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

Cook, Malcolm MEC at Stowers-Institute.org
Mon Feb 23 12:51:04 EST 2004

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

So, should we rewrite those fragments in Bio::Tools:GFF as:
 $name = $feat->seq_id() || 'SEQ'



Malcolm Cook
Database Applications Manager, Bioinformatics
Stowers Institute for Medical Research 

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