From 9846c4f16109358b2774a3868004a0df3297f417 Mon Sep 17 00:00:00 2001 From: mboudet <mateo.boudet@gmail.com> Date: Thu, 5 Oct 2023 14:02:19 +0200 Subject: [PATCH 01/36] Test add annotation name --- cli/genoboo.js | 6 ++++++ imports/api/genes/geneCollection.js | 16 +++++++++++----- imports/api/genomes/annotation/addAnnotation.js | 11 +++++++++-- .../api/genomes/annotation/addAnnotation.test.js | 6 ++++++ .../annotation/parser/annotationParserGff3.js | 8 +++++--- imports/api/genomes/genomeCollection.js | 15 +++++++++------ imports/api/jobqueue/process-annotation.js | 5 ++++- imports/startup/server/fixtures/addTestData.js | 2 ++ 8 files changed, 52 insertions(+), 17 deletions(-) diff --git a/cli/genoboo.js b/cli/genoboo.js index bbf85cc3..8b28df82 100755 --- a/cli/genoboo.js +++ b/cli/genoboo.js @@ -322,6 +322,10 @@ addAnnotation '-n, --name <genome-name>', 'Reference genome name to which the annotation should be added.', ) + .option( + '--annot <annotation-ame>', + 'Annotation name', + ) .option( '-r, --re_protein <pattern>', 'Replacement string for the protein name using capturing groups defined by --re_protein_capture. Make sure to use JS-style groups ($1 for group 1)', @@ -352,6 +356,7 @@ addAnnotation password, port = 3000, name, + annot, re_protein, re_protein_capture, attr_protein, @@ -389,6 +394,7 @@ addAnnotation { fileName, genomeName: name, + annotationName: annot, re_protein, re_protein_capture: correctProteinCapture, attr_protein, diff --git a/imports/api/genes/geneCollection.js b/imports/api/genes/geneCollection.js index cc093e3e..bd13b122 100644 --- a/imports/api/genes/geneCollection.js +++ b/imports/api/genes/geneCollection.js @@ -73,9 +73,7 @@ const SubfeatureSchema = new SimpleSchema( ID: { type: String, index: true, - unique: true, - // denyUpdate: true, - label: 'Unique subfeature ID', + label: 'Subfeature ID', }, protein_id: { type: String, @@ -129,9 +127,8 @@ const GeneSchema = new SimpleSchema( { ID: { type: String, - unique: true, index: true, - label: 'Unique gene ID', + label: 'Gene ID', }, editing: { type: String, @@ -161,6 +158,11 @@ const GeneSchema = new SimpleSchema( index: true, label: 'Reference genome DB identifier (_id in genome collection)', }, + annotationName: { + type: String, + index: true, + label: 'Annotation name', + }, orthogroup: { type: OrthogroupSchema, index: true, @@ -207,8 +209,12 @@ const GeneSchema = new SimpleSchema( // Extend the gene schema with base features. GeneSchema.extend(IntervalBaseSchema); + Genes.attachSchema(GeneSchema); +Genes.createIndex({ID: 'text', 'annotationName': 'text'}, {name: 'Id and annotation index', unique: true}) +Genes.createIndex({'subfeatures.$.ID': 'text', 'annotationName': 'text'}, {name: 'SubId and annotation index', unique: true}) + export { Genes, GeneSchema, diff --git a/imports/api/genomes/annotation/addAnnotation.js b/imports/api/genomes/annotation/addAnnotation.js index b3ef47f9..55de26a3 100644 --- a/imports/api/genomes/annotation/addAnnotation.js +++ b/imports/api/genomes/annotation/addAnnotation.js @@ -15,6 +15,9 @@ const addAnnotation = new ValidatedMethod({ genomeName: { type: String, }, + annotationName: { + type: String, + }, re_protein: { type: String, optional: true, @@ -36,7 +39,7 @@ const addAnnotation = new ValidatedMethod({ noRetry: true, }, run({ - fileName, genomeName, re_protein, re_protein_capture, attr_protein, verbose, + fileName, genomeName, annotationName, re_protein, re_protein_capture, attr_protein, verbose, }) { if (!this.userId || !Roles.userIsInRole(this.userId, 'admin')) { throw new Meteor.Error('not-authorized'); @@ -46,8 +49,11 @@ const addAnnotation = new ValidatedMethod({ if (!existingGenome) { throw new Meteor.Error(`Unknown genome name: ${genomeName}`); } + if (typeof existingGenome.annotationTrack !== 'undefined') { - throw new Meteor.Error(`Genome ${genomeName} already has an annotation track`); + if (existingGenome.annotationTrack.some(annot => annot.name === annotationName)){ + throw new Meteor.Error(`Genome ${genomeName} already has an annotation track with the name ${annotationName}`); + } } const genomeId = existingGenome._id; @@ -58,6 +64,7 @@ const addAnnotation = new ValidatedMethod({ { fileName, genomeName, + annotationName, genomeId, re_protein, re_protein_capture, diff --git a/imports/api/genomes/annotation/addAnnotation.test.js b/imports/api/genomes/annotation/addAnnotation.test.js index 900b4914..68286cb1 100644 --- a/imports/api/genomes/annotation/addAnnotation.test.js +++ b/imports/api/genomes/annotation/addAnnotation.test.js @@ -31,6 +31,7 @@ describe('AddAnnotation', function testAnnotation() { const toAnnot = { fileName: 'assets/app/data/Bnigra.gff3', genomeName: 'Test Genome', + annotationName: 'Test annotation', verbose: false, }; @@ -54,6 +55,7 @@ describe('AddAnnotation', function testAnnotation() { const gene = genes[0]; chai.assert.equal(gene.ID, 'BniB01g000010.2N'); + chai.assert.equal(gene.annotationName, 'Test annotation'); chai.assert.equal(gene.seqid, 'B1'); chai.assert.equal(gene.source, 'AAFC_GIFS'); chai.assert.equal(gene.strand, '-'); @@ -73,6 +75,7 @@ describe('AddAnnotation', function testAnnotation() { const toAnnot = { fileName: 'assets/app/data/Bnigra_min.gff3', genomeName: 'Test Genome', + annotationName: 'Test annotation', verbose: false, }; @@ -94,6 +97,7 @@ describe('AddAnnotation', function testAnnotation() { const toAnnot = { fileName: 'assets/app/data/Bnigra_min.gff3', genomeName: 'Test Genome', + annotationName: 'Test annotation', verbose: false, re_protein_capture: '^Bni(.*?)$', re_protein: 'testprot-$1' @@ -117,6 +121,7 @@ describe('AddAnnotation', function testAnnotation() { const toAnnot = { fileName: 'assets/app/data/Bnigra_min.gff3', genomeName: 'Test Genome', + annotationName: 'Test annotation', verbose: false, attr_protein: 'protid' }; @@ -138,6 +143,7 @@ describe('AddAnnotation', function testAnnotation() { const toAnnot = { fileName: 'assets/app/data/Bnigra_min.gff3', genomeName: 'Test Genome', + annotationName: 'Test annotation', verbose: false, attr_protein: 'protid2' }; diff --git a/imports/api/genomes/annotation/parser/annotationParserGff3.js b/imports/api/genomes/annotation/parser/annotationParserGff3.js index 1984140b..8964cb47 100644 --- a/imports/api/genomes/annotation/parser/annotationParserGff3.js +++ b/imports/api/genomes/annotation/parser/annotationParserGff3.js @@ -17,10 +17,11 @@ import { Genes, GeneSchema } from '../../../genes/geneCollection'; * @param {Boolean} verbose - View more details. */ class AnnotationProcessor { - constructor(filename, genomeID, re_protein=undefined, re_protein_capture="^(.*?)$", attr_protein=undefined, verbose = true) { + constructor(filename, annotationName, genomeID, re_protein=undefined, re_protein_capture="^(.*?)$", attr_protein=undefined, verbose = true) { this.filename = filename; this.genomeID = genomeID; this.verbose = verbose; + this.annotationName = annotationName // Protein ID stuff // Regex options . @@ -501,6 +502,7 @@ class AnnotationProcessor { const features = { ID: identifier, genomeId: this.genomeID, + annotationName: this.annotationName, seqid: seqidGff, source: sourceGff, type: typeGff, @@ -594,9 +596,9 @@ class AnnotationProcessor { genomeCollection.update({ _id: this.genomeID, }, { - $set: { + $push: { annotationTrack: { - name: this.filename.split('/').pop(), + name: this.annotationName, }, }, }); diff --git a/imports/api/genomes/genomeCollection.js b/imports/api/genomes/genomeCollection.js index 7ead8563..c8b62309 100644 --- a/imports/api/genomes/genomeCollection.js +++ b/imports/api/genomes/genomeCollection.js @@ -70,24 +70,27 @@ const genomeSchema = new SimpleSchema({ label: 'Organism name', }, annotationTrack: { - type: Object, + type: Array, optional: true, - label: 'Genome annotation', + label: 'Genome annotations', + }, + 'annotationTrack.$': { + type: Object }, - 'annotationTrack.name': { + 'annotationTrack.$.name': { type: String, label: 'Annotation track name', }, - 'annotationTrack.blastDb': { + 'annotationTrack.$.blastDb': { type: Object, optional: true, label: 'Annotation track BLAST database identifiers', }, - 'annotationTrack.blastDb.nucl': { + 'annotationTrack.$.blastDb.nucl': { type: String, label: 'Nucleotide BLAST database', }, - 'annotationTrack.blastDb.prot': { + 'annotationTrack.$.blastDb.prot': { type: String, label: 'Protein BLAST database', }, diff --git a/imports/api/jobqueue/process-annotation.js b/imports/api/jobqueue/process-annotation.js index 028a6591..f7522e1a 100644 --- a/imports/api/jobqueue/process-annotation.js +++ b/imports/api/jobqueue/process-annotation.js @@ -14,17 +14,19 @@ jobQueue.processJobs( const { fileName, genomeName, + annotationName, genomeId, re_protein, re_protein_capture, attr_protein, verbose, } = job.data; - logger.log(`Adding annotation file "${fileName}" to genome "${genomeName}"`); + logger.log(`Adding annotation file "${fileName}" with name "${annotationName}" to genome "${genomeName}"`); if(verbose){ logger.log('file :', fileName); logger.log('name :', genomeName); + logger.log('annotation name : ', annotationName) logger.log('re_protein :', re_protein); logger.log('re_protein_capture', re_protein_capture); logger.log('attr_protein', attr_protein); @@ -33,6 +35,7 @@ jobQueue.processJobs( const lineProcessor = new AnnotationProcessor( fileName, + annotationName, genomeId, re_protein, re_protein_capture, diff --git a/imports/startup/server/fixtures/addTestData.js b/imports/startup/server/fixtures/addTestData.js index 150cc595..a2eb5695 100644 --- a/imports/startup/server/fixtures/addTestData.js +++ b/imports/startup/server/fixtures/addTestData.js @@ -68,6 +68,7 @@ export function addTestGenome(annot=false) { start: 0, end: 23320, genomeId: genomeId, + annotationName: "Annotation name", permission: 'admin', isPublic: false }) @@ -87,6 +88,7 @@ export function addTestGenome(annot=false) { start: 13640, end: 15401, genomeId: genomeId, + annotationName: "Annotation name", score: '.', subfeatures: [subfeature, cds], seq: 'AAAA', From 977863e6b9d005b81da64abeba0e76b07be1dde5 Mon Sep 17 00:00:00 2001 From: mboudet <mateo.boudet@gmail.com> Date: Thu, 5 Oct 2023 14:19:16 +0200 Subject: [PATCH 02/36] Fix index maybe --- imports/api/genes/geneCollection.js | 2 +- imports/startup/server/fixtures/addDefaultAttributes.js | 4 ++++ 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/imports/api/genes/geneCollection.js b/imports/api/genes/geneCollection.js index bd13b122..c2698501 100644 --- a/imports/api/genes/geneCollection.js +++ b/imports/api/genes/geneCollection.js @@ -213,7 +213,7 @@ GeneSchema.extend(IntervalBaseSchema); Genes.attachSchema(GeneSchema); Genes.createIndex({ID: 'text', 'annotationName': 'text'}, {name: 'Id and annotation index', unique: true}) -Genes.createIndex({'subfeatures.