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
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 LAIZET
Plateforme Genome Transcriptome
Tel: 05 57 12 27 75
Equipe Genetique
69 route d'Arcachon
33612 CESTAS

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