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, J. On Aug 31, 2012, at 4:15 AM, Björn Grüning wrote:

Hi,

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?

Thanks! Bjoern

-- 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.gruening@pharmazie.uni-freiburg.de Web: http://www.pharmaceutical-bioinformatics.org/

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