$.ID': 'text', 'annotationName': 'text'}, {name: 'SubId and annotation index', unique: true}) +Genes.createIndex({'subfeatures.ID': 'text', 'annotationName': 'text'}, {name: 'SubId and annotation index', unique: true}) export { Genes, diff --git a/imports/startup/server/fixtures/addDefaultAttributes.js b/imports/startup/server/fixtures/addDefaultAttributes.js index 07f0c459..04c59d6b 100644 --- a/imports/startup/server/fixtures/addDefaultAttributes.js +++ b/imports/startup/server/fixtures/addDefaultAttributes.js @@ -31,6 +31,10 @@ const PERMANENT_ATTRIBUTES = [ name: 'Genome', query: 'genomeId', }, + { + name: 'Annotation', + query: 'annotationName', + }, ]; export default function addDefaultAttributes() { From 5f50090af4ff177aa96cc5e70e9b561e4d7f1618 Mon Sep 17 00:00:00 2001 From: mboudet <mateo.boudet@gmail.com> Date: Thu, 5 Oct 2023 14:28:22 +0200 Subject: [PATCH 03/36] Test --- imports/api/genes/geneCollection.js | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/imports/api/genes/geneCollection.js b/imports/api/genes/geneCollection.js index c2698501..0b352739 100644 --- a/imports/api/genes/geneCollection.js +++ b/imports/api/genes/geneCollection.js @@ -212,8 +212,7 @@ GeneSchema.extend(IntervalBaseSchema); Genes.attachSchema(GeneSchema); -Genes.createIndex({ID: 'text', 'annotationName': 'text'}, {name: 'Id and annotation index', unique: true}) -Genes.createIndex({'subfeatures.ID': 'text', 'annotationName': 'text'}, {name: 'SubId and annotation index', unique: true}) +Genes.createIndex({ID: 'text', 'annotationName': 'text', 'subfeatures.ID': 'text'}, {name: 'Id and annotation index', unique: true}) export { Genes, From f48dafff8f5b99ff1d7dab285a09951c46e8736c Mon Sep 17 00:00:00 2001 From: mboudet <mateo.boudet@gmail.com> Date: Mon, 9 Oct 2023 15:31:08 +0000 Subject: [PATCH 04/36] fix test --- imports/api/genes/geneCollection.js | 5 ++- .../genomes/annotation/addAnnotation.test.js | 41 ++++++++++++++++++- .../startup/server/fixtures/addTestData.js | 3 +- 3 files changed, 44 insertions(+), 5 deletions(-) diff --git a/imports/api/genes/geneCollection.js b/imports/api/genes/geneCollection.js index 0b352739..578adb8a 100644 --- a/imports/api/genes/geneCollection.js +++ b/imports/api/genes/geneCollection.js @@ -1,5 +1,6 @@ import SimpleSchema from 'simpl-schema'; import { Mongo } from 'meteor/mongo'; +import logger from '/imports/api/util/logger.js'; const VALID_SUBFEATURE_TYPES = [ 'transcript', @@ -209,10 +210,10 @@ const GeneSchema = new SimpleSchema( // Extend the gene schema with base features. GeneSchema.extend(IntervalBaseSchema); - Genes.attachSchema(GeneSchema); -Genes.createIndex({ID: 'text', 'annotationName': 'text', 'subfeatures.ID': 'text'}, {name: 'Id and annotation index', unique: true}) +Genes.createIndex({ID: 1, annotationName: 1}, {name: 'Id and annotation index', unique: true}) +Genes.createIndex({'subfeatures.ID': 1, annotationName: 1}, {name: 'SubId and annotation index', unique: true}) export { Genes, diff --git a/imports/api/genomes/annotation/addAnnotation.test.js b/imports/api/genomes/annotation/addAnnotation.test.js index 68286cb1..66c14718 100644 --- a/imports/api/genomes/annotation/addAnnotation.test.js +++ b/imports/api/genomes/annotation/addAnnotation.test.js @@ -28,7 +28,7 @@ describe('AddAnnotation', function testAnnotation() { this.timeout(10000); const { genomeId, genomeSeqId } = addTestGenome(); - const toAnnot = { + let toAnnot = { fileName: 'assets/app/data/Bnigra.gff3', genomeName: 'Test Genome', annotationName: 'Test annotation', @@ -66,6 +66,45 @@ describe('AddAnnotation', function testAnnotation() { chai.assert.lengthOf(gene.subfeatures, 13, 'Number of subfeatures is not 13'); }); + it('Should add multiple copies of genes with different annotation names', function addAnnotationGff3() { + // Increase timeout + this.timeout(10000); + + const { genomeId, genomeSeqId } = addTestGenome(); + let toAnnot = { + fileName: 'assets/app/data/Bnigra.gff3', + genomeName: 'Test Genome', + annotationName: 'Test annotation', + verbose: false, + }; + + // Should fail for non-logged in + chai.expect(() => { + addAnnotation._execute({}, toAnnot); + }).to.throw('[not-authorized]'); + + // Should fail for non admin user + chai.expect(() => { + addAnnotation._execute(userContext, toAnnot); + }).to.throw('[not-authorized]'); + + // Add annotation. + addAnnotation._execute(adminContext, toAnnot); + + + toAnnot = { + fileName: 'assets/app/data/Bnigra.gff3', + genomeName: 'Test Genome', + annotationName: 'Test annotation2', + verbose: false, + }; + + addAnnotation._execute(adminContext, toAnnot); + + const genes = Genes.find({ genomeId: genomeId }).fetch(); + + chai.assert.lengthOf(genes, 10, 'Number of created genes is not 10'); + }); it('Should add a default -protein label to the mRNA protein_id', function addAnnotationGff3() { // Increase timeout diff --git a/imports/startup/server/fixtures/addTestData.js b/imports/startup/server/fixtures/addTestData.js index a2eb5695..70924a1d 100644 --- a/imports/startup/server/fixtures/addTestData.js +++ b/imports/startup/server/fixtures/addTestData.js @@ -51,7 +51,7 @@ export function addTestUsers() { export function addTestGenome(annot=false) { - const annotObj = annot ? { name: 'myfilename.gff'} : undefined + const annotObj = annot ? [{ name: 'myfilename.gff'}] : undefined const genomeId = genomeCollection.insert({ name: "Test Genome", @@ -68,7 +68,6 @@ export function addTestGenome(annot=false) { start: 0, end: 23320, genomeId: genomeId, - annotationName: "Annotation name", permission: 'admin', isPublic: false }) From 8beb9c66b76716d48b17ee91e6a83ab64d6f6435 Mon Sep 17 00:00:00 2001 From: mboudet <mateo.boudet@gmail.com> Date: Tue, 10 Oct 2023 16:48:25 +0200 Subject: [PATCH 05/36] Test UI --- imports/ui/singleGenePage/SingleGenePage.jsx | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/imports/ui/singleGenePage/SingleGenePage.jsx b/imports/ui/singleGenePage/SingleGenePage.jsx index 983cce10..99394ead 100644 --- a/imports/ui/singleGenePage/SingleGenePage.jsx +++ b/imports/ui/singleGenePage/SingleGenePage.jsx @@ -40,10 +40,19 @@ function isNotFound({ gene }) { return typeof gene === 'undefined'; } -function geneDataTracker({ match, genomeDataCache }) { +function isMultiple({ gene }) { + return gene.length > 1; +} + +function Multiple( {gene} ){ + return <div>Multiple annotation</div>; +} + +function geneDataTracker({ match, genomeDataCache, location }) { const { geneId } = match.params; + const { annotation } = new URLSearchParams(location.search); const geneSub = Meteor.subscribe('singleGene', { geneId }); - const gene = Genes.findOne({ ID: geneId }); + const gene = Genes.find({ ID: geneId, annotationName: annotation }).fetch(); const loading = !geneSub.ready(); return { loading, @@ -83,6 +92,7 @@ function SingleGenePage({ gene, genome = {} }) { <h4 className="title is-size-4 has-text-weight-light"> {`${gene.ID} `} <small className="text-muted">{genome.name}</small> + <small className="text-muted">{gene.annotationName}</small> </h4> <div className="tabs is-boxed"> <ul> From 0becbda5000d43520322e14b984249ac7fa1c048 Mon Sep 17 00:00:00 2001 From: mboudet <mateo.boudet@gmail.com> Date: Tue, 10 Oct 2023 15:47:43 +0000 Subject: [PATCH 06/36] Fix ui --- imports/api/genes/geneCollection.js | 7 +++++-- imports/ui/singleGenePage/SingleGenePage.jsx | 11 ++++++++--- 2 files changed, 13 insertions(+), 5 deletions(-) diff --git a/imports/api/genes/geneCollection.js b/imports/api/genes/geneCollection.js index 578adb8a..03595b8b 100644 --- a/imports/api/genes/geneCollection.js +++ b/imports/api/genes/geneCollection.js @@ -212,8 +212,11 @@ GeneSchema.extend(IntervalBaseSchema); Genes.attachSchema(GeneSchema); -Genes.createIndex({ID: 1, annotationName: 1}, {name: 'Id and annotation index', unique: true}) -Genes.createIndex({'subfeatures.ID': 1, annotationName: 1}, {name: 'SubId and annotation index', unique: true}) +if (Meteor.isServer) { + Genes.createIndex({ID: 1, annotationName: 1}, {name: 'Id and annotation index', unique: true}) + Genes.createIndex({'subfeatures.ID': 1, annotationName: 1}, {name: 'SubId and annotation index', unique: true}) +} + export { Genes, diff --git a/imports/ui/singleGenePage/SingleGenePage.jsx b/imports/ui/singleGenePage/SingleGenePage.jsx index 99394ead..042d1f40 100644 --- a/imports/ui/singleGenePage/SingleGenePage.jsx +++ b/imports/ui/singleGenePage/SingleGenePage.jsx @@ -50,9 +50,14 @@ function Multiple( {gene} ){ function geneDataTracker({ match, genomeDataCache, location }) { const { geneId } = match.params; - const { annotation } = new URLSearchParams(location.search); + const annotation = new URLSearchParams(location.search).get("annotation"); const geneSub = Meteor.subscribe('singleGene', { geneId }); - const gene = Genes.find({ ID: geneId, annotationName: annotation }).fetch(); + let gene + if (annotation) { + gene = Genes.findOne({ ID: geneId, annotationName: annotation }); + } else { + gene = Genes.findOne({ ID: geneId }); + } const loading = !geneSub.ready(); return { loading, @@ -91,7 +96,7 @@ function SingleGenePage({ gene, genome = {} }) { <header className="has-background-light"> <h4 className="title is-size-4 has-text-weight-light"> {`${gene.ID} `} - <small className="text-muted">{genome.name}</small> + <small className="text-muted">{genome.name} </small> <small className="text-muted">{gene.annotationName}</small> </h4> <div className="tabs is-boxed"> From efa2da0dc87ebf770d20f21013ad75bb9fc4a38d Mon Sep 17 00:00:00 2001 From: mboudet <mateo.boudet@gmail.com> Date: Wed, 11 Oct 2023 11:56:08 +0200 Subject: [PATCH 07/36] Some more stuff --- cli/genoboo.js | 52 ++++- imports/api/genes/addInterproscan.js | 18 +- .../api/genes/alignment/addSimilarSequence.js | 7 +- imports/api/genes/alignment/alignment.test.js | 3 + .../genes/alignment/parser/pairwiseParser.js | 13 +- .../api/genes/alignment/parser/xmlParser.js | 16 +- .../alignment/similarSequenceCollection.js | 4 + imports/api/genes/eggnog/addEggnog.js | 32 ++- imports/api/genes/eggnog/eggnog.test.js | 1 + imports/api/genes/eggnog/eggnogCollection.js | 4 + imports/api/genes/hectar/addHectar.js | 33 ++- imports/api/genes/hectar/hectar.test.js | 1 + imports/api/genes/hectar/hectarCollection.js | 4 + imports/api/genes/interproscan.js | 219 ------------------ .../genes/interproscan/interproscan.test.js | 2 + .../interproscan/interproscanCollection.js | 6 +- imports/api/genes/parseGff3Interproscan.js | 7 +- imports/api/genes/parseTsvInterproscan.js | 7 +- imports/api/publications.js | 5 +- imports/ui/singleGenePage/ProteinDomains.jsx | 4 +- 20 files changed, 167 insertions(+), 271 deletions(-) delete mode 100644 imports/api/genes/interproscan.js diff --git a/cli/genoboo.js b/cli/genoboo.js index 8b28df82..36f307a3 100755 --- a/cli/genoboo.js +++ b/cli/genoboo.js @@ -318,11 +318,11 @@ addAnnotation .arguments('<file>') .option('-u, --username <username>', 'GeneNoteBook admin username') .option('-p, --password <password>', 'GeneNoteBook admin password') - .option( + .requiredOption( '-n, --name <genome-name>', 'Reference genome name to which the annotation should be added.', ) - .option( + .requiredOption( '--annot <annotation-ame>', 'Annotation name', ) @@ -439,6 +439,10 @@ running GeneNoteBook server.` '--port [port]', 'Port on which GeneNoteBook is running. Default: 3000' ) + .option( + '--annot <annotation-ame>', + 'Annotation name', + ) .option( '-fmt, --format [parser]', `Choose a parser for the diamond output format. Parses .xml, .txt @@ -461,7 +465,7 @@ running GeneNoteBook server.` .action( ( file, - { username, password, port = 3000, format, algorithm, matrix, database } + { username, password, port = 3000, annot, format, algorithm, matrix, database } ) => { if (typeof file !== 'string') addDiamond.help(); @@ -496,6 +500,7 @@ file extension is not "xml", "txt"`); fileName, parser: parserType, program: 'diamond', + annot: annot, algorithm: algorithm, matrix: matrix, database: database, @@ -531,6 +536,10 @@ running GeneNoteBook server.` '-p, --password <adminPassword>', 'GeneNoteBook admin password' ) + .option( + '--annot <annotation-ame>', + 'Annotation name', + ) .option( '--port [port]', 'Port on which GeneNoteBook is running. Default: 3000' @@ -554,7 +563,7 @@ running GeneNoteBook server.` .action( ( file, - { username, password, port = 3000, format, algorithm, matrix, database } + { username, password, port = 3000, annot, format, algorithm, matrix, database } ) => { if (typeof file !== 'string') addBlast.help(); @@ -590,6 +599,7 @@ file extension is not "xml", "txt"`); parser: parserType, program: 'blast', algorithm: algorithm, + annot: annot, matrix: matrix, database: database, } @@ -625,6 +635,10 @@ addExpression '-d, --sample-description <description>', 'Description of the experiment' ) + .option( + '--annot <annotation-ame>', + 'Annotation name', + ) .option( '-r, --replicas <replicas...>', 'Comma-separated column positions, which are part of the same replica group. Can be set multiple times for multiple groups. The replica group name will be the first column, unless replica-names is set' @@ -645,7 +659,7 @@ addExpression const replicas = opts.replicas || []; const replicaNames = opts.replicaNames || []; const isPublic = opts.public; - + const annot = opts.annot if (!(fileName && username && password)) { program.help(); } @@ -654,6 +668,7 @@ addExpression { fileName, description, + annot, replicas, replicaNames, isPublic @@ -686,6 +701,10 @@ addExpression '-d, --sample-description <description>', 'Description of the experiment' ) + .option( + '--annot <annotation-ame>', + 'Annotation name', + ) .option( '--public', 'Set the generated replica groups as public. Default: false', @@ -698,6 +717,7 @@ addExpression const replicaGroup = opts.replicaGroup || fileName; const description = opts.sampleDescription || 'description'; const isPublic = opts.public + const anot = opts.annot if (!(fileName && username && password)) { program.help(); @@ -707,6 +727,7 @@ addExpression { fileName, sampleName, + annot: annot, replicaGroup, description, isPublic @@ -734,12 +755,16 @@ addInterproscan '--port [port]', 'Port on which GeneNoteBook is running. Default: 3000' ) + .option( + '--annot <annotation-ame>', + 'Annotation name', + ) .option( '--format [parser]', `Choose a parser for the interproscan output files. Parses .gff3 and .tsv extensions.` ) - .action((file, { username, password, port = 3000, format }) => { + .action((file, { username, password, port = 3000, format, annot }) => { if (typeof file !== 'string') addInterproscan.help(); const fileName = path.resolve(file); @@ -772,6 +797,7 @@ file extension is not "tsv", "gff3" or "xml".`); { fileName, parser: parserType, + annot: annot } ); }) @@ -800,11 +826,15 @@ addEggnog '-p, --password <adminPassword>', 'GeneNoteBook admin password' ) + .option( + '--annot <annotation-ame>', + 'Annotation name', + ) .option( '--port [port]', 'Port on which GeneNoteBook is running. Default: 3000' ) - .action((file, { username, password, port = 3000 }) => { + .action((file, { username, password, port = 3000, annot }) => { if (typeof file !== 'string') addEggnog.help(); const fileName = path.resolve(file); @@ -814,6 +844,7 @@ addEggnog new GeneNoteBookConnection({ username, password, port }).call('addEggnog', { fileName, + annot: annot }); }) .on('--help', () => { @@ -839,11 +870,15 @@ addHectar '-p, --password <adminPassword>', 'GeneNoteBook admin password' ) + .option( + '--annot <annotation-ame>', + 'Annotation name', + ) .option( '--port [port]', 'Port on which GeneNoteBook is running. Default: 3000' ) - .action((file, { username, password, port = 3000 }) => { + .action((file, { username, password, port = 3000, annot }) => { if (typeof file !== 'string') addHectar.help(); const fileName = path.resolve(file); @@ -853,6 +888,7 @@ addHectar new GeneNoteBookConnection({ username, password, port }).call('addHectar', { fileName, + annot: annot }); }) .on('--help', () => { diff --git a/imports/api/genes/addInterproscan.js b/imports/api/genes/addInterproscan.js index ad762466..fa53caa4 100644 --- a/imports/api/genes/addInterproscan.js +++ b/imports/api/genes/addInterproscan.js @@ -12,14 +12,16 @@ import { Meteor } from 'meteor/meteor'; * @method finalize */ class InterproscanProcessor { - constructor() { + constructor(annot) { this.bulkOp = interproscanCollection.rawCollection().initializeUnorderedBulkOp(); this.geneBulkOp = Genes.rawCollection().initializeUnorderedBulkOp(); this.currentProt = "" this.currentGene = "" this.currentContent = [] this.currentDB = [] - this.currentOnto = [] + this.currentOnto = [], + this.currentAnnotationName = "", + this.annot = annot } finalize = () => { @@ -47,11 +49,13 @@ class InterproscanProcessor { this.bulkOp.find({ gene_id: this.currentGene, protein_id: this.currentProt, + annotationName: this.currentAnnotationName }).upsert().update( { $set: { gene_id: this.currentGene, protein_id: this.currentProt, + annotationName: this.currentAnnotationName, protein_domains: this.currentContent }, }, @@ -63,7 +67,7 @@ class InterproscanProcessor { } if (this.currentDB != [] || this.currentOnto != []){ - this.geneBulkOp.find({ID: this.currentGene}).update({ + this.geneBulkOp.find({ID: this.currentGene, annotationName: this.currentAnnotationName}).update({ $addToSet: { 'attributes.Ontology_term': { $each: this.currentOnto }, 'attributes.Dbxref': { $each: this.currentDB } @@ -80,6 +84,10 @@ const addInterproscan = new ValidatedMethod({ name: 'addInterproscan', validate: new SimpleSchema({ fileName: { type: String }, + annot: { + type: String, + optional: true, + }, parser: { type: String, allowedValues: ['tsv', 'gff3'], @@ -88,7 +96,7 @@ const addInterproscan = new ValidatedMethod({ applyOptions: { noRetry: true, }, - run({ fileName, parser }) { + run({ fileName, annot, parser }) { if (!this.userId) { throw new Meteor.Error('not-authorized'); } @@ -96,7 +104,7 @@ const addInterproscan = new ValidatedMethod({ throw new Meteor.Error('not-authorized'); } - const job = new Job(jobQueue, 'addInterproscan', { fileName, parser }); + const job = new Job(jobQueue, 'addInterproscan', { fileName, annot, parser }); const jobId = job.priority('high').save(); // Continue with synchronous processing diff --git a/imports/api/genes/alignment/addSimilarSequence.js b/imports/api/genes/alignment/addSimilarSequence.js index abceca55..aee77c88 100644 --- a/imports/api/genes/alignment/addSimilarSequence.js +++ b/imports/api/genes/alignment/addSimilarSequence.js @@ -19,6 +19,10 @@ const addSimilarSequence = new ValidatedMethod({ optional: true, allowedValues: ['blast', 'diamond'], }, + annot: { + type: String, + optional: true, + }, algorithm: { type: String, optional: true, @@ -44,7 +48,7 @@ const addSimilarSequence = new ValidatedMethod({ applyOptions: { noRetry: true, }, - run({ fileName, parser, program, algorithm, matrix, database }) { + run({ fileName, annot, parser, program, algorithm, matrix, database }) { if (!this.userId) { throw new Meteor.Error('not-authorized'); } @@ -57,6 +61,7 @@ const addSimilarSequence = new ValidatedMethod({ 'addDiamond', { fileName, + annot, parser, program, algorithm, diff --git a/imports/api/genes/alignment/alignment.test.js b/imports/api/genes/alignment/alignment.test.js index 70c0ff96..6b2fa963 100644 --- a/imports/api/genes/alignment/alignment.test.js +++ b/imports/api/genes/alignment/alignment.test.js @@ -45,6 +45,7 @@ describe('alignment', function testAlignment() { algorithm: 'blastx', matrix: 'blosum62', database: 'nr', + annot: "Annotation name" }; // Should fail for non-logged in @@ -85,6 +86,7 @@ describe('alignment', function testAlignment() { algorithm: 'blastx', matrix: 'BLOSUM90', database: 'nr', + annot: "Annotation name" }; // Should fail for non-logged in @@ -126,6 +128,7 @@ describe('alignment', function testAlignment() { algorithm: 'blastx', matrix: 'BLOSUM90', database: 'nr', + annot: "Annotation name" }; // Should fail for non-logged in diff --git a/imports/api/genes/alignment/parser/pairwiseParser.js b/imports/api/genes/alignment/parser/pairwiseParser.js index 66037ba0..7fe08ade 100644 --- a/imports/api/genes/alignment/parser/pairwiseParser.js +++ b/imports/api/genes/alignment/parser/pairwiseParser.js @@ -7,7 +7,7 @@ class Pairwise { constructor({ iteration_query, query_length, - position_query, + position_query }){ this.iteration_query = iteration_query; this.query_length = query_length; @@ -28,7 +28,7 @@ class Pairwise { * @param {string} database - The reference database (Non-redundant protein sequences (nr)). */ class PairwiseProcessor { - constructor(program, algorithm, matrix, database) { + constructor(program, algorithm, matrix, database, annot) { this.genesDb = Genes.rawCollection(); this.pairWise = new Pairwise({}); this.program = program; @@ -36,6 +36,7 @@ class PairwiseProcessor { this.matrix = matrix; this.database = database; this.similarSeqBulkOp = similarSequencesCollection.rawCollection().initializeUnorderedBulkOp(); + this.annot = annot; } /** @@ -68,7 +69,8 @@ class PairwiseProcessor { /** Update or insert pairwise. */ this.similarSeqBulkOp.find({ iteration_query: this.pairWise.iteration_query, - protein_id: this.pairWise.iteration_query + protein_id: this.pairWise.iteration_query, + annotationName: this.annot, }).upsert().update( { $set: { @@ -77,6 +79,7 @@ class PairwiseProcessor { matrix_ref: this.matrix, database_ref: this.database, iteration_query: this.pairWise.iteration_query, + annotationName: this.annot, protein_id: this.pairWise.iteration_query, query_len: this.pairWise.query_length, iteration_hits: this.pairWise.iteration_hits, @@ -361,7 +364,8 @@ class PairwiseProcessor { this.similarSeqBulkOp.find({ iteration_query: this.pairWise.iteration_query, - protein_id: this.pairWise.iteration_query + protein_id: this.pairWise.iteration_query, + annotationName: this.annot, }).upsert().update( { $set: { @@ -370,6 +374,7 @@ class PairwiseProcessor { matrix_ref: this.matrix, database_ref: this.database, iteration_query: this.pairWise.iteration_query, + annotationName: this.annot, protein_id: this.pairWise.iteration_query, query_len: this.pairWise.query_length, iteration_hits: this.pairWise.iteration_hits, diff --git a/imports/api/genes/alignment/parser/xmlParser.js b/imports/api/genes/alignment/parser/xmlParser.js index cebe7c3c..c88147de 100644 --- a/imports/api/genes/alignment/parser/xmlParser.js +++ b/imports/api/genes/alignment/parser/xmlParser.js @@ -16,12 +16,13 @@ import logger from '/imports/api/util/logger.js'; */ class XmlProcessor { - constructor(program, algorithm, matrix, database) { + constructor(program, algorithm, matrix, database, annot) { this.genesDb = Genes.rawCollection(); this.program = program; this.algorithm = algorithm; this.matrix = matrix; this.database = database; + this.annot = annot; this.similarSeqBulkOp = similarSequencesCollection.rawCollection().initializeUnorderedBulkOp(); } @@ -101,9 +102,16 @@ class XmlProcessor { await Promise.all(splitIterationQuery.map(async (iter) => { /** Chek if the queries exist in the genes collection. */ - const subfeatureIsFound = await this.genesDb.findOne({ $or: [{'subfeatures.ID': iter}, {'subfeatures.protein_id': iter}] }); + + let geneQuery = { $or: [{'subfeatures.ID': iter}, {'subfeatures.protein_id': iter}] } + if (typeof this.annot !== "undefined"){ + geneQuery['annotationName'] = this.annot + } + + const subfeatureIsFound = await this.genesDb.findOne(geneQuery); if (typeof subfeatureIsFound !== 'undefined' && subfeatureIsFound !== null) { /** Get the total query sequence length. */ + const annotationName = subfeatureIsFound.annotationName const queryLen = blastIteration[i]['iteration_query-len'] /** Get the root tag of hit sequences. */ @@ -185,7 +193,8 @@ class XmlProcessor { /** Mongo bulk-operation. */ this.similarSeqBulkOp.find({ iteration_query: geneIdentifier, - protein_id: iter + protein_id: iter, + annotationName: annotationName }).upsert().update( { $set: { @@ -197,6 +206,7 @@ class XmlProcessor { protein_id: iter, query_len: queryLen, iteration_hits: iterations, + annotationName: annotationName }, }, { diff --git a/imports/api/genes/alignment/similarSequenceCollection.js b/imports/api/genes/alignment/similarSequenceCollection.js index d0e0c918..b902b752 100644 --- a/imports/api/genes/alignment/similarSequenceCollection.js +++ b/imports/api/genes/alignment/similarSequenceCollection.js @@ -26,6 +26,10 @@ const similarSequencesSchema = new SimpleSchema({ type: String, label: 'Protein_id', }, + annotationName: { + type: String, + label: 'Annotation name', + }, iteration_hits: { type: Array, label: 'List of iteration hits.', diff --git a/imports/api/genes/eggnog/addEggnog.js b/imports/api/genes/eggnog/addEggnog.js index 573eb5ff..4f00d17d 100644 --- a/imports/api/genes/eggnog/addEggnog.js +++ b/imports/api/genes/eggnog/addEggnog.js @@ -90,38 +90,42 @@ class EggnogProcessor { // If subfeatures is found in genes database (e.g: ID = // MMUCEDO_000002-T1). - const subfeatureIsFound = Genes.findOne({ + + let geneQuery = { $or: [ { 'subfeatures.ID': queryName }, { 'subfeatures.protein_id': queryName }, ], - }); + } + if (typeof this.annot !== "undefined"){ + geneQuery['annotationName'] = this.annot + } + + const subfeatureIsFound = Genes.findOne(geneQuery); if (typeof subfeatureIsFound !== 'undefined') { // Increment eggnog. this.nEggnog += 1; + let annotationName = subfeatureIsFound.annotationName + annotations['annotationName'] = annotationName // Update or insert if no matching documents were found. const documentEggnog = eggnogCollection.upsert( - { query_name: queryName }, // selector. + { query_name: queryName, annotationName }, // selector. annotations, // modifier. ); // Update eggnogId in genes database. if (typeof documentEggnog.insertedId !== 'undefined') { // Eggnog _id is created. - return this.genesDb.update({ - $or: [ - { 'subfeatures.ID': queryName }, - { 'subfeatures.protein_id': queryName }, - ]}, + return this.genesDb.update(geneQuery, { $set: { eggnogId: documentEggnog.insertedId } }, ); } else { // Eggnog already exists. - const eggnogIdentifiant = eggnogCollection.findOne({ query_name: queryName })._id; + const eggnogIdentifiant = eggnogCollection.findOne({ query_name: queryName, annotationName })._id; return this.genesDb.update( - { $or: [{'subfeatures.ID': queryName}, {'subfeatures.protein_id': queryName}] }, + geneQuery, { $set: { eggnogId: eggnogIdentifiant } }, ); } @@ -139,11 +143,15 @@ const addEggnog = new ValidatedMethod({ name: 'addEggnog', validate: new SimpleSchema({ fileName: { type: String }, + annot: { + type: String, + optional: true, + }, }).validator(), applyOptions: { noRetry: true, }, - run({ fileName }) { + run({ fileName, annot }) { if (!this.userId) { throw new Meteor.Error('not-authorized'); } @@ -152,7 +160,7 @@ const addEggnog = new ValidatedMethod({ } logger.log('file :', { fileName }); - const job = new Job(jobQueue, 'addEggnog', { fileName }); + const job = new Job(jobQueue, 'addEggnog', { fileName, annot }); const jobId = job.priority('high').save(); let { status } = job.doc; diff --git a/imports/api/genes/eggnog/eggnog.test.js b/imports/api/genes/eggnog/eggnog.test.js index cc0cd260..9a08f565 100644 --- a/imports/api/genes/eggnog/eggnog.test.js +++ b/imports/api/genes/eggnog/eggnog.test.js @@ -33,6 +33,7 @@ describe('eggnog', function testEggnog() { const eggNogParams = { fileName: 'assets/app/data/Bnigra_eggnog.tsv', + annot: "Annotation name" }; // Should fail for non-logged in diff --git a/imports/api/genes/eggnog/eggnogCollection.js b/imports/api/genes/eggnog/eggnogCollection.js index 2c6ef1a5..5c766caa 100644 --- a/imports/api/genes/eggnog/eggnogCollection.js +++ b/imports/api/genes/eggnog/eggnogCollection.js @@ -6,6 +6,10 @@ const eggnogSchema = new SimpleSchema({ type: String, label: 'Query sequence name.', }, + annotationName: { + type: String, + label: 'Annotation name', + }, seed_eggNOG_ortholog: { type: String, label: 'Best protein match in eggNOG.', diff --git a/imports/api/genes/hectar/addHectar.js b/imports/api/genes/hectar/addHectar.js index 7c8ebf6d..c3bd8a17 100644 --- a/imports/api/genes/hectar/addHectar.js +++ b/imports/api/genes/hectar/addHectar.js @@ -63,39 +63,44 @@ class HectarProcessor { } // If subfeatures is found in genes database (e.g: ID = // MMUCEDO_000002-T1). - const subfeatureIsFound = Genes.findOne({ + + let geneQuery = { $or: [ { 'subfeatures.ID': proteinId }, { 'subfeatures.protein_id': proteinId }, ], - }); + } + if (typeof this.annot !