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 though... >> 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. Agreed. >> 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. OK. >>> 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... Thanks, Peter
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