[Bioperl-l] Bio::SeqFeature->feature_seq

[Ewan Birney]

On Tue, 10 Sep 2002, Hilmar Lapp wrote:

> Sounds good.
>
> To tell you the truth I anticipate confusion about what $feat->seq()
> does and what $feat->feature_seq() would do, and why they don't always
> do the same, and when they actually do the same and when not. I'm still
> not 100% convinced that $feat->seq() shouldn't simply do what you
> describe for $feat->feature_seq(), even though the remote seq fetching
> is maybe too fancy for $feat->seq().

I am sure we will get confusion, but I *know* that some people are relying
on $feat->seq() provides extent-of-feature semantics. So... I don't know
what to do - break backward compatibility so that new users have an easier
learning curve or try to finesse new users with the right documentation to
the right function names.


More than happy to hear opinions, but I think we are in a bit of a bind...





>
> My $0.02.
>
> 	-hilmar
>
> > -----Original Message-----
> > From: Ewan Birney [mailto:birney@ebi.ac.uk]
> > Sent: Tuesday, September 10, 2002 11:09 AM
> > To: bioperl-l@bioperl.org
> > Subject: [Bioperl-l] Bio::SeqFeature->feature_seq
> >
> >
> >
> >
> > Here is the proposed spec for a new function on SeqFeatureI,
> > to provide more "magic" for the users.
> >
> > the main use case is to be able to get out the "cdna" from a join'd
> > embl/genbank record without too much horsing around.
> >
> >
> > Notice it does not throw on remote locations with no db. Thoughts?
> >
> >
> >   Title   : feature_seq
> >
> >   Usage   : $seq = $feature->feature_seq()
> >             $seq =
> > $feature_with_remote_locations->feature_seq($db_for_seqs)
> >
> >   Function: Provides a sequence of the feature which is the most
> >             semantically "relevant" feature for this
> > sequence. A default
> >             implementation is provided which for simple cases
> > returns just
> >             the sequence, but for split cases, loops over the
> > split location
> >             to return the sequence. In the case of split
> > locations with
> >             remote locations, eg
> >
> >             join(AB000123:5567-5589,80..1144)
> >
> >             in the case when a database object is passed in,
> > it will attempt
> >             to retrieve the sequence from the database
> > object, and "Do the right thing",
> >             however if no database object is provided, it
> > will generate the correct
> >             number of N's (DNA) or X's (protein, though this
> > is unlikely).
> >             This function is deliberately "magical"
> > attempting to second guess
> >             what a user wants as "the" sequence for this feature
> >
> >             Implementing classes are free to override this
> > method with their
> >             own magic if they have a better idea what the user wants
> >
> >   Args    : [optional] A Bio::DB::RandomAccessI compliant object
> >   Returns : A Bio::Seq
> >
> >
> >
> >
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> >
>