I will modify the gff file as you mentioned and update galaxy.
Thanks a lot.
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
================================================
Le 29/10/2012 15:59, Jeremy Goecks a écrit :
Whatever the file type I set for the gff file (gff3, gff or gtf), I
get the transcript_id 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'
This was due to an incomplete feature. Turns out that GFF support
hadn't been included in feature search; I've added it in -central
changeset fa045aad74e9:
https://bitbucket.org/galaxy/galaxy-central/changeset/fa045aad74e90f16995e0cbb670a59e6b9becbed
Is the gff file not correct?
I believe there is an issue with your GFF: it is using non-standard
identifiers in the attributes (last) column. To the best of my
knowledge, 'name' is not a valid field for connecting features in GFF3
(which is my best guess for the file version), but your GFF uses this
field anyways.
To fix this issue, I replaced 'name' with 'ID' (which is compliant
GFF3) from the command line:
--
% sed s/name/ID/ ~/Downloads/test.gff > ~/Downloads/test_with_ids.gff
--
and this fixed the issue.
Finally, there is a sed wrapper in the toolshed should you want to do
this conversion in Galaxy:
http://toolshed.g2.bx.psu.edu/repository/browse_categories?sort=name&operation=view_or_manage_repository&f-deleted=False&f-free-text-search=sed&id=9652a50c5a932f3e
Best,
J.
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