> 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):
> line 91, in
> 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:
> 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:
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