[Bioperl-l] starts and ends of features

[govind chandra (JIC)]

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