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

[Hilmar Lapp]

Looks like the way to go. -hilmar

On Monday, February 23, 2004, at 11:53  AM, Cook, Malcolm wrote:

> 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
>> -------------------------------------------------------------
>>
>>
>>
>
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>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------