shine dalgarno fixes #2516

nathandunn · 2020-09-28T18:52:43Z

Shine Dalgarno evidence should be moveable without a refresh
- create a separate method that mimics set_exon_boundary without calculating the CDS
  - in AnnotTrack.js (842) switch for method to call set_shine_dalgarno_boundaries`
  - in AEC and RHS, create methods that mirror set_exon_boundaries called setShineDalgarnoBoundaries
  - om RHS method, should be the same, but looks for SD and mRNA explicitly and does not recalculate CDS or non-canonical splice site . . . conversely, we could use set_exon_boundaries and see if the method is a SD? . . . hmm
~~terminator should be moveable like RR and TE~~ moved to unable to resize terminators manually #2521
clean

make sure that Shine Dalgarno has mRNA listed as a parent (the reverse is true)
GFF3 export should list mRNA as parent Shine Dalgarno
check with FASTA export
after a refresh, deletion of the Shine Dalgarno should not cause a problem or cause a refresh
deletion of gene with Shine Dalgarno should not cause a problem or cause a referesh

shine dalgarno should be a child of the mRNA, treat as a type of an exon
deletion of the Shine Dalgarno should not cause a problem or cause a refresh (this is true for the initial creation)
fix addition of Shine Dalgarno Canvas track
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
~~allow changing of type (no)~~
allow independent creation

nathandunn · 2020-10-06T21:05:35Z

So, when we create a the gene here from the Shine Dalgarno:

The input sub features are created correctly (mRNA with a child exon and Shine Dalgarno sequence):

  var afeat ;
                    console.log('getting into aadding mRNA features');
                    if(biotype === 'mRNA'){
                        featureToAdd = JSONUtils.handleCigarSubFeatures(featureToAdd,biotype);
                        afeat = JSONUtils.createApolloFeature(featureToAdd, biotype, true);
                        console.log('adding feature',featureToAdd,afeat)
                        featuresToAdd.push(afeat);
                    }

This is when we create a gene, which gets converted to an identical mRNA.

However, createApolloFeature properly calculates the Shine Dalgarno, but for the exon it adds a sub exon and a sub CDS, neither of which we want.

nathandunn · 2020-10-09T22:38:24Z

input sequence:

{"track":"ACHIV102_cov_229.2","features":[{"location":{"fmin":20957,"fmax":22306,"strand":1},"type":{"cv":{"name":"sequence"},"name":"mRNA"},"name":"ACHIV102_cov_229.2.orf00043","orig_id":"ACHIV102_cov_229.2.orf00043","children":[{"location":{"fmin":20957,"fmax":20960,"strand":1},"type":{"cv":{"name":"sequence"},"name":"shine_dalgarno_sequence"},"orig_id":"ACHIV102_cov_229.2.cds_orf00043.rbs-0"},{"location":{"fmin":20968,"fmax":22306,"strand":1},"type":{"cv":{"name":"sequence"},"name":"exon"},"orig_id":"ACHIV102_cov_229.2.orf00043.exon","children":[{"location":{"fmin":20968,"fmax":22306,"strand":1},"type":{"cv":{"name":"sequence"},"name":"CDS"}}]}]}],"operation":"add_transcript","clientToken":"9755865001478805356695905165"}

return value:

{"features":[{"owner":"ndunn@me.com","parent_name":"ACHIV102_cov_229.2.orf00043","uniquename":"abca13e0-6693-44c5-9835-f856fac54c2d","type":{"cv":{"name":"sequence"},"name":"mRNA"},"parent_type":{"cv":{"name":"sequence"},"name":"gene"},"date_creation":1602283010350,"sequence":"ACHIV102_cov_229.2","children":[{"owner":"None","parent_name":"ACHIV102_cov_229.2.orf00043-00001","uniquename":"abca13e0-6693-44c5-9835-f856fac54c2d-non_canonical_three_prime_splice_site-20968","type":{"cv":{"name":"sequence"},"name":"non_canonical_three_prime_splice_site"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1602283011020,"sequence":"ACHIV102_cov_229.2","parent_id":"abca13e0-6693-44c5-9835-f856fac54c2d","name":"abca13e0-6693-44c5-9835-f856fac54c2d-non_canonical_three_prime_splice_site-20968","location":{"strand":1,"id":967,"fmin":20968,"fmax":20968},"id":967,"properties":[],"date_last_modified":1602283011043},{"owner":"None","parent_name":"ACHIV102_cov_229.2.orf00043-00001","uniquename":"f351ff97-c101-48a6-af7c-b959d8d3d7aa","type":{"cv":{"name":"sequence"},"name":"Shine_Dalgarno_sequence"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1602283010279,"sequence":"ACHIV102_cov_229.2","parent_id":"abca13e0-6693-44c5-9835-f856fac54c2d","name":"f351ff97-c101-48a6-af7c-b959d8d3d7aa","location":{"strand":1,"id":963,"fmin":20957,"fmax":20960},"id":963,"properties":[{"name":"orig_id","type":{"cv":{"name":"feature_property"}},"value":"ACHIV102_cov_229.2.cds_orf00043.rbs-0"}],"date_last_modified":1602283010315},{"owner":"None","parent_name":"ACHIV102_cov_229.2.orf00043-00001","uniquename":"7d24352b-95e8-4a51-96c0-62ade478f757","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1602283010344,"sequence":"ACHIV102_cov_229.2","children":[{"owner":"None","parent_name":"7d24352b-95e8-4a51-96c0-62ade478f757","uniquename":"6f5bd196-2f94-4afd-80d2-191cb8e729e4","type":{"cv":{"name":"sequence"},"name":"CDS"},"parent_type":{"cv":{"name":"sequence"},"name":"exon"},"date_creation":1602283010337,"sequence":"ACHIV102_cov_229.2","parent_id":"7d24352b-95e8-4a51-96c0-62ade478f757","name":"6f5bd196-2f94-4afd-80d2-191cb8e729e4","location":{"strand":1,"id":965,"fmin":20968,"fmax":22306},"id":965,"properties":[],"date_last_modified":1602283010632}],"parent_id":"abca13e0-6693-44c5-9835-f856fac54c2d","name":"7d24352b-95e8-4a51-96c0-62ade478f757","location":{"strand":1,"id":964,"fmin":20968,"fmax":22306},"id":964,"properties":[{"name":"orig_id","type":{"cv":{"name":"feature_property"}},"value":"ACHIV102_cov_229.2.orf00043.exon"}],"date_last_modified":1602283010631},{"owner":"None","parent_name":"ACHIV102_cov_229.2.orf00043-00001","uniquename":"abca13e0-6693-44c5-9835-f856fac54c2d-CDS","type":{"cv":{"name":"sequence"},"name":"CDS"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1602283010615,"sequence":"ACHIV102_cov_229.2","parent_id":"abca13e0-6693-44c5-9835-f856fac54c2d","name":"abca13e0-6693-44c5-9835-f856fac54c2d-CDS","location":{"strand":1,"is_fmin_partial":true,"id":966,"fmin":20968,"fmax":22306},"id":966,"properties":[],"date_last_modified":1602283010689}],"parent_id":"26dfb8a0-df3c-4cb7-9fa6-ec5d2f28fdb8","name":"ACHIV102_cov_229.2.orf00043-00001","location":{"strand":1,"id":962,"fmin":20957,"fmax":22306},"id":962,"properties":[{"name":"orig_id","type":{"cv":{"name":"feature_property"}},"value":"ACHIV102_cov_229.2.orf00043"}],"date_last_modified":1602283011055}],"sequenceAlterationEvent":false,"operation":"ADD"}

nathandunn · 2020-10-09T22:40:17Z

Based on this, the return type is correct. gene -> mRNA -> (exon, SD, CDS, non-can SS)

The gff3 is:

##gff-version 3
##sequence-region ACHIV102_cov_229.2 1 42452
ACHIV102_cov_229.2	.	gene	20958	22306	.	+	.	owner=ndunn@me.com;ID=26dfb8a0-df3c-4cb7-9fa6-ec5d2f28fdb8;date_last_modified=2020-10-09;Name=ACHIV102_cov_229.2.orf00043;date_creation=2020-10-09
ACHIV102_cov_229.2	.	mRNA	20958	22306	.	+	.	owner=ndunn@me.com;Parent=26dfb8a0-df3c-4cb7-9fa6-ec5d2f28fdb8;ID=abca13e0-6693-44c5-9835-f856fac54c2d;orig_id=ACHIV102_cov_229.2.orf00043;date_last_modified=2020-10-09;Name=ACHIV102_cov_229.2.orf00043-00001;date_creation=2020-10-09
ACHIV102_cov_229.2	.	non_canonical_three_prime_splice_site	20969	20969	.	+	.	Parent=abca13e0-6693-44c5-9835-f856fac54c2d;ID=abca13e0-6693-44c5-9835-f856fac54c2d-non_canonical_three_prime_splice_site-20968;Name=abca13e0-6693-44c5-9835-f856fac54c2d-non_canonical_three_prime_splice_site-20968
ACHIV102_cov_229.2	.	Shine_Dalgarno_sequence	20958	20960	.	+	.	ID=f351ff97-c101-48a6-af7c-b959d8d3d7aa;orig_id=ACHIV102_cov_229.2.cds_orf00043.rbs-0;date_last_modified=2020-10-09;Name=f351ff97-c101-48a6-af7c-b959d8d3d7aa;date_creation=2020-10-09
ACHIV102_cov_229.2	.	exon	20969	22306	.	+	.	Parent=abca13e0-6693-44c5-9835-f856fac54c2d;ID=7d24352b-95e8-4a51-96c0-62ade478f757;Name=7d24352b-95e8-4a51-96c0-62ade478f757
ACHIV102_cov_229.2	.	CDS	20969	22306	.	+	0	Parent=abca13e0-6693-44c5-9835-f856fac54c2d;ID=abca13e0-6693-44c5-9835-f856fac54c2d-CDS;Name=abca13e0-6693-44c5-9835-f856fac54c2d-CDS
###

