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GMOD
import / export entire gene evidence as model (should work) with output evidence with gene models
related to #2234
make work for GFF3 track
- [ ] create annotation with that track, making sure that it sends the Gene as a parent ID
- [ ] in JSONUtils.copyOfficialData build a parent_id (with the unique object) and a parent object
- [ ] in https://github.com/GMOD/Apollo/blob/develop/grails-app/services/org/bbop/apollo/FeatureService.groovy#L1293 make sure that we pull in the additional properties if there (gene_product, provenance, comments, dbxref, etc. etct.)
- [x] exported GFF3 should contain all of the attributes
- [x] confirm that GFF3 native can have the parent feature attached properly from the exported GFF
- [ ] confirm that GFF3 JSON (as gene top) can have the parent feature attached properly
- [ ] confirm that GFF3 JSON (as mRNA top) can have the parent feature attached properly
- [x] export GFF3 with full gene, transcript, etc.
- [x] implement #2400 to add GO
- [x] import GFF3 as evidence (maybe with GFF3 native) to see that it renders
- [x] make new track the
official track - [x] verify that details show the genes
Adding a transcript always looks like this:
{"track":"Group11.18","features":[{"location":{"fmin":2859758,"fmax":2864902,"strand":-1},"type":{"cv":{"name":"sequence"},"name":"mRNA"},"name":"GB44997-RA","orig_id":"GB44997-RA","children":[{"location":{"fmin":2859758,"fmax":2860165,"strand":-1},"type":{"cv":{"name":"sequence"},"name":"exon"}},{"location":{"fmin":2860270,"fmax":2860452,"strand":-1},"type":{"cv":{"name":"sequence"},"name":"exon"}},{"location":{"fmin":2860516,"fmax":2860592,"strand":-1},"type":{"cv":{"name":"sequence"},"name":"exon"}},{"location":{"fmin":2861367,"fmax":2861438,"strand":-1},"type":{"cv":{"name":"sequence"},"name":"exon"}},{"location":{"fmin":2862068,"fmax":2862242,"strand":-1},"type":{"cv":{"name":"sequence"},"name":"exon"}},{"location":{"fmin":2862326,"fmax":2862541,"strand":-1},"type":{"cv":{"name":"sequence"},"name":"exon"}},{"location":{"fmin":2863109,"fmax":2863254,"strand":-1},"type":{"cv":{"name":"sequence"},"name":"exon"}},{"location":{"fmin":2863347,"fmax":2863542,"strand":-1},"type":{"cv":{"name":"sequence"},"name":"exon"}},{"location":{"fmin":2863764,"fmax":2863937,"strand":-1},"type":{"cv":{"name":"sequence"},"name":"exon"}},{"location":{"fmin":2864002,"fmax":2864160,"strand":-1},"type":{"cv":{"name":"sequence"},"name":"exon"}},{"location":{"fmin":2864240,"fmax":2864362,"strand":-1},"type":{"cv":{"name":"sequence"},"name":"exon"}},{"location":{"fmin":2864487,"fmax":2864902,"strand":-1},"type":{"cv":{"name":"sequence"},"name":"exon"}},{"location":{"fmin":2859758,"fmax":2864579,"strand":-1},"type":{"cv":{"name":"sequence"},"name":"CDS"}}]}],"operation":"add_transcript","clientToken":"14470703356983923241302701874"}
So the parent is not included. We need to include the parent and make sure it renders properly.
