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

[Hilmar Lapp]

You mean replace can('seqname') by can('seq_id')?

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.

	-hilmar

On Monday, February 23, 2004, at 09:51  AM, Cook, Malcolm wrote:

> Dear Matthew, Ewan, et al1
>
> I see in three places in  Bio::Tools::GFF the following:
>
>   if( $feat->can('seqname') ) {
>        $name = $feat->seq_id();
>        $name ||= 'SEQ';
>    } else {
>        $name = 'SEQ';
>    }
>
> However, in Bio::SeqFeature::Generic we learn that
>
> 	$self->warn("-seqname is deprecated. Please use -seq_id
> instead.");
>
> So, should we rewrite those fragments in Bio::Tools:GFF as:
>  $name = $feat->seq_id() || 'SEQ'
>
> ??
>
> Thanks,
>
> Malcolm Cook
> Database Applications Manager, Bioinformatics
> Stowers Institute for Medical Research
>
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>
-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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