nathandunn · 2020-10-09T22:45:01Z

getFeatures returns the correct mRNA and the Shine Dalgarno as well. I think the SD lacks a parent:

{"features":[{"owner":"ndunn@me.com","parent_name":"ACHIV102_cov_229.2.orf00043","uniquename":"d5b76d11-596c-4643-948c-9d10dd97c866","type":{"cv":{"name":"sequence"},"name":"mRNA"},"parent_type":{"cv":{"name":"sequence"},"name":"gene"},"date_creation":1602283363275,"sequence":"ACHIV102_cov_229.2","children":[{"owner":"None","parent_name":"ACHIV102_cov_229.2.orf00043-00001","uniquename":"d5b76d11-596c-4643-948c-9d10dd97c866-non_canonical_three_prime_splice_site-20968","type":{"cv":{"name":"sequence"},"name":"non_canonical_three_prime_splice_site"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1602283363347,"sequence":"ACHIV102_cov_229.2","parent_id":"d5b76d11-596c-4643-948c-9d10dd97c866","name":"d5b76d11-596c-4643-948c-9d10dd97c866-non_canonical_three_prime_splice_site-20968","location":{"strand":1,"id":988,"fmin":20968,"fmax":20968},"id":988,"properties":[],"date_last_modified":1602283363355},{"owner":"None","parent_name":"ACHIV102_cov_229.2.orf00043-00001","uniquename":"34a89e03-d2b7-4471-adce-86bd92817a49","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1602283363273,"sequence":"ACHIV102_cov_229.2","children":[{"owner":"None","parent_name":"34a89e03-d2b7-4471-adce-86bd92817a49","uniquename":"9b3731b3-4f72-4836-939b-c29aa86cc719","type":{"cv":{"name":"sequence"},"name":"CDS"},"parent_type":{"cv":{"name":"sequence"},"name":"exon"},"date_creation":1602283363271,"sequence":"ACHIV102_cov_229.2","parent_id":"34a89e03-d2b7-4471-adce-86bd92817a49","name":"9b3731b3-4f72-4836-939b-c29aa86cc719","location":{"strand":1,"id":986,"fmin":20968,"fmax":22306},"id":986,"properties":[],"date_last_modified":1602283363308}],"parent_id":"d5b76d11-596c-4643-948c-9d10dd97c866","name":"34a89e03-d2b7-4471-adce-86bd92817a49","location":{"strand":1,"id":985,"fmin":20968,"fmax":22306},"id":985,"properties":[{"name":"orig_id","type":{"cv":{"name":"feature_property"}},"value":"ACHIV102_cov_229.2.orf00043.exon"}],"date_last_modified":1602283363307},{"owner":"None","parent_name":"ACHIV102_cov_229.2.orf00043-00001","uniquename":"40675c0f-41d9-4f67-8561-ddf2766ede0c","type":{"cv":{"name":"sequence"},"name":"Shine_Dalgarno_sequence"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1602283363253,"sequence":"ACHIV102_cov_229.2","parent_id":"d5b76d11-596c-4643-948c-9d10dd97c866","name":"40675c0f-41d9-4f67-8561-ddf2766ede0c","location":{"strand":1,"id":984,"fmin":20957,"fmax":20960},"id":984,"properties":[{"name":"orig_id","type":{"cv":{"name":"feature_property"}},"value":"ACHIV102_cov_229.2.cds_orf00043.rbs-0"}],"date_last_modified":1602283363263},{"owner":"None","parent_name":"ACHIV102_cov_229.2.orf00043-00001","uniquename":"d5b76d11-596c-4643-948c-9d10dd97c866-CDS","type":{"cv":{"name":"sequence"},"name":"CDS"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1602283363299,"sequence":"ACHIV102_cov_229.2","parent_id":"d5b76d11-596c-4643-948c-9d10dd97c866","name":"d5b76d11-596c-4643-948c-9d10dd97c866-CDS","location":{"strand":1,"is_fmin_partial":true,"id":987,"fmin":20968,"fmax":22306},"id":987,"properties":[],"date_last_modified":1602283363318}],"parent_id":"56f03ae1-ea1d-4032-aab7-a48e9e5b180a","name":"ACHIV102_cov_229.2.orf00043-00001","location":{"strand":1,"id":983,"fmin":20957,"fmax":22306},"id":983,"properties":[{"name":"orig_id","type":{"cv":{"name":"feature_property"}},"value":"ACHIV102_cov_229.2.orf00043"}],"date_last_modified":1602283363360},{"owner":"None","parent_name":"ACHIV102_cov_229.2.orf00043-00001","uniquename":"40675c0f-41d9-4f67-8561-ddf2766ede0c","type":{"cv":{"name":"sequence"},"name":"Shine_Dalgarno_sequence"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1602283363253,"sequence":"ACHIV102_cov_229.2","parent_id":"d5b76d11-596c-4643-948c-9d10dd97c866","name":"40675c0f-41d9-4f67-8561-ddf2766ede0c","location":{"strand":1,"id":984,"fmin":20957,"fmax":20960},"id":984,"properties":[{"name":"orig_id","type":{"cv":{"name":"feature_property"}},"value":"ACHIV102_cov_229.2.cds_orf00043.rbs-0"}],"date_last_modified":1602283363263}],"clientToken":"9755865001478805356695905165","track":"ACHIV102_cov_229.2","operation":"get_features"}