{"data":{"seq_id":"Group11.18","source":null,"type":"gene","start":2859758,"end":2864902,"score":null,"strand":-1,"phase":null,"owner":"[email protected]","id":"a7648887-db04-48b2-a408-7902608afee7","date_last_modified":"2020-03-10","name":"GB44997-RA","date_creation":"2020-03-10","subfeatures":[{"data":{"seq_id":"Group11.18","source":null,"type":"mRNA","start":2859758,"end":2864902,"score":null,"strand":-1,"phase":null,"owner":"[email protected]","parent":"a7648887-db04-48b2-a408-7902608afee7","id":"5fa27908-0f06-4667-9fd6-5ae7d9770d18","orig_id":"GB44997-RA","date_last_modified":"2020-03-10","name":"GB44997-RA-00001","date_creation":"2020-03-10","subfeatures":[{"data":{"seq_id":"Group11.18","source":null,"type":"exon","start":2864240,"end":2864362,"score":null,"strand":-1,"phase":null,"parent":"5fa27908-0f06-4667-9fd6-5ae7d9770d18","id":"01812965-063c-4256-96d5-c40533b0a3bf","name":"01812965-063c-4256-96d5-c40533b0a3bf"},"_uniqueID":"a7648887-db04-48b2-a408-7902608afee7_0_1"},{"data":{"seq_id":"Group11.18","source":null,"type":"CDS","start":2864487,"end":2864579,"score":null,"strand":-1,"phase":"0","parent":"5fa27908-0f06-4667-9fd6-5ae7d9770d18","id":"2161b5c5-c6cf-4429-97a8-32141016eeb4","name":"2161b5c5-c6cf-4429-97a8-32141016eeb4"},"_uniqueID":"a7648887-db04-48b2-a408-7902608afee7_0_2"},{"data":{"seq_id":"Group11.18","source":null,"type":"CDS","start":2864240,"end":2864362,"score":null,"strand":-1,"phase":"1","parent":"5fa27908-0f06-4667-9fd6-5ae7d9770d18","id":"2161b5c5-c6cf-4429-97a8-32141016eeb4","name":"2161b5c5-c6cf-4429-97a8-32141016eeb4"},"_uniqueID":"a7648887-db04-48b2-a408-7902608afee7_0_3"},{"data":{"seq_id":"Group11.18","source":null,"type":"CDS","start":2864002,"end":2864160,"score":null,"strand":-1,"phase":"2","parent":"5fa27908-0f06-4667-9fd6-5ae7d9770d18","id":"2161b5c5-c6cf-4429-97a8-32141016eeb4","name":"2161b5c5-c6cf-4429-97a8-32141016eeb4"},"_uniqueID":"a7648887-db04-48b2-a408-7902608afee7_0_4"},{"data":{"seq_id":"Group11.18","source":null,"type":"CDS","start":2863764,"end":2863937,"score":null,"strand":-1,"phase":"0","parent":"5fa27908-0f06-4667-9fd6-5ae7d9770d18","id":"2161b5c5-c6cf-4429-97a8-32141016eeb4","name":"2161b5c5-c6cf-4429-97a8-32141016eeb4"},"_uniqueID":"a7648887-db04-48b2-a408-7902608afee7_0_5"},{"data":{"seq_id":"Group11.18","source":null,"type":"CDS","start":2863347,"end":2863542,"score":null,"strand":-1,"phase":"1","parent":"5fa27908-0f06-4667-9fd6-5ae7d9770d18","id":"2161b5c5-c6cf-4429-97a8-32141016eeb4","name":"2161b5c5-c6cf-4429-97a8-32141016eeb4"},"_uniqueID":"a7648887-db04-48b2-a408-7902608afee7_0_6"},{"data":{"seq_id":"Group11.18","source":null,"type":"CDS","start":2863109,"end":2863254,"score":null,"strand":-1,"phase":"1","parent":"5fa27908-0f06-4667-9fd6-5ae7d9770d18","id":"2161b5c5-c6cf-4429-97a8-32141016eeb4","name":"2161b5c5-c6cf-4429-97a8-32141016eeb4"},"_uniqueID":"a7648887-db04-48b2-a408-7902608afee7_0_7"},{"data":{"seq_id":"Group11.18","source":null,"type":"CDS","start":2862326,"end":2862541,"score":