== "undefined"){ + geneQuery['annotationName'] = this.annot + } + + const subfeatureIsFound = Genes.findOne(geneQuery); if (typeof subfeatureIsFound !== 'undefined') { console.log("if loop" + typeof subfeatureIsFound); + let annotationName = subfeatureIsFound.annotationName // Increment hectar. this.nHectar += 1; + annotations['annotationName'] = annotationName + // Update or insert if no matching documents were found. const documentHectar = hectarCollection.upsert( - { protein_id: proteinId }, // selector. + { protein_id: proteinId, annotationName }, // selector. annotations, // modifier. ); // Update hectarId in genes database. if (typeof documentHectar.insertedId !== 'undefined') { // Hectar _id is created. - return this.genesDb.update({ - $or: [ - { 'subfeatures.ID': proteinId }, - { 'subfeatures.protein_id': proteinId }, - ]}, + return this.genesDb.update(geneQuery, { $set: { hectarId: documentHectar.insertedId } }, ); } else { // Hectar already exists. - const hectarIdentifiant = hectarCollection.findOne({ protein_id: proteinId })._id; + const hectarIdentifiant = hectarCollection.findOne({ protein_id: proteinId, annotationName })._id; return this.genesDb.update( - { $or: [{'subfeatures.ID': proteinId}, {'subfeatures.protein_id': proteinId}] }, + geneQuery, { $set: { hectarId: hectarIdentifiant } }, ); } @@ -113,11 +118,15 @@ const addHectar = new ValidatedMethod({ name: 'addHectar', validate: new SimpleSchema({ fileName: { type: String }, + annot: { + type: String, + optional: true, + }, }).validator(), applyOptions: { noRetry: true, }, - run({ fileName }) { + run({ fileName, annot }) { if (!this.userId) { throw new Meteor.Error('not-authorized'); } @@ -126,7 +135,7 @@ const addHectar = new ValidatedMethod({ } logger.log('file :', { fileName }); - const job = new Job(jobQueue, 'addHectar', { fileName }); + const job = new Job(jobQueue, 'addHectar', { fileName, annot }); const jobId = job.priority('high').save(); let { status } = job.doc; diff --git a/imports/api/genes/hectar/hectar.test.js b/imports/api/genes/hectar/hectar.test.js index dbc210f8..beb1c11f 100644 --- a/imports/api/genes/hectar/hectar.test.js +++ b/imports/api/genes/hectar/hectar.test.js @@ -33,6 +33,7 @@ describe('hectar', function testHectar() { const hectarParams = { fileName: 'assets/app/data/Bnigra_hectar.tab', + annot: "Annotation name" }; // Should fail for non-logged in diff --git a/imports/api/genes/hectar/hectarCollection.js b/imports/api/genes/hectar/hectarCollection.js index bf7dad3f..5033f203 100644 --- a/imports/api/genes/hectar/hectarCollection.js +++ b/imports/api/genes/hectar/hectarCollection.js @@ -6,6 +6,10 @@ const hectarSchema = new SimpleSchema({ type: String, label: 'Query sequence name and type.', }, + annotationName: { + type: String, + label: 'Annotation name', + }, predicted_targeting_category: { type: String, label: 'Predicted sub-cellular localization.', diff --git a/imports/api/genes/interproscan.js b/imports/api/genes/interproscan.js deleted file mode 100644 index 0df060b9..00000000 --- a/imports/api/genes/interproscan.js +++ /dev/null @@ -1,219 +0,0 @@ -/* import { Meteor } from 'meteor/meteor'; -import { Roles } from 'meteor/alanning:roles'; - -import request from 'request'; -import Future from 'fibers/future'; - -import { getGeneSequences } from '/imports/api/util/util.js'; - -import { Genes } from '/imports/api/genes/gene_collection.js'; - -const revcomp = (seq) => { - const comp = { - 'A':'T','a':'t', - 'T':'A','t':'a', - 'C':'G','c':'g', - 'G':'C','g':'c', - 'N':'N','n':'n' - } - const revSeqArray = seq.split('').reverse() - const revCompSeqArray = revSeqArray.map( (nuc) => { - return comp[nuc] - }) - const revCompSeq = revCompSeqArray.join('') - return revCompSeq -} - -const translate = (seq) => { - const trans = { - 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', - 'AGG': 'R', 'AGC': 'S', 'GTA': 'V', - 'AGA': 'R', 'ACT': 'T', 'GTG': 'V', - 'AGT': 'S', 'CCA': 'P', 'CCC': 'P', - 'GGT': 'G', 'CGA': 'R', 'CGC': 'R', - 'TAT': 'Y', 'CGG': 'R', 'CCT': 'P', - 'GGG': 'G', 'GGA': 'G', 'GGC': 'G', - 'TAA': '*', 'TAC': 'Y', 'CGT': 'R', - 'TAG': '*', 'ATA': 'I', 'CTT': 'L', - 'ATG': 'M', 'CTG': 'L', 'ATT': 'I', - 'CTA': 'L', 'TTT': 'F', 'GAA': 'E', - 'TTG': 'L', 'TTA': 'L', 'TTC': 'F', - 'GTC': 'V', 'AAG': 'K', 'AAA': 'K', - 'AAC': 'N', 'ATC': 'I', 'CAT': 'H', - 'AAT': 'N', 'GTT': 'V', 'CAC': 'H', - 'CAA': 'Q', 'CAG': 'Q', 'CCG': 'P', - 'TCT': 'S', 'TGC': 'C', 'TGA': '*', - 'TGG': 'W', 'TCG': 'S', 'TCC': 'S', - 'TCA': 'S', 'GAG': 'E', 'GAC': 'D', - 'TGT': 'C', 'GCA': 'A', 'GCC': 'A', - 'GCG': 'A', 'GCT': 'A', 'CTC': 'L', - 'GAT': 'D'} - const codonArray = seq.match(/.{1,3}/g) - const pepArray = codonArray.map( (codon) => { - let aminoAcid = 'X' - if (codon.indexOf('N') < 0){ - aminoAcid = trans[codon] - } - return aminoAcid - }) - const pep = pepArray.join('') - return pep -} - -const makeFasta = (gene) => { - let transcripts = gene.subfeatures.filter( (subfeature) => { return subfeature.type === 'mRNA' }) - let sequences = transcripts.map( (transcript) => { - let transcriptSeq = `>${transcript.ID}\n`; - let transcriptPep = `>${transcript.ID}\n`; - let cdsArray = gene.subfeatures.filter( (sub) => { - return sub.parents.indexOf(transcript.ID) >= 0 && sub.type === 'CDS' - }).sort( (a,b) => { - return a.start - b.start - }) - - let refStart = 10e99; - //let referenceSubscription = Meteor.subscribe('references',gene.seqid) - - //find all reference fragments overlapping the mRNA feature - let referenceArray = References.find({ - header: gene.seqid, - $and: [ - { start: {$lte: gene.end} }, - { end: {$gte: gene.start} } - ] - }).fetch() - - if (referenceArray.length){ - let reference = referenceArray.sort( (a,b) => { - //sort on start coordinate - return a.start - b.start - }).map( (ref) => { - //find starting position of first reference fragment - refStart = Math.min(refStart,ref.start) - return ref.seq - }).join('') - - seq = cdsArray.map( (cds, index) => { - let start = cds.start - refStart - 1; - let end = cds.end - refStart; - return reference.slice(start,end) - }).join('') - - let phase; - if (this.strand === '-'){ - seq = revcomp(seq) - phase = cdsArray[cdsArray.length -1].phase - } else { - phase = cdsArray[0].phase - } - - if ([1,2].indexOf(phase) >= 0){ - seq = seq.slice(phase) - } - - let pep = translate(seq.toUpperCase()); - - transcriptSeq += seq; - - transcriptPep += pep; - transcriptPep = transcriptPep.split('*').join('X') - } - return {ID:transcript.ID, seq: transcriptSeq, pep: transcriptPep} - }) - return sequences -} - -function submitInterpro(sequenceId,peptide){ - const submitJob = new Future(); - - request.post({ - url: 'http://www.ebi.ac.uk/Tools/services/rest/iprscan5/run/', - form: { - email: 'rens.holmer@gmail.com', - title: `genebook protein ${sequenceId}`, - sequence: peptide - } - }, (error, response, jobId) => { - console.log('error:', error); // Print the error if one occurred - console.log('statusCode:', response && response.statusCode); // Print the response status code if a response was received - console.log('requestId:', jobId); - submitJob.return(jobId) - }) - - const jobId = submitJob.wait() - - return jobId -} - -function pollInterpro(jobId,cb){ - const statusRequest = new Future(); - const url = `http://www.ebi.ac.uk/Tools/services/rest/iprscan5/status/${jobId}`; - console.log(`Trying ${url}`) - request.get(url, (error,response,body) => { - console.log(error) - console.log(body) - statusRequest.return(body) - }) - const status = statusRequest.wait() - if (status === 'RUNNING'){ - //figure out a way to call the function with a parameter - Meteor.setTimeout(function(){return pollInterpro(jobId,cb)}, 100000) - } else { - cb(status) - } -} - -function getInterproResults(jobId){ - const future = new Future(); - const url = `http://www.ebi.ac.uk/Tools/services/rest/iprscan5/result/${jobId}/json` - console.log(`Trying ${url}`) - request.get(url, (error,response,body) => { - let interproAnnotation = JSON.parse(body) - future.return(interproAnnotation) - }) - const results = future.wait() - return results -} - -Meteor.methods({ - interproscan(geneId){ - if (! this.userId) { - throw new Meteor.Error('not-authorized'); - } - if (! Roles.userIsInRole(this.userId,'admin')){ - throw new Meteor.Error('not-authorized'); - } - - //this.unblock(); - const gene = Genes.findOne({ID: geneId}) - const sequences = getGeneSequences(gene) - const results = sequences.map((sequence) => { - - // interproscan does not like stop codons, just replace all with X - let pep = sequence.pep.split('*').join('X') - - const jobId = submitInterpro(sequence.ID, pep); - - const fut = new Future(); - pollInterpro(jobId, (status) => { - console.log(`pollInterpro: ${status}`) - fut.return(status) - }) - - const finished = fut.wait(); - - let results; - - if (finished === 'FINISHED'){ - results = getInterproResults(jobId) - console.log(results) - Genes.update({'subfeatures.ID':sequence.ID},{$set:{interproscan:results[0].matches}}) - } - - return results - }) - - return results - } -}) -*/ diff --git a/imports/api/genes/interproscan/interproscan.test.js b/imports/api/genes/interproscan/interproscan.test.js index 1bfbc627..6add689b 100644 --- a/imports/api/genes/interproscan/interproscan.test.js +++ b/imports/api/genes/interproscan/interproscan.test.js @@ -41,6 +41,7 @@ describe('interproscan', function testInterproscan() { const interproParams = { fileName: 'assets/app/data/Bnigra_interproscan.tsv', parser: "tsv", + annot: "Annotation name" }; // Should fail for