The error suggests that Trackster thinks the dataset is in GTF format, not GFF format.
Galaxy attempts to guess a format when a file is uploaded. If transcript_id and gene_id are present in the attributes column, Galaxy will assign it a GTF format. (In GTF format, attributes transcript_id and gene_id are required.) So far, this heuristic has worked well, but perhaps it's problematic in your case?
You can manually change the format of a dataset in the main Galaxy UI by clicking on the pencil icon next to a dataset, selecting the Datatype tab, and choosing GFF. Once you've changed the format to GFF, you should be able to view it in Trackster.
J.
23, 2012, at 9:08 AM, Yec'han Laizet wrote:
Hello,
when I try to load a gff file in trackster on a galaxy instance (ubuntu server), I get the following error:
Traceback (most recent call last): File "/home/pgtgal/galaxy-dist/lib/galaxy/datatypes/converters/interval_to_fli.py", line 91, in main() File "/home/pgtgal/galaxy-dist/lib/galaxy/datatypes/converters/interval_to_fli.py", line 30, in main for feature in read_unordered_gtf( open( in_fname, 'r' ) ): File "/home/pgtgal/galaxy-dist/lib/galaxy/datatypes/util/gff_util.py", line 375, in read_unordered_gtf transcript_id = line_attrs[ 'transcript_id' ] KeyError: 'transcript_id'
I guess it's because not all the lines in the file have a transcript_id. Is it a specification in gff file format?
I made it work by changing the line 65 of /home/pgtgal/galaxy-dist/lib/galaxy/datatypes/util/gff_util.py by this:
transcript_id = line_attrs.get('transcript_id' , 0)
You may want to change the default 0 value by something more pertinent... if it is really a bug and not a mistake from myself.
Best regards
Yec'han
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Yec'han LAIZET Ingenieur Plateforme Genome Transcriptome Tel: 05 57 12 27 75 _________________________________ INRA-UMR BIOGECO 1202 Equipe Genetique 69 route d'Arcachon 33612 CESTAS ================================================
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