null,"strand":-1,"phase":"0","parent":"5fa27908-0f06-4667-9fd6-5ae7d9770d18","id":"2161b5c5-c6cf-4429-97a8-32141016eeb4","name":"2161b5c5-c6cf-4429-97a8-32141016eeb4"},"_uniqueID":"a7648887-db04-48b2-a408-7902608afee7_0_8"},{"data":{"seq_id":"Group11.18","source":null,"type":"CDS","start":2862068,"end":2862242,"score":null,"strand":-1,"phase":"1","parent":"5fa27908-0f06-4667-9fd6-5ae7d9770d18","id":"2161b5c5-c6cf-4429-97a8-32141016eeb4","name":"2161b5c5-c6cf-4429-97a8-32141016eeb4"},"_uniqueID":"a7648887-db04-48b2-a408-7902608afee7_0_9"},{"data":{"seq_id":"Group11.18","source":null,"type":"CDS","start":2861367,"end":2861438,"score":null,"strand":-1,"phase":"1","parent":"5fa27908-0f06-4667-9fd6-5ae7d9770d18","id":"2161b5c5-c6cf-4429-97a8-32141016eeb4","name":"2161b5c5-c6cf-4429-97a8-32141016eeb4"},"_uniqueID":"a7648887-db04-48b2-a408-7902608afee7_0_10"},{"data":{"seq_id":"Group11.18","source":null,"type":"CDS","start":2860516,"end":2860592,"score":null,"strand":-1,"phase":"2","parent":"5fa27908-0f06-4667-9fd6-5ae7d9770d18","id":"2161b5c5-c6cf-4429-97a8-32141016eeb4","name":"2161b5c5-c6cf-4429-97a8-32141016eeb4"},"_uniqueID":"a7648887-db04-48b2-a408-7902608afee7_0_11"},{"data":{"seq_id":"Group11.18","source":null,"type":"CDS","start":2860270,"end":2860452,"score":null,"strand":-1,"phase":"1","parent":"5fa27908-0f06-4667-9fd6-5ae7d9770d18","id":"2161b5c5-c6cf-4429-97a8-32141016eeb4","name":"2161b5c5-c6cf-4429-97a8-32141016eeb4"},"_uniqueID":"a7648887-db04-48b2-a408-7902608afee7_0_12"},{"data":{"seq_id":"Group11.18","source":null,"type":"CDS","start":2859758,"end":2860165,"score":null,"strand":-1,"phase":"2","parent":"5fa27908-0f06-4667-9fd6-5ae7d9770d18","id":"2161b5c5-c6cf-4429-97a8-32141016eeb4","name":"2161b5c5-c6cf-4429-97a8-32141016eeb4"},"_uniqueID":"a7648887-db04-48b2-a408-7902608afee7_0_13"},{"data":{"seq_id":"Group11.18","source":null,"type":"exon","start":2864487,"end":2864902,"score":null,"strand":-1,"phase":null,"parent":"5fa27908-0f06-4667-9fd6-5ae7d9770d18","id":"ac356fe9-eada-4d84-8860-429bd69fa3d9","name":"ac356fe9-eada-4d84-8860-429bd69fa3d9"},"_uniqueID":"a7648887-db04-48b2-a408-7902608afee7_0_14"},{"data":{"seq_id":"Group11.18","source":null,"type":"exon","start":2860516,"end":2860592,"score":null,"strand":-1,"phase":null,"parent":"5fa27908-0f06-4667-9fd6-5ae7d9770d18","id":"1f50a7f3-9b3c-4233-8719-b06d8df7954f","name":"1f50a7f3-9b3c-4233-8719-b06d8df7954f"},"_uniqueID":"a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So, from @cmdcolin feedback, if you use ./flatfile-to-json.pl and you use type=gene using feature.parent should provide the gene data within JBrowse.
Testing with the GFF3 uploads, though, we have even better news. Within a GFF3 upload, we have access to all of the top-level genes, that can be added to the parent_id object if an official track:
When I add a loaded GFF3, much of the evidence comes through:
{"data":{"121":"asdsad","seq_id":"Group11.18","source":null,"type":"gene","start":2859758,"end":2864902,"score":null,"strand":-1,"phase":null,"owner":"[email protected]","symbol":"mygenesymbol","description":"description of gene","name":"GB44997-RA-00001a","date_creation":"2020-03-11","provenance":"rank=1;field=NAME;db_xref=asfa:lkj;evidence=ECO:0000269;note=null;based_on=[\"as:12313\"]","alias":["syn1","syn2"],"note":"dfasdfasdf","gene_product":"rank=1;term=my gene product;db_xref=asdf:1212122;evidence=ECO:0000353;alternate=true;note=[];based_on=[\"asdf:1212\"]","id":"00bd7a2a-617e-48de-bc6e-4fa454f3d518","date_last_modified":"2020-03-11","dbxref":"asdf:111212","status":"accepted","subfeatures":[{"data":{"seq_id":"Group11.18","source":null,"type":"mRNA","start":2859758,"end":2864902,"score":null,"strand":-1,"phase":null,"owner":"[email protected]","parent":"00bd7a2a-617e-48de-bc6e-4fa454f3d518","id":"e163a393-fa70-4b10-91f8-3d08eecb9005","orig_id":"5fa27908-0f06-4667-9fd6-5ae7d9770d18","date_last_modified":"2020-03-11","name":"GB44997-RA-00001-00001","date_creation":"2020-03-11","subfeatures":[{"data":{"seq_id":"Group11.18","source":null,"type":"exon","start":2864487,"end":2864902,"score":null,"strand":-1,"phase":null,"parent":"e163a393-fa70-4b10-91f8-3d08eecb9005","id":"b2650bf5-c4b6-446a-8539-51503c0c5215","name":"ac356fe9-eada-4d84-8860-429bd69fa3d9"},"_uniqueID":"00bd7a2a-617e-48de-bc6e-4fa454f3d518_52_57"},{"data":{"seq_id":"Group11.18","source":null,"type":"CDS","start":2864487,"end":2864579,"score":null,"strand":-1,"phase":"0","parent":"e163a393-fa70-4b10-91f8-3d08eecb9005","id":"7fb9abb0-4836-4615-be08-b238741cc688","name":"7fb9abb0-4836-4615-be08-b238741cc688"},"_uniqueID":"00bd7a2a-617e-48de-bc6e-4fa454f3d518_52_62"},{"data":{"seq_id":"Group11.18","source":null,"type":"exon","start":2864240,"end":2864362,"score":null,"strand":-1,"phase":null,"parent":"e163a393-fa70-4b10-91f8-3d08eecb9005","id":"049b77a0-9079-46ee-afff-5267aa9c3c62","name":"01812965-063c-4256-96d5-c40533b0a3bf"},"_uniqueID":"00bd7a2a-617e-48de-bc6e-4fa454f3d518_52_53"},{"data":{"seq_id":"Group11.18","source":null,"type":"CDS","start":2864240,"end":2864362,"score":null,"strand":-1,"phase":"1","parent":"e163a393-fa70-4b10-91f8-3d08eecb9005","id":"7fb9abb0-4836-4615-be08-b238741cc688","name":"7fb9abb0-4836-4615-be08-b238741cc688"},"_uniqueID":"00bd7a2a-617e-48de-bc6e-4fa454f3d518_52_63"},{"data":{"seq_id":"Group11.18","source":null,"type":"CDS","start":2864002,"end":2864160,"score":null,"strand":-1,"phase":"2","parent":"e163a393-fa70-4b10-91f8-3d08eecb9005","id":"7fb9abb0-4836-4615-be08-b238741cc688","name":"7fb9abb0-4836-4615-be08-b238741cc688"},"_uniqueID":"00bd7a2a-617e-48de-bc6e-4fa454f3d518_52_64"},{"data":{"seq_id":"Group11.18","source":null,"type":"exon","start":2864002,"end":2864160,"score":null,"strand":-1,"phase":null,"parent":"e163a393-fa70-4b10-91f8-3d08eecb9005","id":"5d3f4fa0-2fcf-4f68-bda8-014bf7deada9","name":"367218ff-1eb1-47ce-b69e-a533b56413e0"},"_uniqueID":"00bd7a2a-617e-48de-bc6e-4fa454f3d518_52_76"},{"data":{"seq_id":"Group11.18","source":null,"type":"exon","start":2863764