[Bioperl-l] sub_SeqFeature written

[Ewan Birney]

On Fri, 30 Aug 2002, Michael Muratet wrote:

> Greetings All
> 
> I'm working on project in which a sub-feature would be very handy. I was
> working with Bio::SeqFeature::Generic and using the add_sub_SeqFeature
> method. It adds the subfeature and you can retrieve it, but when you
> write the sequence object out via SeqIO(... -file => 'EMBL') the
> subfeatures are not written to the file. Looking at embl.pm in SeqIO, it
> appears as though the hash containing subfeatures is never referenced
> and therefore never written. Did I miss something, or is this something
> that is yet to be implemented?


No ... it is a hang-up/screw up when we moved over to the location view of
composite features.


Hmmm. The relevant lines are in embl.pm at 558-587 (main trunk code). You
will need to put in a sub_SeqFeatures() call and then call
from_SeqFeature() code on each one. Easy enough to do, just a little
frustrating.



I'll file this as bug for 1.2






> 
> Thanks.
> 
> Mike
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