[Bioperl-l] Re: SeqFeatureI::display_name

[Hilmar Lapp]

On Saturday, November 8, 2003, at 04:18  PM, Marc Logghe wrote:

> The returned persistent feature objects seem not to know about their 
> parent; I mean, the display_name is undef. What should I change to the 
> query in order to fill that slot ?
>

Display_name is not populated from some property of the parent 
bioentry; it is a property of the seqfeature (see also 
Bio::SeqFeatureI::display_name). Bioperl itself doesn't use the 
display_name property when you create those features from databank 
files via the SeqIO path. Only Bio::Graphics/Bio::DB::GFF uses it I 
think.

Maybe the GFF parser will populate it too, possibly only when reading 
GFF3? Does anybody know off hand?

So, for all features that were loaded into the database using a SeqIO 
parser the display_name property will be undefined.

Now, the other thing you're noticing is that the seqfeature adaptor 
will not automatically load the corresponding sequence and attach it to 
the feature. This is so that sequence object serialization does not 
enter a circular loop, because when storing sequences their features 
will be serialized too. Your way out is either to retrieve sequences 
from the query, not features, and then filter out those features you 
didn't want, or the code needs to be changed to allow that optionally 
the sequence is retrieved for each feature.

	-hilmar
-- 
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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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