if Shine Dalgarno is attached as evidence it gets rendered as an exon

[nathandunn]

This is treated correctly coming form the UI (Canvas I think), but not using the load_gff3 script.

This fixed the initial drag up issue: GMOD/Apollo#2516

I think the JSON sent over is correct, but maybe mis-associated with the gene instead of the transcript.

[MoffMade]

Just confirmed on our workflows, any evidence that has an associated Shine Dalgarno is using a Canvas feature in the JBrowse/Apollo UI

[nathandunn]

Not sure if it will be related to this: https://github.com/GMOD/Apollo/issues/2144

However, it probably has to be that the Shine_dalgarno must be associated at the right level via the python-apollo manipulation.

[nathandunn]

Both dragging up and right-click adding with html and canvas produce the correct output:

[nathandunn]

Using: arrow annotations load_gff3 shinedalgarno2 test1.gff3 with gff3:

##gff-version 3
##sequence-region ACHIV102_cov_229.2 1 42452
ACHIV102_cov_229.2	.	gene	20958	22306	.	+	.	[email protected];ID=c2bdb72a-b116-43df-8ca4-fd07a8a46a7e;date_last_modified=2021-01-29;Name=ACHIV102_cov_229.2.orf00043;date_creation=2021-01-29
ACHIV102_cov_229.2	.	mRNA	20958	22306	.	+	.	[email protected];Parent=c2bdb72a-b116-43df-8ca4-fd07a8a46a7e;ID=14c936aa-a03a-42f5-b03c-9648aa9aa0c5;date_last_modified=2021-01-29;Name=ACHIV102_cov_229.2.orf00043-00002;date_creation=2021-01-29
ACHIV102_cov_229.2	.	Shine_Dalgarno_sequence	20958	20960	.	+	.	Parent=14c936aa-a03a-42f5-b03c-9648aa9aa0c5;ID=d6047ece-fa1e-4429-b9b4-b70c369a8006;Name=d6047ece-fa1e-4429-b9b4-b70c369a8006
ACHIV102_cov_229.2	.	exon	20969	22306	.	+	.	Parent=14c936aa-a03a-42f5-b03c-9648aa9aa0c5;ID=e02f1b38-e5c7-4d92-8d44-89d1599c756f;Name=e02f1b38-e5c7-4d92-8d44-89d1599c756f
ACHIV102_cov_229.2	.	non_canonical_three_prime_splice_site	20969	20969	.	+	.	Parent=14c936aa-a03a-42f5-b03c-9648aa9aa0c5;ID=14c936aa-a03a-42f5-b03c-9648aa9aa0c5-non_canonical_three_prime_splice_site-20968;Name=14c936aa-a03a-42f5-b03c-9648aa9aa0c5-non_canonical_three_prime_splice_site-20968
ACHIV102_cov_229.2	.	CDS	20969	22306	.	+	0	Parent=14c936aa-a03a-42f5-b03c-9648aa9aa0c5;ID=14c936aa-a03a-42f5-b03c-9648aa9aa0c5-CDS;Name=14c936aa-a03a-42f5-b03c-9648aa9aa0c5-CDS
###

transfer the shine_dalgarno into an exon:

[nathandunn]

this should be working now: