Dragging feature boundaries not working as expected for Shine-Dalgarno and CDS #2515

MoffMade · 2020-09-24T20:53:45Z

We're experiencing some issues dragging the boundaries on gene annotations called from evidence with both a Shine-Dalgarno_sequence and a CDS.

Gene with SD+CDS
- Shine Dalgarno boundary
  - Away from CDS > New Shine Dalgarno is created at new boundary separate from original gene feature
  - Towards CDS > Nothing, no logs
- CDS Boundary, nothing happens either way, error popup in UI with "Cannot get property 'id' on null object" and gets this error in logs

ERROR apollo.AnnotationEditorController  - CAUGHT ERROR through websocket call: java.lang.reflect.InvocationTargetException
ERROR apollo.AnnotationEditorController  - THROWING PARENT ERROR instead through reflection: java.lang.NullPointerException: Cannot get property 'id' on null object
ERROR apollo.AnnotationEditorController  - exception java.lang.NullPointerException: Cannot get property 'id' on null object
ERROR apollo.AnnotationEditorController  - exception message Cannot get property 'id' on null object
ERROR apollo.AnnotationEditorController  - username cory.maughmer@tamu.edu
ERROR apollo.AnnotationEditorController  - error destination message: /topic/AnnotationNotification/user/cory.maughmer@tamu.edu

Gene with no SD, only CDS works as expected
tRNA and terminator boundaries drag as expected

Screenshot of error:

This same error message appears when attempting to "split" a gene with both SD and CDS

The text was updated successfully, but these errors were encountered:

nathandunn · 2020-09-24T21:54:45Z

Can you right-click on the annotation and add the GFF3 for all components in there?

MoffMade · 2020-09-24T22:20:16Z

##gff-version 3
##sequence-region ACHIV102_cov_229.2 1 42452
ACHIV102_cov_229.2	.	gene	32061	32519	.	+	.	owner=meiliu@tamu.edu,cory.maughmer@tamu.edu;ID=1b3e7cb5-bb0a-4ce3-aaf7-367c2a51bdfa;date_last_modified=2020-09-23;Name=ACHIV102_cov_229.2.orf00066;date_creation=2020-09-01
ACHIV102_cov_229.2	.	mRNA	32061	32519	.	+	.	owner=cory.maughmer@tamu.edu;Parent=1b3e7cb5-bb0a-4ce3-aaf7-367c2a51bdfa;ID=f3831d22-8c02-4524-ad1d-2f1965e87696;orig_id=ACHIV102_cov_229.2.orf00066;date_last_modified=2020-09-23;Name=ACHIV102_cov_229.2.orf00066-00002;date_creation=2020-09-23
ACHIV102_cov_229.2	.	exon	32073	32519	.	+	.	Parent=f3831d22-8c02-4524-ad1d-2f1965e87696;ID=ea90c5ba-3525-4566-83f0-6b419b344e99;Name=ea90c5ba-3525-4566-83f0-6b419b344e99
ACHIV102_cov_229.2	.	CDS	32073	32519	.	+	0	Parent=f3831d22-8c02-4524-ad1d-2f1965e87696;ID=f3831d22-8c02-4524-ad1d-2f1965e87696-CDS;Name=f3831d22-8c02-4524-ad1d-2f1965e87696-CDS
ACHIV102_cov_229.2	.	Shine_Dalgarno_sequence	32061	32068	.	+	.	Parent=f3831d22-8c02-4524-ad1d-2f1965e87696;ID=0bdce2de-0d43-4ec3-a149-51b4cc60dad3;Name=0bdce2de-0d43-4ec3-a149-51b4cc60dad3
###

This is the GFF for the specific example in the screenshot but it's happening across most organisms we've created since the update to 2.6.1

nathandunn · 2020-09-25T15:57:03Z

@MoffMade I'm not seeing it initially, but I'm sure I don't have the same setup.

Can you email me a tarball of the jbrowse directory you are using so I can emulate it. If you could also indicate from which track and how you generated the annotation, that would be helpful.

I'm assuming you are running off of the latest.

MoffMade · 2020-09-25T16:15:58Z

Sure thing, let me pull it and I'll send it your way. We're running a fork of 2.6.1 with a couple of docker changes and css modifications.

This issue is occurring on features promoted to gene annotations from any of the tracks that have both a Shine-Dalgarno and a Exon/CDS

nathandunn · 2020-09-28T18:04:10Z

Should be noted that the GFF3 I get is fairly similar, with nothing of note incorrect:

##gff-version 3
##sequence-region ACHIV102_cov_229.2 1 42452
ACHIV102_cov_229.2	testing	gene	20958	22306	.	+	.	owner=ndunn@me.com;ID=40b1041e-fe11-4d43-85a9-f4001dfbfbe9;date_last_modified=2020-09-25;Name=ACHIV102_cov_229.2.orf00043;date_creation=2020-09-25
ACHIV102_cov_229.2	testing	mRNA	20958	22306	.	+	.	owner=ndunn@me.com;Parent=40b1041e-fe11-4d43-85a9-f4001dfbfbe9;ID=229784f8-0098-4af6-b54c-db4e1b0b7082;orig_id=ACHIV102_cov_229.2.orf00043;date_last_modified=2020-09-25;Name=ACHIV102_cov_229.2.orf00043-00001;date_creation=2020-09-25
ACHIV102_cov_229.2	testing	exon	20969	22306	.	+	.	Parent=229784f8-0098-4af6-b54c-db4e1b0b7082;ID=c1101238-04fe-4742-8f98-2139e0e9d272;Name=c1101238-04fe-4742-8f98-2139e0e9d272
ACHIV102_cov_229.2	testing	Shine_Dalgarno_sequence	20956	20960	.	+	.	Parent=229784f8-0098-4af6-b54c-db4e1b0b7082;ID=5aa0b906-84fb-4dd3-982c-0d8d94a133db;Name=5aa0b906-84fb-4dd3-982c-0d8d94a133db
ACHIV102_cov_229.2	testing	non_canonical_three_prime_splice_site	20969	20969	.	+	.	Parent=229784f8-0098-4af6-b54c-db4e1b0b7082;ID=229784f8-0098-4af6-b54c-db4e1b0b7082-non_canonical_three_prime_splice_site-20968;Name=229784f8-0098-4af6-b54c-db4e1b0b7082-non_canonical_three_prime_splice_site-20968
ACHIV102_cov_229.2	testing	CDS	20969	22306	.	+	0	Parent=229784f8-0098-4af6-b54c-db4e1b0b7082;ID=229784f8-0098-4af6-b54c-db4e1b0b7082-CDS;Name=229784f8-0098-4af6-b54c-db4e1b0b7082-CDS
###

However, when I look at the child / parent feature relationship for the exon being edited, the parent is also the same exon . . .

parent Feature{id=612, symbol='null', description='null', name='c1101238-04fe-4742-8f98-2139e0e9d272', uniqueName='c1101238-04fe-4742-8f98-2139e0e9d272', sequenceLength=null, status=null, dateCreated=2020-09-25 18:37:25.707, lastUpdated=2020-09-25 18:37:25.949} -> SO:0000147 -> exon
child Feature{id=614, symbol='null', description='null', name='bcaf9c39-d35f-40ff-a874-4b738f4173c5', uniqueName='bcaf9c39-d35f-40ff-a874-4b738f4173c5', sequenceLength=null, status=null, dateCreated=2020-09-25 18:37:25.701, lastUpdated=2020-09-25 18:37:25.949} -> SO:0000147 -> exon

for child feature relationships of feature:

input exon Feature{id=614, symbol='null', description='null', name='bcaf9c39-d35f-40ff-a874-4b738f4173c5', uniqueName='bcaf9c39-d35f-40ff-a874-4b738f4173c5', sequenceLength=null, status=null, dateCreated=2020-09-25 18:37:25.701, lastUpdated=2020-09-25 18:37:25.949}

nathandunn · 2020-09-28T18:04:28Z

However, the `bcaf...' does not show up in the GFF3.

nathandunn · 2020-09-28T18:38:58Z

So, the issue is that it goes from gene -> mRNA -> exon -> exon . . . I'm not sure why its creating the second exon or why it was created at that level.

