Hello,

Is it possible to load a unique gff file with the annotations of several chromosomes for my custom build in one step (one gff file)?


With the current version of galaxy, it seems that I can load a gff file referring only to one chromosome. That's pretty tedious to load 43 gff files separatly for my custom build...

If I try, I get this error:

Traceback (most recent call last):
File "~/galaxy-dist/lib/galaxy/datatypes/converters/interval_to_fli.py", line 91, in
    main()
File "~/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 "~/galaxy-dist/lib/galaxy/datatypes/util/gff_util.py", line 389, in read_unordered_gtf
    feature = GFFFeature( None, intervals=intervals )
File "~/galaxy-dist/lib/galaxy/datatypes/util/gff_util.py", line 65, in __init__
    ( interval.chrom, self.chrom ) )
ValueError: interval chrom does not match self chrom: SAGS2 != SAGS1

Thanks

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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