Downloading GFF3 programmatically in Apollo

[Nathan Dunn]

For those of you using scripts to download GFF3 from sequences, I had a user ask about ways to do this programmatically over an entire sequence or organism (as opposed to indicating individual servers). 

I had a few answers that I thought I’d share, but all rely on using the existing web services:

1 - use arrow and / or the  python apollo library: https://pypi.org/project/apollo/  (useful for many automation scripts)

arrow io write_downloadable --export_type GFF3 Merlin2 

{

    "uuid": "1f805f46-3e30-4941-9032-192b1d6fecbc",

    "exportType": "GFF3",

    "seqType": "peptide",

    "format": "text",

    "filename": "Annotations.gff3"

}

arrow io download —output_format text 1f805f46-3e30-4941-9032-192b1d6fecbc > annotations.gff

2 -  Conversely, I have a shell and a groovy script that do this, as well:

https://github.com/GMOD/Apollo/tree/develop/docs/web_services/examples

From the groovy (install via https://sdkman.io/ ideally):

groovy get_gff3.groovy -ignoressl -organism Merlin2 -url http://demo.genomearchitect.org/Apollo-staging -username natha...@lbl.gov -password demo

I don’t hav a reciprocal example in a shell script, but “getGff3.sh” is close.  I’m sure you can adapt the groovy to do something similar. 

3 - Roll your own over the existing web services:

http://demo.genomearchitect.org/Apollo2/WebServices/

Specifically the IO and Annotation / getGff3 services. 

Cheers,

Nathan