On Fri, Aug 12, 2011 at 2:45 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> On Fri, Aug 12, 2011 at 2:25 PM, Jeremy Goecks <jeremy.goe...@emory.edu> 
> wrote:
>>> Actual result: Red error against the gff file,
>>> Unspecified genome build, click the pencil icon in the history item to
>>> set the genome build
>>>
>>> The fact I'm using a FASTA file from my history should mean the genome
>>> build is irrelevant as that only applies to "locally cached genomes"
>>> (right?).
>>
>> Correct. Fixed in galaxy-central changeset 07de40a5a0b9
>>
>> Thanks,
>> J.
>
> Great. Could you try that example on the latest galaxy-central please?
> I have revision 06f0bca6de24 and get the following error using the
> steps given earlier:
>
> Traceback (most recent call last):
>  File 
> "/home/pjcock/repositories/galaxy-central/tools/extract/extract_genomic_dna.py",
> line 261, in
>    if __name__ == "__main__": __main__()
>  File 
> "/home/pjcock/repositories/galaxy-central/tools/extract/extract_genomic_dna.py",
> line 128, in __main__
>    chrom = feature.chrom
> AttributeError: 'Header' object has no attribute 'chrom'
>
> Thanks,
>
> Peter
>
> P.S. Perhaps you could apply this fix before tacking the above issue?
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-August/006366.html
> That would save me having to merge it after the trunk changes.
>

I think I've found another problem in exploring possible workarounds,

1. Goto http://usegalaxy.org (or a local Galaxy running galaxy-dist or
galaxy-central)

2. Import this GFF3 file,
ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Nanoarchaeum_equitans_Kin4_M_uid58009/NC_005213.gff

3. Click on the pencil for this dataset to "Edit Attributes"

4. Under "Convert to new format", "Convert GFF to Interval Index", convert

Expected result:
New interval file

Actual result:

Traceback (most recent call last):
  File 
"/home/pjcock/repositories/galaxy-central/lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py",
line 39, in
    main()
  File 
"/home/pjcock/repositories/galaxy-central/lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py",
line 26, in main
    for feature in list( reader_wrapper ):
  File 
"/home/pjcock/repositories/galaxy-central/lib/galaxy/datatypes/util/gff_util.py",
line 213, in next
    group = interval.attributes.get( 'group', None )
AttributeError: 'Comment' object has no attribute 'attributes'

On the bright side, convert to BED seems to work.

Let me know if you want me to file bugs for these issues since
that seems to be the new policy - email first, then file bug.
Personally I fear that risks issues being forgotten about and
never being filed, but we'll see.

Peter

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