,"end":2863937,"score":null,"strand":-1,"phase":null,"parent":"e163a393-fa70-4b10-91f8-3d08eecb9005","id":"875d6c57-9825-4495-a6d2-008eed438da7","name":"cf022cfc-06d6-44d8-b763-d4ac3765f7c4"},"_uniqueID":"00bd7a2a-617e-48de-bc6e-4fa454f3d518_52_54"},{"data":{"seq_id":"Group11.18","source":null,"type":"CDS","start":2863764,"end":2863937,"score":null,"strand":-1,"phase":"0","parent":"e163a393-fa70-4b10-91f8-3d08eecb9005","id":"7fb9abb0-4836-4615-be08-b238741cc688","name":"7fb9abb0-4836-4615-be08-b238741cc688"},"_uniqueID":"00bd7a2a-617e-48de-bc6e-4fa454f3d518_52_65"},{"data":{"seq_id":"Group11.18","source":null,"type":"CDS","start":2863347,"end":2863542,"score":null,"strand":-1,"phase":"1","parent":"e163a393-fa70-4b10-91f8-3d08eecb9005","id":"7fb9abb0-4836-4615-be08-b238741cc688","name":"7fb9abb0-4836-4615-be08-b238741cc688"},"_uniqueID":"00bd7a2a-617e-48de-bc6e-4fa454f3d518_52_66"},{"data":{"seq_id":"Group11.18","source":null,"type":"exon","start":2863347,"end":2863542,"score":null,"strand":-1,"phase":null,"parent":"e163a393-fa70-4b10-91f8-3d08eecb9005","id":"e76bf1fc-6d4d-4fa2-8cf5-f5e0fe3af4b5","name":"8d558ee0-a67b-48ca-8ce3-b60aee1e5374"},"_uniqueID":"00bd7a2a-617e-48de-bc6e-4fa454f3d518_52_75"},{"data":{"seq_id":"Group11.18","source":null,"type":"CDS","start":2863109,"end":2863254,"score":null,"strand":-1,"phase":"1","parent":"e163a393-fa70-4b10-91f8-3d08eecb9005","id":"7fb9abb0-4836-4615-be08-b238741cc688","name":"7fb9abb0-4836-4615-be08-b238741cc688"},"_uniqueID":"00bd7a2a-617e-48de-bc6e-4fa454f3d518_52_67"},{"data":{"seq_id":"Group11.18","source":null,"type":"exon","start":2863109,"end":2863254,"score":null,"strand":-1,"phase":null,"parent":"e163a393-fa70-4b10-91f8-3d08eecb9005","id":"f661050f-e2c5-41bc-a7bd-d14c05f73585","name":"4210a2d5-07a5-45b2-9426-37a4c1cb5b6a"},"_uniqueID":"00bd7a2a-617e-48de-bc6e-4fa454f3d518_52_74"},{"data":{"seq_id":"Group11.18","source":null,"type":"exon","start":2862326,"end":2862541,"score":null,"strand":-1,"phase":null,"parent":"e163a393-fa70-4b10-91f8-3d08eecb9005","id":"4697c3d5-8753-44cb-841d-3ce9d46747ef","name":"567a4d75-9554-4ab6-9761-62b432526bcc"},"_uniqueID":"00bd7a2a-617e-48de-bc6e-4fa454f3d518_52_59"},{"data":{"seq_id":"Group11.18","source":null,"type":"CDS","start":2862326,"end":2862541,"score":null,"strand":-1,"phase":"0","parent":"e163a393-fa70-4b10-91f8-3d08eecb9005","id":"7fb9abb0-4836-4615-be08-b238741cc688","name":"7fb9abb0-4836-4615-be08-b238741cc688"},"_uniqueID":"00bd7a2a-617e-48de-bc6e-4fa454f3d518_52_68"},{"data":{"seq_id":"Group11.18","source":null,"type":"exon","start":2862068,"end":2862242,"score":null,"strand":-1,"phase":null,"parent":"e163a393-fa70-4b10-91f8-3d08eecb9005","id":"bf1ec343-dd01-4115-b199-b040ba164109","name":"69553015-8e90-45c1-aeef-5185ee28053a"},"_uniqueID":"00bd7a2a-617e-48de-bc6e-4fa454f3d518_52_55"},{"data":{"seq_id":"Group11.18","source":null,"type":"CDS","start":2862068,"end":2862242,"score":null,"strand":-1,"phase":"1","parent":"e163a393-fa70-4b10-91f8-3d08eecb9005","id