[Bioperl-l] Truncate sequence with features

Heikki Lehvaslaiho heikki at sanbi.ac.za
Fri Jun 9 03:35:12 EDT 2006


Roy,

The definitive document describing the locations is the feature table 
definition:

http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#3.5

but you probably know that already.


Two questions come to mind:

1. Can you parse your joint location using bioperl without errors?

2. Is there a practical advantage in including a location which has no 
relevance to the sequence in hand?

I notice that the /partial qualifier is deprecated and the docs suggest using 
</> signs to indicate that the sequence is partial, so I guess what you are 
doing is  correct.

	-Heikki

On Thursday 08 June 2006 18:31, Roy Chaudhuri wrote:
> 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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> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
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     _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
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