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

[Lincoln Stein]

Bio::Graphics doesn't depend on a seq_id as far as I know.  Please let me know 
if you have evidence otherwise.

Lincoln


On Tuesday 24 February 2004 10:28 pm, Hilmar Lapp wrote:
> 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 ...
>
> 	-hilmar
>
> > Thanks, Dave
> >
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-- 
Lincoln Stein
lstein at cshl.edu
Cold Spring Harbor Laboratory
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