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galaxy-genome-annotation / python-apollo

Python library for talking to Apollo API
MIT License
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if Shine Dalgarno is attached as evidence it gets rendered as an exon #48

Closed nathandunn closed 3 years ago

nathandunn commented 3 years ago

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: https://github.com/GMOD/Apollo/pull/2516

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

MoffMade commented 3 years ago

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

nathandunn commented 3 years ago

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 commented 3 years ago

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

image

image

nathandunn commented 3 years ago

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   .   +   .   owner=ndunn@me.com;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   .   +   .   owner=ndunn@me.com;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:

image

nathandunn commented 3 years ago

this should be working now: image