non-logged in @@ -89,6 +90,7 @@ describe('interproscan', function testInterproscan() { const interproParams = { fileName: 'assets/app/data/Bnigra_interproscan.gff', parser: "gff3", + annot: "Annotation name" }; // Should fail for non-logged in diff --git a/imports/api/genes/interproscan/interproscanCollection.js b/imports/api/genes/interproscan/interproscanCollection.js index 65a2ede8..3d9f577c 100644 --- a/imports/api/genes/interproscan/interproscanCollection.js +++ b/imports/api/genes/interproscan/interproscanCollection.js @@ -11,6 +11,10 @@ const interproscanSchema = new SimpleSchema({ type: String, label: 'Linked protein ID', }, + annotationName: { + type: String, + label: 'Annotation name', + }, protein_domains: { type: Array, label: 'Interproscan protein domains', @@ -20,7 +24,7 @@ const interproscanSchema = new SimpleSchema({ type: Object, label: 'Interproscan protein domain', blackbox: true, - }, + } }); const interproscanCollection = new Mongo.Collection('interproscan'); diff --git a/imports/api/genes/parseGff3Interproscan.js b/imports/api/genes/parseGff3Interproscan.js index 5d4a11dd..c4b42914 100644 --- a/imports/api/genes/parseGff3Interproscan.js +++ b/imports/api/genes/parseGff3Interproscan.js @@ -57,9 +57,14 @@ class ParseGff3File extends InterproscanProcessor { this.currentProt = seqId this.currentGene = "" - let gene = Genes.findOne({ $or: [{'subfeatures.ID': seqId}, {'subfeatures.protein_id': seqId}] }); + let geneQuery = { $or: [{'subfeatures.ID': seqId}, {'subfeatures.protein_id': seqId}] } + if (typeof this.annot !== "undefined"){ + geneQuery['annotationName'] = this.annot + } + let gene = Genes.findOne(geneQuery); if (typeof gene !== "undefined"){ this.currentGene = gene.ID + this.currentAnnotationName = gene.annotationName } this.currentContent = [] diff --git a/imports/api/genes/parseTsvInterproscan.js b/imports/api/genes/parseTsvInterproscan.js index 8f26694e..e4737c43 100644 --- a/imports/api/genes/parseTsvInterproscan.js +++ b/imports/api/genes/parseTsvInterproscan.js @@ -30,9 +30,14 @@ class ParseTsvFile extends InterproscanProcessor { this.currentProt = seqId this.currentGene = "" - let gene = Genes.findOne({ $or: [{'subfeatures.ID': seqId}, {'subfeatures.protein_id': seqId}] }); + let geneQuery = { $or: [{'subfeatures.ID': seqId}, {'subfeatures.protein_id': seqId}] } + if (typeof this.annot !== "undefined"){ + geneQuery['annotationName'] = this.annot + } + let gene = Genes.findOne(geneQuery); if (typeof gene !== "undefined"){ this.currentGene = gene.ID + this.currentAnnotationName = gene.annotationName } this.currentContent = [] diff --git a/imports/api/publications.js b/imports/api/publications.js index cc594cdb..eed47fe7 100644 --- a/imports/api/publications.js +++ b/imports/api/publications.js @@ -217,6 +217,7 @@ Meteor.publish({ alignment(gene) { const diamond = similarSequencesCollection.find( { + annotationName: gene.annotationName, $or: [ { iteration_query: gene.ID }, { iteration_query: { $in: gene.children } }, @@ -225,8 +226,8 @@ Meteor.publish({ ); return diamond; }, - interpro(query){ - return interproscanCollection.find({gene_id: query}) + interpro(gene){ + return interproscanCollection.find({gene_id: gene.ID, annotationName: gene.annotationName}) }, orthogroups(ID) { return orthogroupCollection.find({ _id: ID }); diff --git a/imports/ui/singleGenePage/ProteinDomains.jsx b/imports/ui/singleGenePage/ProteinDomains.jsx index e8f8144a..00211331 100644 --- a/imports/ui/singleGenePage/ProteinDomains.jsx +++ b/imports/ui/singleGenePage/ProteinDomains.jsx @@ -295,7 +295,7 @@ function NoProteinDomains({ showHeader }) { } function InterproDataTracker({ gene }) { - const interproSub = Meteor.subscribe('interpro', gene.ID); + const interproSub = Meteor.subscribe('interpro', gene); const loading = !interproSub.ready(); const proteinDomains = interproscanCollection.find({}).fetch() @@ -372,7 +372,7 @@ function ProteinDomains({ ); }) - let axisTransform = `translate(0,${15 + currentTranslate})` + let axisTransform = `translate(0,${15 + currentTranslate})` let gTransform = `translate(0,${40 + currentTranslate})` let data = ( From 454a4a0e470d6327ebc5c2656ac4914a84be409b Mon Sep 17 00:00:00 2001 From: mboudet <mateo.boudet@gmail.com> Date: Wed, 11 Oct 2023 14:20:25 +0000 Subject: [PATCH 08/36] fixing ui --- imports/api/api.js | 1 - imports/api/genes/parseGff3Interproscan.js | 2 ++ 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/imports/api/api.js b/imports/api/api.js index 1c889783..ddcecfb2 100644 --- a/imports/api/api.js +++ b/imports/api/api.js @@ -17,7 +17,6 @@ import './genomes/removeGenome.js'; import './genomes/annotation/removeAnnotationTrack.js'; import './genomes/annotation/addAnnotation.js'; -import './genes/interproscan.js'; import './genes/addInterproscan.js'; import './genes/eggnog/addEggnog.js'; import './genes/hectar/addHectar.js'; diff --git a/imports/api/genes/parseGff3Interproscan.js b/imports/api/genes/parseGff3Interproscan.js index c4b42914..a6a72f58 100644 --- a/imports/api/genes/parseGff3Interproscan.js +++ b/imports/api/genes/parseGff3Interproscan.js @@ -62,6 +62,8 @@ class ParseGff3File extends InterproscanProcessor { geneQuery['annotationName'] = this.annot } let gene = Genes.findOne(geneQuery); + logger.log(gene) + logger.log(geneQuery) if (typeof gene !== "undefined"){ this.currentGene = gene.ID this.currentAnnotationName = gene.annotationName From fcaeca96702b8066afb47e1110884f175758bede Mon Sep 17 00:00:00 2001 From: mboudet <mateo.boudet@gmail.com> Date: Wed, 11 Oct 2023 16:55:18 +0200 Subject: [PATCH 09/36] Test check gene in pairwise parser --- .../genes/alignment/parser/pairwiseParser.js | 30 ++++++++++++++++--- 1 file changed, 26 insertions(+), 4 deletions(-) diff --git a/imports/api/genes/alignment/parser/pairwiseParser.js b/imports/api/genes/alignment/parser/pairwiseParser.js index 7fe08ade..37f3d489 100644 --- a/imports/api/genes/alignment/parser/pairwiseParser.js +++ b/imports/api/genes/alignment/parser/pairwiseParser.js @@ -31,6 +31,7 @@ class PairwiseProcessor { constructor(program, algorithm, matrix, database, annot) { this.genesDb = Genes.rawCollection(); this.pairWise = new Pairwise({}); + this.currentGene = "" this.program = program; this.algorithm = algorithm; this.matrix = matrix; @@ -63,6 +64,22 @@ class PairwiseProcessor { this.pairWise.iteration_query = queryClean; } + let geneQuery = { + $or: [ + { 'subfeatures.ID': this.pairWise.iteration_query }, + { 'subfeatures.protein_id': this.pairWise.iteration_query }, + ], + } + if (typeof this.annot !== "undefined"){ + geneQuery['annotationName'] = this.annot + } + + this.currentGene = Genes.findOne(geneQuery); + if (typeof this.currentGene === 'undefined'){ + logger.warn(`Warning ! No sub-feature was found for ${this.pairWise.iteration_query}.`); + return + } + /** In the case where a new pairwise must be created. */ if (typeof this.pairWise.iteration_query !== 'undefined' && this.pairWise.iteration_query !== queryClean) { @@ -70,7 +87,7 @@ class PairwiseProcessor { this.similarSeqBulkOp.find({ iteration_query: this.pairWise.iteration_query, protein_id: this.pairWise.iteration_query, - annotationName: this.annot, + annotationName: this.currentGene.annotationName, }).upsert().update( { $set: { @@ -79,7 +96,7 @@ class PairwiseProcessor { matrix_ref: this.matrix, database_ref: this.database, iteration_query: this.pairWise.iteration_query, - annotationName: this.annot, + annotationName: this.currentGene.annotationName, protein_id: this.pairWise.iteration_query, query_len: this.pairWise.query_length, iteration_hits: this.pairWise.iteration_hits, @@ -97,6 +114,11 @@ class PairwiseProcessor { this.pairWise.iteration_query = queryClean; this.pairWise.iteration_hits = []; } + + if (typeof this.currentGene === 'undefined'){ + return + } + if (/Length/.test(line)) { /** * Get and clean the length of the query sequence according to the program used. @@ -365,7 +387,7 @@ class PairwiseProcessor { this.similarSeqBulkOp.find({ iteration_query: this.pairWise.iteration_query, protein_id: this.pairWise.iteration_query, - annotationName: this.annot, + annotationName: this.currentGene.annotationName, }).upsert().update( { $set: { @@ -374,7 +396,7 @@ class PairwiseProcessor { matrix_ref: this.matrix, database_ref: this.database, iteration_query: this.pairWise.iteration_query, - annotationName: this.annot, + annotationName: this.currentGene.annotationName, protein_id: this.pairWise.iteration_query, query_len: this.pairWise.query_length, iteration_hits: this.pairWise.iteration_hits, From 943565f20cb59f61ffe77d618f1a3ac081d182fd Mon Sep 17 00:00:00 2001 From: mboudet <mateo.boudet@gmail.com> Date: Wed, 11 Oct 2023 16:07:34 +0000 Subject: [PATCH 10/36] fix tests --- imports/api/genes/alignment/alignment.test.js | 6 +++++- imports/api/genes/alignment/parser/pairwiseParser.js | 4 ++++ 2 files changed, 9 insertions(+), 1 deletion(-) diff --git a/imports/api/genes/alignment/alignment.test.js b/imports/api/genes/alignment/alignment.test.js index 6b2fa963..0d3f2d11 100644 --- a/imports/api/genes/alignment/alignment.test.js +++ b/imports/api/genes/alignment/alignment.test.js @@ -1,4 +1,4 @@ -7/* eslint-env mocha */ +/* eslint-env mocha */ import chai from 'chai'; import { Meteor } from 'meteor/meteor'; import logger from '/imports/api/util/logger.js'; @@ -79,6 +79,8 @@ describe('alignment', function testAlignment() { // Increase timeout this.timeout(20000); + addTestGenome(annot=true) + const diamondParams = { fileName: 'assets/app/data/Diamond_blastx_bnigra.txt', parser: 'txt', @@ -121,6 +123,8 @@ describe('alignment', function testAlignment() { // Increase timeout this.timeout(20000); + addTestGenome(annot=true) + const diamondParams = { fileName: 'assets/app/data/BLAST_blastx_bnigra.txt', parser: 'txt', diff --git a/imports/api/genes/alignment/parser/pairwiseParser.js b/imports/api/genes/alignment/parser/pairwiseParser.js index 37f3d489..a706034f 100644 --- a/imports/api/genes/alignment/parser/pairwiseParser.js +++ b/imports/api/genes/alignment/parser/pairwiseParser.js @@ -384,6 +384,10 @@ class PairwiseProcessor { */ lastPairwise = () => { + if (typeof this.annot !