nathandunn · 2020-10-09T23:39:49Z

For sending boundaries sending this:

{"track":"ACHIV102_cov_229.2","features":[{"uniquename":"76b20483-a63d-4d16-b64c-d6195325935e","location":{"fmin":20953,"fmax":20961}}],"operation":"set_boundaries","clientToken":"9755865001478805356695905165"}

and returning this:

{"features":[{"owner":"ndunn@me.com","parent_name":"ACHIV102_cov_229.2.orf00043-00001","uniquename":"76b20483-a63d-4d16-b64c-d6195325935e","type":{"cv":{"name":"sequence"},"name":"Shine_Dalgarno_sequence"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1602286580182,"sequence":"ACHIV102_cov_229.2","parent_id":"f0a2ea96-6730-4014-93fc-ad8af83f5ad4","name":"76b20483-a63d-4d16-b64c-d6195325935e","location":{"strand":1,"id":1050,"fmin":20953,"fmax":20961},"id":1050,"properties":[{"name":"orig_id","type":{"cv":{"name":"feature_property"}},"value":"ACHIV102_cov_229.2.cds_orf00043.rbs-0"}],"date_last_modified":1602286583476}],"sequenceAlterationEvent":false,"operation":"UPDATE"}

some minor changes

dbbe370

nathandunn changed the title ~~some minor changes~~ shine dalgarno fixes Oct 5, 2020

nathandunn added 3 commits October 5, 2020 15:50

Merge branch 'develop' into fix-2515

ff56dd6

updated the PR to re-include shine dalgarno

663c840

fixed real path

8fa1364

no longer creating sub features

93d4e8c

nathandunn mentioned this pull request Oct 7, 2020

Display gene name rather than mRNA name #2519

Closed

nathandunn added 2 commits October 9, 2020 09:14

Merge branch 'develop' into fix-2515

db4f8ac

Merge branch 'develop' into fix-2515

e4be450

nathandunn added 2 commits October 9, 2020 16:07

fixed feature retrieval

26b9c90

removed test

dd49339

nathandunn added 7 commits October 9, 2020 21:49

added a bit of cleanup

2196af8

added shine_dalgarno_hooks

732476a

handling correct ontology type

4cd2b12

modified popup time

e1ac90d

cleaned it up

cf6c99f

removed the ability to add a shine_dalgarno if not part of a gene model

f6800b9

updated changelog

da21068

nathandunn merged commit 191c72d into develop Oct 12, 2020

nathandunn mentioned this pull request Oct 12, 2020

add Shine-dalgarno so that gene region is not modified #2506

Closed

nathandunn mentioned this pull request Jan 26, 2021

if Shine Dalgarno is attached as evidence it gets rendered as an exon galaxy-genome-annotation/python-apollo#48

Closed

cmdcolin deleted the fix-2515 branch December 7, 2023 19:58

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

shine dalgarno fixes #2516

shine dalgarno fixes #2516

nathandunn commented Sep 28, 2020 •

edited

Loading

nathandunn commented Oct 6, 2020

nathandunn commented Oct 9, 2020

nathandunn commented Oct 9, 2020

nathandunn commented Oct 9, 2020

nathandunn commented Oct 9, 2020

shine dalgarno fixes #2516

shine dalgarno fixes #2516

Conversation

nathandunn commented Sep 28, 2020 • edited Loading

nathandunn commented Oct 6, 2020

nathandunn commented Oct 9, 2020

nathandunn commented Oct 9, 2020

nathandunn commented Oct 9, 2020

nathandunn commented Oct 9, 2020

nathandunn commented Sep 28, 2020 •

edited

Loading