The error suggests that Trackster thinks the dataset is in GTF format, not GFF
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.
23, 2012, at 9:08 AM, Yec'han Laizet wrote:
> 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):
> line 91, in
> 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 LAIZET
> 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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