use of seq_id. was: [Bioperl-l] Bio::Tools::GFF use of seqname

Hilmar Lapp hlapp at
Tue Feb 24 22:28:48 EST 2004

On Tuesday, February 24, 2004, at 01:55  AM, Dave Howorth wrote:

> Hilmar Lapp wrote:
>> Actually, $feat->can('seq_id') must be true at all times iff 
>> $feat->isa("Bio::SeqFeatureI"), so it's kind of superfluous to test 
>> for it.
> Where does this come from, please?  In the SeqFeatureI documentation 
> it says seq_id 'is an attribute such that you *can* store the ID' (my 
> emphasis).  You seem to be saying that if I'm creating a bunch of 
> (sub) features just so I can use Bio::Graphics, I must attach a seq_id 
> to each and every one.

I'm not saying anything about the value of the attribute. 
$feat->can('seq_id') will be true if you can call $feat->seq_id(), 
which you will always be able to since it's defined in 
Bio::SeqFeatureI. Whether that method returns garbage or something 
useful is another story. I'm not sure whether you have to set seq_id() 
to something meaningful in order to remain compatible with 
Bio::Graphics, but I'd guess you do. Lincoln?

> I have an inverse question that I haven't managed to find an answer to 
> yet. If I'm displaying these sub-features as segments, how can I 
> attach some text to the feature that will be displayed alongside each 
> individual segment?

This one is for Lincoln ...


> Thanks, Dave
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at
Hilmar Lapp                            email: lapp at
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757

More information about the Bioperl-l mailing list