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

[Cook, Malcolm]

Actually, I mean replace the 6 lines with the single line:

 $name = $feat->seq_id() || 'SEQ'

>-----Original Message-----
>From: Hilmar Lapp [mailto:hlapp at gmx.net] 
>Sent: Monday, February 23, 2004 12:19 PM
>To: Cook, Malcolm
>Cc: Bioperl; birney at sanger.ac.uk; mrp at sanger.ac.uk
>Subject: Re: [Bioperl-l] Bio::Tools::GFF use of seqname
>
>
>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
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at portal.open-bio.org
>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>-- 
>-------------------------------------------------------------
>Hilmar Lapp                            email: lapp at gnf.org
>GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
>-------------------------------------------------------------
>
>
>