[Bioperl-l] feature additional tag order in GFF

[Ewan Birney]

On Fri, 18 Oct 2002, Jason Stajich wrote:

> Because of the way Bio::DB::GFF gets its info about a feature's name, it
> seems that it is best to have the 'Sequence' or 'Target' field first when
> loading GFF data into the db so it can determine the name of the feature
> properly (I'd also be happy to implement it so that the GFF tries to pull
> the data from a Target/Sequence field first before relying on the 1st
> field for that info -- Thoughts Lincoln?).
>
> Currently when writing out GFF strings for a feature (SeqFeature::Generic)
> we do foreach my $tag ( $feature->all_tags ) { .. } The order of the tags
> as determined by all_tags is just straight from keys
> %{$self->{_internal_hash}} so the order cannot be reliably determined
> either based on insert order or name.
>
> Does it make more sense to provide a Get/Set method
> my @tags = $feature->tag_order( \@tagnames )
> which allows us to specify the tag order (in the absence of being set we
> rely on the old way of just grabbing the hash keys).
>
> This has the side-effect of allowing one to NOT specify all of the tags in
> that tag_order list which would effectively allow one to filter the tags
> which are output -- which could be a good thing as with the blast2gff
> script I am finishing off, bitscore,percentid,fraction_identitical, etc
> are all stored as tags in the SeqFeature::Similarity object and we may not
> really want to see all of them as additional tags in the GFF extra tag
> section.
>
> Thoughts?  I've implemented a local tag_order to serve my own purpose just
> curious if people think this is a sensible broadly applicable method?

I think... this is sane, but I wonder if there is a cleaner solution than
this. ...



>
> -jason
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
>
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