[Bioperl-l] starts and ends of features

[Heikki Lehvaslaiho]

Hi Govind,

Check the modules in directory Bio/Location for explanation how
Bioperl handles this.

	-Heikki

"govind chandra (JIC)" wrote:
> 
> Hello,
> 
> I can get the start and end points of a feature by using $feature->start()
> and $feature->end() methods which I think are implemented in SeqFeatureI.
> Some features have a range like this <1..947 which means that the beginning
> of the feature lies beyond the beginning of the submitted sequence. Likewise
> some features are 9567..>10280 which means that the end of the feature lies
> beyond the end of the submitted sequence.
> 
> When I am getting features it is important know whether the feature lies
> completely within the specified range or extend beyond the range. The
> start() and end() methods return integers and get rid of any > or < marks
> that may be there. Which is probably the right thing to do considering that
> the integers may be used for extracting out subsequences. I would greatly
> appreciate some king of 'flag' to indicate whether the feature lies entirely
> within the range specified or extends beyond it. I would imagine something
> like the strand() method. A return value of 0 indicating that the feature is
> contained entirely within the range specified, 1 meaning it extends beyond
> the beginning of the range and -1 meaning it extends beyond the end of the
> range specified.
> 
> If a method already exists for the above I will greatly appreciate being
> made aware of it. Otherwise if someone (Ewan?) can provide a quick patch it
> will be great.
> 
> Bye
> 
> Govind
> (Govind Chandra)
> ScoDB, JIC
> Norwich
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     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
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