[gt-users] method to either delete a child from a FeatureNode, or to update its type

[La Rota, Mauricio]

Thanks Gordon,

This did the job.  Thanks a second time for the explanation of how it works.

-M

> -----Original Message-----
> From: gt-users-bounces at genometools.org [mailto:gt-users-
> bounces at genometools.org] On Behalf Of Gordon Gremme
> Sent: Thursday, April 30, 2009 6:13 AM
> To: GenomeTools Users
> Subject: Re: [gt-users] method to either delete a child from a
> FeatureNode, or to update its type
> 
> Hi Mauricio,
> 
> > Is there a way to update the type of an already existing child feature?
> What about to remove it and recreate a correct one?
> 
> there wasn't any, but I just added a set_type method to the C lib and
> the python bindings ;-)
> I didn't need one before...
> 
> 
> >  I  am trying to correct the type for the wrongly labeled UTRs in the
> GFF files I am working with (I sent two sample GFF files yesterday in the
> thread "A series of questions regarding GenomeTools C and its Python
> interface")  and since I don't see a way to modify (or have access to) a
> FeatureNode's type with something like FeatureNode.setType() I was instead
> trying to remove the child node (with fn.__del__) and recreating a new one
> in its place.
> >
> > Of the two choices, it might be cleaner just o update the type.  The
> sample GFF contains some gene models for which the UTRs labels are
> reversed (5' should be 3' or viceversa).
> >
> > Please see my python function below where I was trying to take a pointer
> to the current child_feature, checking it and returning the same one if
> nothing needed updating or destroying it and recreating a new one.  See
> line annotated with "****"
> 
> Your code didn't work, because the feature iterator gives you new
> references during the traversal. I.e., fn.__del__() just deletes the
> new reference but leaves the traversed feature intact. You would have
> to modify the traversed feature (i.e., remove a child), but that isn't
> available in the Python bindings yet. In the C library I have a method
> which removes a leaf (i.e., a feature without any children), because
> in this case it is clear what to do.
> 
> But in your case, just using set_type is the better solution anyway.
> 
> Gordon
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