Re: [Gmod-ajax] how I set multiple reference sequences

[Mitch S. <mit...@be...>]

On 08/07/2009 02:14 AM, du zhou wrote:
> Thank you for reply.
> Yes, it works. One more question is that can I set the refseq without
> fasta files of DNA sequences? In other word, can I use the GFF file
> only as refseq?
> I tried ”bin/prepare-refseqs.pl --gff
> docs/tutorial/data_files/volvox.gff3“, but it gave out "found no ref
> seqs at bin/prepare-refseqs.pl line 199.", and same happened when I
> tried "bin/prepare-refseqs.pl --gff
> docs/tutorial/data_files/volvox.gff3 --noseq"
> Thank you~

If you have a GFF file with sequence-region directives in it, you can
use that file with
bin/prepare-refseqs.pl --gff <file> --refs <comma-separated list of ref
seq names>

See the "Other Syntax" section of
http://www.sequenceontology.org/gff3.shtml
for details about sequence-region.

I'll document that better, and maybe add an example file to make it
easier to demonstrate how to use it. You're right that the example GFF
file that we currently have doesn't work for that use.

I added that functionality originally because I wanted it for testing,
but I'm interested in real use cases. Is there no sequence for your
organism? Or are your users just not interested in the sequence? What
data are you starting from, and what format is it in?

Regards,
Mitch