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
================================================
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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