== "undefined") { + return + } + this.similarSeqBulkOp.find({ iteration_query: this.pairWise.iteration_query, protein_id: this.pairWise.iteration_query, From 16d10ad9989e86750d5cf2c6dee6af08c785e889 Mon Sep 17 00:00:00 2001 From: mboudet <mateo.boudet@gmail.com> Date: Wed, 11 Oct 2023 17:02:16 +0000 Subject: [PATCH 11/36] add proper redirect to gene with annotation --- imports/ui/genetable/GeneTableBody.jsx | 6 +++--- imports/ui/genetable/columns/GeneLink.jsx | 10 ++++++++-- 2 files changed, 11 insertions(+), 5 deletions(-) diff --git a/imports/ui/genetable/GeneTableBody.jsx b/imports/ui/genetable/GeneTableBody.jsx index dd3d8b1d..29258bc7 100644 --- a/imports/ui/genetable/GeneTableBody.jsx +++ b/imports/ui/genetable/GeneTableBody.jsx @@ -122,11 +122,11 @@ function Loading({ selectedColumns, ...props }) { } function AttributeColumn({ - attributeName, attributeValue, geneId, genomeDataCache, + attributeName, attributeValue, gene, genomeDataCache, }) { switch (attributeName) { case 'Gene ID': - return <GeneLink geneId={geneId} />; + return <GeneLink gene={gene} />; case 'Genome': return ( <GenomeName @@ -179,7 +179,7 @@ function GeneTableRow({ <AttributeColumn attributeName={attributeName} attributeValue={attributeValue} - geneId={gene.ID} + gene={gene} genomeDataCache={genomeDataCache} /> </td> diff --git a/imports/ui/genetable/columns/GeneLink.jsx b/imports/ui/genetable/columns/GeneLink.jsx index e338df1e..05b199a8 100644 --- a/imports/ui/genetable/columns/GeneLink.jsx +++ b/imports/ui/genetable/columns/GeneLink.jsx @@ -3,9 +3,15 @@ import { Meteor } from 'meteor/meteor'; import React from 'react'; import { Link } from 'react-router-dom'; -export default function GeneLink({ geneId }) { +export default function GeneLink({ gene }) { + const geneId = gene.ID + + const query = new URLSearchParams(); + query.set("annotation", gene.annotationName); + const url = `/gene/${geneId}?${query.toString()}` + return ( - <Link to={`/gene/${geneId}`} className="genelink" title={geneId}> + <Link to={url} className="genelink" title={geneId}> { geneId } </Link> ); From b562bea7cc98f3416ed8dbae523968206a5212fa Mon Sep 17 00:00:00 2001 From: mboudet <mateo.boudet@gmail.com> Date: Wed, 11 Oct 2023 19:11:04 +0200 Subject: [PATCH 12/36] Fix interpro import + add warnings --- imports/api/genes/addInterproscan.js | 2 +- imports/api/genes/parseGff3Interproscan.js | 4 ++-- imports/api/genes/parseTsvInterproscan.js | 2 ++ 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/imports/api/genes/addInterproscan.js b/imports/api/genes/addInterproscan.js index fa53caa4..777ad49f 100644 --- a/imports/api/genes/addInterproscan.js +++ b/imports/api/genes/addInterproscan.js @@ -33,7 +33,7 @@ class InterproscanProcessor { if (this.bulkOp.length > 0){ return this.bulkOp.execute(); } - return { nMatched: 0 } + return { nUpserted: 0 } } updateGenes = () => { diff --git a/imports/api/genes/parseGff3Interproscan.js b/imports/api/genes/parseGff3Interproscan.js index a6a72f58..4f3a23ee 100644 --- a/imports/api/genes/parseGff3Interproscan.js +++ b/imports/api/genes/parseGff3Interproscan.js @@ -62,11 +62,11 @@ class ParseGff3File extends InterproscanProcessor { geneQuery['annotationName'] = this.annot } let gene = Genes.findOne(geneQuery); - logger.log(gene) - logger.log(geneQuery) if (typeof gene !== "undefined"){ this.currentGene = gene.ID this.currentAnnotationName = gene.annotationName + } else { + logger.warn(`Warning ! No sub-feature was found for ${seqId}.`) } this.currentContent = [] diff --git a/imports/api/genes/parseTsvInterproscan.js b/imports/api/genes/parseTsvInterproscan.js index e4737c43..6043e037 100644 --- a/imports/api/genes/parseTsvInterproscan.js +++ b/imports/api/genes/parseTsvInterproscan.js @@ -38,6 +38,8 @@ class ParseTsvFile extends InterproscanProcessor { if (typeof gene !== "undefined"){ this.currentGene = gene.ID this.currentAnnotationName = gene.annotationName + } else { + logger.warn(logger.warn(`Warning ! No sub-feature was found for ${seqId}.`)) } this.currentContent = [] From 65ad83e41b40a72eaa046ad8838e682ebb8cbcf4 Mon Sep 17 00:00:00 2001 From: mboudet <mateo.boudet@gmail.com> Date: Thu, 12 Oct 2023 11:05:52 +0200 Subject: [PATCH 13/36] Actually add annot in methods --- imports/api/genes/eggnog/addEggnog.js | 3 ++- imports/api/genes/hectar/addHectar.js | 3 ++- imports/api/genes/interproscan/interproscanCollection.js | 1 + imports/api/jobqueue/process-eggnog.js | 4 ++-- imports/api/jobqueue/process-hectar.js | 4 ++-- imports/api/jobqueue/process-interproscan.js | 6 +++--- imports/api/jobqueue/process-similarsequences.js | 6 +++--- 7 files changed, 15 insertions(+), 12 deletions(-) diff --git a/imports/api/genes/eggnog/addEggnog.js b/imports/api/genes/eggnog/addEggnog.js index 4f00d17d..a6a2f1ab 100644 --- a/imports/api/genes/eggnog/addEggnog.js +++ b/imports/api/genes/eggnog/addEggnog.js @@ -8,10 +8,11 @@ import SimpleSchema from 'simpl-schema'; import { Meteor } from 'meteor/meteor'; class EggnogProcessor { - constructor() { + constructor(annot) { // Not a bulk mongo suite. this.genesDb = Genes.rawCollection(); this.nEggnog = 0; + this.annot = annot; } /** diff --git a/imports/api/genes/hectar/addHectar.js b/imports/api/genes/hectar/addHectar.js index c3bd8a17..9981c443 100644 --- a/imports/api/genes/hectar/addHectar.js +++ b/imports/api/genes/hectar/addHectar.js @@ -8,10 +8,11 @@ import SimpleSchema from 'simpl-schema'; import { Meteor } from 'meteor/meteor'; class HectarProcessor { - constructor() { + constructor(annot) { // Not a bulk mongo suite. this.genesDb = Genes.rawCollection(); this.nHectar = 0; + this.annot = annot; } /** diff --git a/imports/api/genes/interproscan/interproscanCollection.js b/imports/api/genes/interproscan/interproscanCollection.js index 3d9f577c..7628ad86 100644 --- a/imports/api/genes/interproscan/interproscanCollection.js +++ b/imports/api/genes/interproscan/interproscanCollection.js @@ -13,6 +13,7 @@ const interproscanSchema = new SimpleSchema({ }, annotationName: { type: String, + index: true, label: 'Annotation name', }, protein_domains: { diff --git a/imports/api/jobqueue/process-eggnog.js b/imports/api/jobqueue/process-eggnog.js index b139a9c3..787ca037 100644 --- a/imports/api/jobqueue/process-eggnog.js +++ b/imports/api/jobqueue/process-eggnog.js @@ -11,10 +11,10 @@ jobQueue.processJobs( payload: 1, }, async (job, callback) => { - const { fileName } = job.data; + const { fileName, annot } = job.data; logger.log(`Add ${fileName} eggnog file.`); - const lineProcessor = new EggnogProcessor(); + const lineProcessor = new EggnogProcessor(annot); const rl = readline.createInterface({ input: fs.createReadStream(fileName, 'utf8'), diff --git a/imports/api/jobqueue/process-hectar.js b/imports/api/jobqueue/process-hectar.js index 4338b288..c7ec44ab 100644 --- a/imports/api/jobqueue/process-hectar.js +++ b/imports/api/jobqueue/process-hectar.js @@ -11,10 +11,10 @@ jobQueue.processJobs( payload: 1, }, async (job, callback) => { - const { fileName } = job.data; + const { fileName, annot } = job.data; logger.log(`Add ${fileName} hectar file.`); - const lineProcessor = new HectarProcessor(); + const lineProcessor = new HectarProcessor(annot); const rl = readline.createInterface({ input: fs.createReadStream(fileName, 'utf8'), diff --git a/imports/api/jobqueue/process-interproscan.js b/imports/api/jobqueue/process-interproscan.js index 41ddbd5b..9f07ffdd 100644 --- a/imports/api/jobqueue/process-interproscan.js +++ b/imports/api/jobqueue/process-interproscan.js @@ -12,7 +12,7 @@ jobQueue.processJobs( payload: 1, }, async (job, callback) => { - const { fileName, parser } = job.data; + const { fileName, parser, annot } = job.data; logger.log(`Add ${fileName} interproscan file.`); const rl = readline.createInterface({ @@ -24,11 +24,11 @@ jobQueue.processJobs( switch (parser) { case 'tsv': logger.log('Format : .tsv'); - lineProcessor = new ParseTsvFile(); + lineProcessor = new ParseTsvFile(annot); break; case 'gff3': logger.log('Format : .gff3'); - lineProcessor = new ParseGff3File(); + lineProcessor = new ParseGff3File(annot); break; } diff --git a/imports/api/jobqueue/process-similarsequences.js b/imports/api/jobqueue/process-similarsequences.js index 7032911b..90b74ae7 100644 --- a/imports/api/jobqueue/process-similarsequences.js +++ b/imports/api/jobqueue/process-similarsequences.js @@ -13,14 +13,14 @@ jobQueue.processJobs( payload: 1, }, async (job, callback) => { - const { fileName, parser, program, algorithm, matrix, database } = job.data; + const { fileName, parser, program, algorithm, matrix, database, annot } = job.data; logger.log(`Add ${fileName} diamond file.