I actually removed most of the Shine Dalgarno code because there were some implementation issues, so its surprising it is working at all. I actually thought we were going to wait on this implementation, but its possible that we can work around this, as well.

nathandunn · 2020-09-28T18:41:38Z

So, the issue here is to fix this by:

eliminate the creation of the extra exon
suppress calculation

nathandunn · 2020-09-28T18:45:12Z

@MoffMade This does work for HTMLFeatures:

##gff-version 3
##sequence-region ACHIV102_cov_229.2 1 42452
ACHIV102_cov_229.2	testing	gene	20958	22306	.	+	.	owner=ndunn@me.com;ID=d883d2c6-28be-400d-85b5-5ca7fffaab87;date_last_modified=2020-09-28;Name=ACHIV102_cov_229.2;date_creation=2020-09-28
ACHIV102_cov_229.2	testing	mRNA	20958	22306	.	+	.	owner=ndunn@me.com;Parent=d883d2c6-28be-400d-85b5-5ca7fffaab87;ID=9d8d5fbc-289e-4ecd-8200-0bd1140b9e86;date_last_modified=2020-09-28;Name=ACHIV102_cov_229.2-00001;date_creation=2020-09-28
ACHIV102_cov_229.2	testing	exon	20974	22306	.	+	.	Parent=9d8d5fbc-289e-4ecd-8200-0bd1140b9e86;ID=5a0aee2a-73a2-4c99-8acd-554a8f8fd468;Name=5a0aee2a-73a2-4c99-8acd-554a8f8fd468
ACHIV102_cov_229.2	testing	non_canonical_three_prime_splice_site	20974	20974	.	+	.	Parent=9d8d5fbc-289e-4ecd-8200-0bd1140b9e86;ID=9d8d5fbc-289e-4ecd-8200-0bd1140b9e86-non_canonical_three_prime_splice_site-20973;Name=9d8d5fbc-289e-4ecd-8200-0bd1140b9e86-non_canonical_three_prime_splice_site-20973
ACHIV102_cov_229.2	testing	Shine_Dalgarno_sequence	20958	20960	.	+	.	Parent=9d8d5fbc-289e-4ecd-8200-0bd1140b9e86;ID=dc8259d4-33d6-4212-aceb-6261b540d383;Name=dc8259d4-33d6-4212-aceb-6261b540d383
ACHIV102_cov_229.2	testing	CDS	20975	22306	.	+	0	Parent=9d8d5fbc-289e-4ecd-8200-0bd1140b9e86;ID=9d8d5fbc-289e-4ecd-8200-0bd1140b9e86-CDS;Name=9d8d5fbc-289e-4ecd-8200-0bd1140b9e86-CDS
###

nathandunn · 2020-09-28T18:49:31Z

You have to drag them up at the same time, and then it works as expected. I think the fix for this is multiple fold.

implement https://github.com/GMOD/Apollo/pull/2143/files to incorproate shine dalgarno explicitly (and include some other things) - which was reverted at some later point
fix addition of Shine Dalgarno Canvas track

nathandunn mentioned this issue Sep 28, 2020

shine dalgarno fixes #2516

Merged

16 tasks

nathandunn mentioned this issue Oct 7, 2020

Display gene name rather than mRNA name #2519

Closed

nathandunn closed this as completed in #2516 Oct 12, 2020

nathandunn mentioned this issue Apr 14, 2021

Index Error [-1] on GFFs with Shine_Dalgarno features of length 3 #2607

Closed

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Dragging feature boundaries not working as expected for Shine-Dalgarno and CDS #2515

Dragging feature boundaries not working as expected for Shine-Dalgarno and CDS #2515

MoffMade commented Sep 24, 2020 •

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Dragging feature boundaries not working as expected for Shine-Dalgarno and CDS #2515

Dragging feature boundaries not working as expected for Shine-Dalgarno and CDS #2515

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