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

[Hilmar Lapp]

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().

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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