l] Truncate sequence with features
roy at colibase.bham.ac.uk
Thu Jun 8 12:31:10 EDT 2006
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
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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