> 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.
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
