On Thursday, August 18, 2011, Jeremy Goecks <jeremy.goe...@emory.edu> wrote:
>> I'm picturing select parameter for FASTA output,
>> Name features using:
>> * build, reference, co-ordinates and strand (default)
>> * name from annotation file (if present)
>> * reference name (useful if working on gene/proteins)
> Agreed.

Great - I may not be able to work on this immediately

>> If name is selected, then a conditional text parameter for
>> GFF type files would be shown to ask which tag(s) to use
>> as the name - a command separated list might work well:
>> http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-August/006432.html
> Yes, this is a limitation of the current Galaxy framework
> but should be able to be implemented without too much trouble.
>> This could default to ID for GFF3, and transcript_id,gene_id
>> for GTF, and whatever else is sensible for GFF2. Or a single
>> default suitable for all: ID,transcript_id,gene_id
>> Maybe we don't need the tag setting to be optional, just
>> hard code it to something like ID,transcript_id,gene_id?
> As a first step, hardcoding is fine.


>> Is it acceptable for the file format conversion tools in Galaxy
>> to have parameters? In this case, a list of tags to use as the
>> feature name, e.g. ID, transcript_id, gene_id
> Not that I know of because Galaxy assumes conversions
> can be done automatically as needed.


>>> Finally, note that all changes made to any GFF code must
>>> work for GFF, GFF3, and GTF formats.
>> That makes life interesting... what are the major sources of
>> legacy GFF files within Galaxy (anything not GFF3)?
> Perhaps I spoke a bit too strongly here. I think that GTFs are
> the primary flavor of GFF files used in Galaxy, and these are
> acquired from UCSC and Ensembl. GFF3 also seem to be
> used quite frequently as well, especially for folks working
> with bacteria and other simple organisms. GFF 2.2 and
> earlier aren't seen much as best I know.

Interesting - thank you!

> So let me rephrase and say that any changes need to be
> compatible with GTF and GFF3.

OK - I'll focus on them.

Meanwhile back to the song-devel mailing list for more
GFF3 spec discussions on things like best practice
for protein annotation using GFF3...


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