":"7fb9abb0-4836-4615-be08-b238741cc688","name":"7fb9abb0-4836-4615-be08-b238741cc688"},"_uniqueID":"00bd7a2a-617e-48de-bc6e-4fa454f3d518_52_69"},{"data":{"seq_id":"Group11.18","source":null,"type":"exon","start":2861367,"end":2861438,"score":null,"strand":-1,"phase":null,"parent":"e163a393-fa70-4b10-91f8-3d08eecb9005","id":"44cc0e7a-8683-42ca-9742-41911b756632","name":"e24e7379-d4c2-40f5-b7f1-18b84d870cdf"},"_uniqueID":"00bd7a2a-617e-48de-bc6e-4fa454f3d518_52_58"},{"data":{"seq_id":"Group11.18","source":null,"type":"CDS","start":2861367,"end":2861438,"score":null,"strand":-1,"phase":"1","parent":"e163a393-fa70-4b10-91f8-3d08eecb9005","id":"7fb9abb0-4836-4615-be08-b238741cc688","name":"7fb9abb0-4836-4615-be08-b238741cc688"},"_uniqueID":"00bd7a2a-617e-48de-bc6e-4fa454f3d518_52_70"},{"data":{"seq_id":"Group11.18","source":null,"type":"exon","start":2860516,"end":2860592,"score":null,"strand":-1,"phase":null,"parent":"e163a393-fa70-4b10-91f8-3d08eecb9005","id":"c8bccf61-c558-4081-a7d3-327ac8d8e08b","name":"1f50a7f3-9b3c-4233-8719-b06d8df7954f"},"_uniqueID":"00bd7a2a-617e-48de-bc6e-4fa454f3d518_52_60"},{"data":{"seq_id":"Group11.18","source":null,"type":"CDS","start":2860516,"end":2860592,"score":null,"strand":-1,"phase":"2","parent":"e163a393-fa70-4b10-91f8-3d08eecb9005","id":"7fb9abb0-4836-4615-be08-b238741cc688","name":"7fb9abb0-4836-4615-be08-b238741cc688"},"_uniqueID":"00bd7a2a-617e-48de-bc6e-4fa454f3d518_52_71"},{"data":{"seq_id":"Group11.18","source":null,"type":"exon","start":2860270,"end":2860452,"score":null,"strand":-1,"phase":null,"parent":"e163a393-fa70-4b10-91f8-3d08eecb9005","id":"5d7ae8c3-a91a-4468-9349-bc9c33c482d2","name":"ef04ed63-3f3e-4dc1-8470-c4a61758ae06"},"_uniqueID":"00bd7a2a-617e-48de-bc6e-4fa454f3d518_52_56"},{"data":{"seq_id":"Group11.18","source":null,"type":"CDS","start":2860270,"end":2860452,"score":null,"strand":-1,"phase":"1","parent":"e163a393-fa70-4b10-91f8-3d08eecb9005","id":"7fb9abb0-4836-4615-be08-b238741cc688","name":"7fb9abb0-4836-4615-be08-b238741cc688"},"_uniqueID":"00bd7a2a-617e-48de-bc6e-4fa454f3d518_52_72"},{"data":{"seq_id":"Group11.18","source":null,"type":"exon","start":2859758,"end":2860165,"score":null,"strand":-1,"phase":null,"parent":"e163a393-fa70-4b10-91f8-3d08eecb9005","id":"f1126bf1-1d16-4186-aa76-d31134aa1a93","name":"494202da-a844-474a-b9b1-03ddac9ed414"},"_uniqueID":"00bd7a2a-617e-48de-bc6e-4fa454f3d518_52_61"},{"data":{"seq_id":"Group11.18","source":null,"type":"CDS","start":2859758,"end":2860165,"score":null,"strand":-1,"phase":"2","parent":"e163a393-fa70-4b10-91f8-3d08eecb9005","id":"7fb9abb0-4836-4615-be08-b238741cc688","name":"7fb9abb0-4836-4615-be08-b238741cc688"},"_uniqueID":"00bd7a2a-617e-48de-bc6e-4fa454f3d518_52_73"}]},"_uniqueID":"00bd7a2a-617e-48de-bc6e-4fa454f3d518_52"}],"orig_id":"00bd7a2a-617e-48de-bc6e-4fa454f3d518"},"_uniqueID":"00bd7a2a-617e-48de-bc6e-4fa454f3d518"}
