I've fixed this in -central changeset 0e3ecd0ea818 with a bit of refactoring
amongst the GFF, GFF3, and GTF datatypes.
Thanks for reporting the issue,
On Aug 31, 2012, at 4:15 AM, Björn Grüning wrote:
> i have found a small problem in gff_filter_by_attribute and not sure how
> to fix it properly.
> gff_filter_by_attribute.xml accepts gff data types but crashes if you
> run it with gff. Because metadata.attribute_types is not defined for gff
> and the dictionary is empty. For gtf files it works, because gtf has
> metadata.attribute_types defined.
> Should we extend the gff data type to also set metadata.attribute_types
> or is it for some reason better to create a gff<->gtf converter and
> chance gff_filter_by_attribute.xml to only accept gtf files?
> Björn Grüning
> Albert-Ludwigs-Universität Freiburg
> Institute of Pharmaceutical Sciences
> Pharmaceutical Bioinformatics
> Hermann-Herder-Strasse 9
> D-79104 Freiburg i. Br.
> Tel.: +49 761 203-4872
> Fax.: +49 761 203-97769
> E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de
> Web: http://www.pharmaceutical-bioinformatics.org/
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