Yes, you should be able to use a single GFF for the complete genome.
This error stems from the same issue as before, namely that Galaxy is treating
your GFF file as GTF.
If you think your GFF is well formatted and there is an issue with Galaxy's
handling of GFF, please send me your GFF and I'll take a look.
Best,
J.
On Oct 23, 2012, at 9:24 AM, Yec'han Laizet wrote:
> 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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