Group11.18 . gene 2859759 2864902 . - . [email protected];symbol=mygenesymbol;description=description of gene;Name=GB44997-RA-00001a;date_creation=2020-03-11;121=asdsad;provenance=rank%3D1%3Bfield%3DNAME%3Bdb_xref%3Dasfa:lkj%3Bevidence%3DECO:0000269%3Bnote%3Dnull%3Bbased_on%3D["as:12313"];Alias=syn1,syn2;Note=dfasdfasdf;gene_product=rank%3D1%3Bterm%3Dmy gene product%3Bdb_xref%3Dasdf:1212122%3Bevidence%3DECO:0000353%3Balternate%3Dtrue%3Bnote%3D[]%3Bbased_on%3D["asdf:1212"];ID=00bd7a2a-617e-48de-bc6e-4fa454f3d518;date_last_modified=2020-03-11;Dbxref=asdf:111212;status=accepted
Group11.18 . mRNA 2859759 2864902 . - . [email protected];Parent=00bd7a2a-617e-48de-bc6e-4fa454f3d518;gene_product=;ID=e163a393-fa70-4b10-91f8-3d08eecb9005;orig_id=5fa27908-0f06-4667-9fd6-5ae7d9770d18;date_last_modified=2020-03-11;Name=GB44997-RA-00001-00001;date_creation=2020-03-11
Group11.18 . exon 2864241 2864362 . - . Parent=e163a393-fa70-4b10-91f8-3d08eecb9005;ID=049b77a0-9079-46ee-afff-5267aa9c3c62;Name=01812965-063c-4256-96d5-c40533b0a3bf
Group11.18 . exon 2863765 2863937 . - . Parent=e163a393-fa70-4b10-91f8-3d08eecb9005;ID=875d6c57-9825-4495-a6d2-008eed438da7;Name=cf022cfc-06d6-44d8-b763-d4ac3765f7c4
Group11.18 . exon 2862069 2862242 . - . Parent=e163a393-fa70-4b10-91f8-3d08eecb9005;ID=bf1ec343-dd01-4115-b199-b040ba164109;Name=69553015-8e90-45c1-aeef-5185ee28053a
Group11.18 . exon 2860271 2860452 . - . Parent=e163a393-fa70-4b10-91f8-3d08eecb9005;ID=5d7ae8c3-a91a-4468-9349-bc9c33c482d2;Name=ef04ed63-3f3e-4dc1-8470-c4a61758ae06
Group11.18 . exon 2864488 2864902 . - . Parent=e163a393-fa70-4b10-91f8-3d08eecb9005;ID=b2650bf5-c4b6-446a-8539-51503c0c5215;Name=ac356fe9-eada-4d84-8860-429bd69fa3d9
Group11.18 . exon 2861368 2861438 . - . Parent=e163a393-fa70-4b10-91f8-3d08eecb9005;ID=44cc0e7a-8683-42ca-9742-41911b756632;Name=e24e7379-d4c2-40f5-b7f1-18b84d870cdf
Group11.18 . exon 2862327 2862541 . - . Parent=e163a393-fa70-4b10-91f8-3d08eecb9005;ID=4697c3d5-8753-44cb-841d-3ce9d46747ef;Name=567a4d75-9554-4ab6-9761-62b432526bcc
Group11.18 . exon 2860517 2860592 . - . Parent=e163a393-fa70-4b10-91f8-3d08eecb9005;ID=c8bccf61-c558-4081-a7d3-327ac8d8e08b;Name=1f50a7f3-9b3c-4233-8719-b06d8df7954f
Group11.18 . exon 2859759 2860165 . - . Parent=e163a393-fa70-4b10-91f8-3d08eecb9005;ID=f1126bf1-1d16-4186-aa76-d31134aa1a93;Name=494202da-a844-474a-b9b1-03ddac9ed414
Group11.18 . CDS 2864488 2864579 . - 0 Parent=e163a393-fa70-4b10-91f8-3d08eecb9005;ID=7fb9abb0-4836-4615-be08-b238741cc688;Name=7fb9abb0-4836-4615-be08-b238741cc688
Group11.18 . CDS 2864241 2864362 . - 1 Parent=e163a393-fa70-4b10-91f8-3d08eecb9005;ID=7fb9abb0-4836-4615-be08-b238741cc688;Name=7fb9abb0-4836-4615-be08-b238741cc688
Group11.18 . CDS 2864003 2864160 . - 2 Parent=e163a393-fa70-4b10-91f8-3d08eecb9005;ID=7fb9abb0-4836-4615-be08-b238741cc688;Name=7fb9abb0-4836-4615-be08-b238741cc688
Group11.18 . CDS 2863765 2863937 . - 0 Parent=e163a393-fa70-4b10-91f8-3d08eecb9005;ID=7fb9abb0-4836-4615-be08-b238741cc688;Name=7fb9abb0-4836-4615-be08-b238741cc688
Group11.18 . CDS 2863348 2863542 . - 1 Parent=e163a393-fa70-4b10-91f8-3d08eecb9005;ID=7fb9abb0-4836-4615-be08-b238741cc688;Name=7fb9abb0-4836-4615-be08-b238741cc688
Group11.18 . CDS 2863110 2863254 . - 1 Parent=e163a393-fa70-4b10-91f8-3d08eecb9005;ID=7fb9abb0-4836-4615-be08-b238741cc688;Name=7fb9abb0-4836-4615-be08-b238741cc688
Group11.18 . CDS 2862327 2862541 . - 0 Parent=e163a393-fa70-4b10-91f8-3d08eecb9005;ID=7fb9abb0-4836-4615-be08-b238741cc688;Name=7fb9abb0-4836-4615-be08-b238741cc688
Group11.18 . CDS 2862069 2862242 . - 1 Parent=e163a393-fa70-4b10-91f8-3d08eecb9005;ID=7fb9abb0-4836-4615-be08-b238741cc688;Name=7fb9abb0-4836-4615-be08-b238741cc688
Group11.18 . CDS 2861368 2861438 . - 1 Parent=e163a393-fa70-4b10-91f8-3d08eecb9005;ID=7fb9abb0-4836-4615-be08-b238741cc688;Name=7fb9abb0-4836-4615-be08-b238741cc688
Group11.18 . CDS 2860517 2860592 . - 2 Parent=e163a393-fa70-4b10-91f8-3d08eecb9005;ID=7fb9abb0-4836-4615-be08-b238741cc688;Name=7fb9abb0-4836-4615-be08-b238741cc688
Group11.18 . CDS 2860271 2860452 . - 1 Parent=e163a393-fa70-4b10-91f8-3d08eecb9005;ID=7fb9abb0-4836-4615-be08-b238741cc688;Name=7fb9abb0-4836-4615-be08-b238741cc688
Group11.18 . CDS 2859759 2860165 . - 2 Parent=e163a393-fa70-4b10-91f8-3d08eecb9005;ID=7fb9abb0-4836-4615-be08-b238741cc688;Name=7fb9abb0-4836-4615-be08-b238741cc688
Group11.18 . exon 2863110 2863254 . - . Parent=e163a393-fa70-4b10-91f8-3d08eecb9005;ID=f661050f-e2c5-41bc-a7bd-d14c05f73585;Name=4210a2d5-07a5-45b2-9426-37a4c1cb5b6a
Group11.18 . exon 2863348 2863542 . - . Parent=e163a393-fa70-4b10-91f8-3d08eecb9005;ID=e76bf1fc-6d4d-4fa2-8cf5-f5e0fe3af4b5;Name=8d558ee0-a67b-48ca-8ce3-b60aee1e5374
Group11.18 . exon 2864003 2864160 . - . Parent=e163a393-fa70-4b10-91f8-3d08eecb9005;ID=5d3f4fa0-2fcf-4f68-bda8-014bf7deada9;Name=367218ff-1eb1-47ce-b69e-a533b56413e0
Comments come through as comma-separated (hmm). Attributes come through as-is, which is probably good. Dbxref also comma-separated:
Group11.18 . gene 2859759 2864902 . - . [email protected];gene key1=gene attr 1;Note=comment 1,gene comment 2;gene key 2=gene attr 2;gene_product=;ID=0e8928c3-ce60-4228-87c6-a02f3fd3d1df;date_last_modified=2020-03-11;Name=GB44997-RA-00001-00001;Dbxref=aaa:1111,bbbb:2222;date_creation=2020-03-11
The JSON created is:
{"data":{"seq_id":"Group11.18","source":null,"type":"gene","start":2859758,"end":2864902,"score":null,"strand":-1,"phase":null,"owner":"[email protected]","gene key1":"gene attr 1","note":["comment 1","gene comment 2"],"gene key 2":"gene attr 2","id":"0e8928c3-ce60-4228-87c6-a02f3fd3d1df","date_last_modified":"2020-03-11","name":"GB44997-RA-00001-00001","dbxref":["aaa:1111","bbbb:2222"],"date_creation":"2020-03-11"}}
And the multiples are treated as arrays when they come in:
All of the data is in there. We just need to copy parent_id using the UUID and copy in the parent object so that generate transcript works properly:
https://github.com/GMOD/Apollo/blob/develop/grails-app/services/org/bbop/apollo/FeatureService.groovy#L413
and
https://github.com/GMOD/Apollo/blob/develop/grails-app/services/org/bbop/apollo/FeatureService.groovy#L1293