`); // Different parser for the xml file. if (parser === 'xml') { const stream = fs.createReadStream(fileName); const xml = new XmlFlow(stream, { normalize: false }); - const lineProcessor = new XmlProcessor(program, algorithm, matrix, database); + const lineProcessor = new XmlProcessor(program, algorithm, matrix, database, annot); const tag = 'blastoutput'; xml.on(`tag:${tag}`, async (obj) => { @@ -48,7 +48,7 @@ jobQueue.processJobs( input: fs.createReadStream(fileName, 'utf8'), }); - const lineProcessor = new PairwiseProcessor(program, algorithm, matrix, database); + const lineProcessor = new PairwiseProcessor(program, algorithm, matrix, database, annot); for await (const line of lineReader) { try { From 322dc94517362a68243b4246019d0ca192e711de Mon Sep 17 00:00:00 2001 From: mboudet <mateo.boudet@gmail.com> Date: Fri, 13 Oct 2023 14:59:41 +0000 Subject: [PATCH 14/36] fix protein display --- imports/ui/singleGenePage/ProteinDomains.jsx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/imports/ui/singleGenePage/ProteinDomains.jsx b/imports/ui/singleGenePage/ProteinDomains.jsx index 00211331..27dec0c2 100644 --- a/imports/ui/singleGenePage/ProteinDomains.jsx +++ b/imports/ui/singleGenePage/ProteinDomains.jsx @@ -298,7 +298,7 @@ function InterproDataTracker({ gene }) { const interproSub = Meteor.subscribe('interpro', gene); const loading = !interproSub.ready(); - const proteinDomains = interproscanCollection.find({}).fetch() + const proteinDomains = interproscanCollection.find({gene_id: gene.ID, annotationName: gene.annotationName}).fetch() return { loading, From 393eebe353ab66986d5df0fab7fa521db1ed871a Mon Sep 17 00:00:00 2001 From: mboudet <mateo.boudet@gmail.com> Date: Fri, 13 Oct 2023 17:42:52 +0200 Subject: [PATCH 15/36] Add some tests & change default attributes --- imports/api/genes/alignment/alignment.test.js | 12 +++++------ .../genes/alignment/parser/pairwiseParser.js | 4 ++-- imports/api/genes/eggnog/eggnog.test.js | 13 ++++++++++-- imports/api/genes/hectar/hectar.test.js | 11 ++++++++-- .../genes/interproscan/interproscan.test.js | 8 ++++---- .../server/fixtures/addDefaultAttributes.js | 14 ++++++++++--- .../startup/server/fixtures/addTestData.js | 20 ++++++++++++++++++- 7 files changed, 62 insertions(+), 20 deletions(-) diff --git a/imports/api/genes/alignment/alignment.test.js b/imports/api/genes/alignment/alignment.test.js index 0d3f2d11..4420bb47 100644 --- a/imports/api/genes/alignment/alignment.test.js +++ b/imports/api/genes/alignment/alignment.test.js @@ -36,7 +36,7 @@ describe('alignment', function testAlignment() { // Increase timeout this.timeout(20000); - addTestGenome(annot=true) + addTestGenome(annot=true, multiple=true) const diamondParams = { fileName: 'assets/app/data/Diamond_blastp_bnigra.xml', @@ -60,7 +60,7 @@ describe('alignment', function testAlignment() { let result = addSimilarSequence._execute(adminContext, diamondParams); - const simSeq = similarSequencesCollection.find({iteration_query: "BniB01g000010.2N"}).fetch(); + const simSeq = similarSequencesCollection.find({iteration_query: "BniB01g000010.2N", annotationName: "Annotation name"}).fetch(); chai.assert.lengthOf(simSeq, 1, "No similar sequence found") const seq = simSeq[0] @@ -79,7 +79,7 @@ describe('alignment', function testAlignment() { // Increase timeout this.timeout(20000); - addTestGenome(annot=true) + addTestGenome(annot=true, multiple=true) const diamondParams = { fileName: 'assets/app/data/Diamond_blastx_bnigra.txt', @@ -105,7 +105,7 @@ describe('alignment', function testAlignment() { //Meteor._sleepForMs(10000); - const simSeq = similarSequencesCollection.find({iteration_query: "BniB01g000010.2N.1-P"}).fetch(); + const simSeq = similarSequencesCollection.find({iteration_query: "BniB01g000010.2N", annotationName: "Annotation name"}).fetch(); chai.assert.lengthOf(simSeq, 1, "No similar sequence found") @@ -123,7 +123,7 @@ describe('alignment', function testAlignment() { // Increase timeout this.timeout(20000); - addTestGenome(annot=true) + addTestGenome(annot=true, multiple=true) const diamondParams = { fileName: 'assets/app/data/BLAST_blastx_bnigra.txt', @@ -147,7 +147,7 @@ describe('alignment', function testAlignment() { let result = addSimilarSequence._execute(adminContext, diamondParams); - const simSeq = similarSequencesCollection.find({iteration_query: "BniB01g000010.2N.1-P"}).fetch(); + const simSeq = similarSequencesCollection.find({iteration_query: "BniB01g000010.2N", annotationName: "Annotation name"}).fetch(); chai.assert.lengthOf(simSeq, 1, "No similar sequence found") const seq = simSeq[0] diff --git a/imports/api/genes/alignment/parser/pairwiseParser.js b/imports/api/genes/alignment/parser/pairwiseParser.js index a706034f..c8fe618b 100644 --- a/imports/api/genes/alignment/parser/pairwiseParser.js +++ b/imports/api/genes/alignment/parser/pairwiseParser.js @@ -384,8 +384,8 @@ class PairwiseProcessor { */ lastPairwise = () => { - if (typeof this.annot !== "undefined") { - return + if (typeof this.currentGene !== "undefined") { + return { ok:"", writeErrors:"", nInserted:0, nUpserted: 0 } } this.similarSeqBulkOp.find({ diff --git a/imports/api/genes/eggnog/eggnog.test.js b/imports/api/genes/eggnog/eggnog.test.js index 9a08f565..ac47bd2d 100644 --- a/imports/api/genes/eggnog/eggnog.test.js +++ b/imports/api/genes/eggnog/eggnog.test.js @@ -6,6 +6,7 @@ import { eggnogCollection } from './eggnogCollection'; import addEggnog from './addEggnog'; import { addTestUsers, addTestGenome } from '../../../startup/server/fixtures/addTestData'; import '../../jobqueue/process-eggnog'; +import { Genes } from '/imports/api/genes/geneCollection.js'; describe('eggnog', function testEggnog() { let adminId; @@ -29,7 +30,7 @@ describe('eggnog', function testEggnog() { // Increase timeout this.timeout(20000); - addTestGenome(annot = true); + addTestGenome(annot = true, multiple = true); const eggNogParams = { fileName: 'assets/app/data/Bnigra_eggnog.tsv', @@ -50,7 +51,7 @@ describe('eggnog', function testEggnog() { chai.assert.equal(result.nInserted, 1) - const eggs = eggnogCollection.find({ query_name: 'BniB01g000010.2N.1-P' }).fetch(); + const eggs = eggnogCollection.find({ query_name: 'BniB01g000010.2N.1-P', annotationName: "Annotation name" }).fetch(); chai.assert.lengthOf(eggs, 1, 'No eggnog data found'); @@ -62,5 +63,13 @@ describe('eggnog', function testEggnog() { chai.assert.lengthOf(egg.eggNOG_OGs, 5); chai.assert.lengthOf(egg.GOs, 18); chai.assert.equal(egg.Description, 'UDP-glucuronic acid decarboxylase'); + + const gene1 = Genes.findOne({ID: 'BniB01g000010.2N.1', annotationName: 'Annotation name'}) + const gene2 = Genes.findOne({ID: 'BniB01g000010.2N.1', annotationName: 'Annotation name 2'}) + + chai.assert.isDefined(gene2.eggnogId, "eggNodeId is not defined for the correct annotation") + chai.assert.isUndefined(gene2.eggnogId, "eggNodeId is defined for the wrong annotation") + + }); }); diff --git a/imports/api/genes/hectar/hectar.test.js b/imports/api/genes/hectar/hectar.test.js index beb1c11f..9dbae5eb 100644 --- a/imports/api/genes/hectar/hectar.test.js +++ b/imports/api/genes/hectar/hectar.test.js @@ -6,6 +6,7 @@ import { hectarCollection } from './hectarCollection'; import addHectar from './addHectar'; import { addTestUsers, addTestGenome } from '../../../startup/server/fixtures/addTestData'; import '../../jobqueue/process-hectar'; +import { Genes } from '/imports/api/genes/geneCollection.js'; describe('hectar', function testHectar() { let adminId; @@ -29,7 +30,7 @@ describe('hectar', function testHectar() { // Increase timeout this.timeout(20000); - addTestGenome(annot = true); + addTestGenome(annot = true, multiple = true); const hectarParams = { fileName: 'assets/app/data/Bnigra_hectar.tab', @@ -50,7 +51,7 @@ describe('hectar', function testHectar() { chai.assert.equal(result.nInserted, 1) - const hecs = hectarCollection.find({ protein_id: 'BniB01g000010.2N.1' }).fetch(); + const hecs = hectarCollection.find({ protein_id: 'BniB01g000010.2N.1', annotationName: "Annotation name" }).fetch(); chai.assert.lengthOf(hecs, 1, 'No hectar data found'); @@ -61,5 +62,11 @@ describe('hectar', function testHectar() { chai.assert.equal(hec.typeII_signal_anchor_score, '0.0228'); chai.assert.equal(hec.mitochondrion_score, '0.1032'); chai.assert.equal(hec.other_score, '0.8968'); + + const gene1 = Genes.findOne({ID: 'BniB01g000010.2N.1', annotationName: 'Annotation name'}) + const gene2 = Genes.findOne({ID: 'BniB01g000010.2N.1', annotationName: 'Annotation name 2'}) + + chai.assert.isDefined(gene2.eggnogId, "eggNodeId is not defined for the correct annotation") + chai.assert.isUndefined(gene2.eggnogId, "eggNodeId is defined for the wrong annotation") }); }); diff --git a/imports/api/genes/interproscan/interproscan.test.js b/imports/api/genes/interproscan/interproscan.test.js index 6add689b..58fb26ab 100644 --- a/imports/api/genes/interproscan/interproscan.test.js +++ b/imports/api/genes/interproscan/interproscan.test.js @@ -36,7 +36,7 @@ describe('interproscan', function testInterproscan() { // Increase timeout this.timeout(20000); - addTestGenome(annot=true) + addTestGenome(annot=true, multiple = true) const interproParams = { fileName: 'assets/app/data/Bnigra_interproscan.tsv', @@ -63,7 +63,7 @@ describe('interproscan', function testInterproscan() { chai.assert.deepEqual(gene.attributes.Dbxref, [ 'InterPro:1236' ]) chai.assert.deepEqual(gene.attributes.Ontology_term, [ 'GO:1238' ]) - const interpros = interproscanCollection.find({gene_id: "BniB01g000010.2N"}).fetch(); + const interpros = interproscanCollection.find({gene_id: "BniB01g000010.2N", annotationName: "Annotation name"}).fetch(); chai.assert.lengthOf(interpros, 1, "No Interpro document found") const protein_domains = interpros[0].protein_domains @@ -85,7 +85,7 @@ describe('interproscan', function testInterproscan() { // Increase timeout this.timeout(20000); - addTestGenome(annot=true) + addTestGenome(annot=true, multiple = true) const interproParams = { fileName: 'assets/app/data/Bnigra_interproscan.gff', @@ -107,7 +107,7 @@ describe('interproscan', function testInterproscan() { let result = addInterproscan._execute(adminContext, interproParams); - const interpros = interproscanCollection.find({gene_id: "BniB01g000010.2N"}).fetch(); + const interpros = interproscanCollection.find({gene_id: "BniB01g000010.2N", annotationName: "Annotation name"}).fetch(); chai.assert.lengthOf(interpros, 1, "No Interpro document found") const protein_domains = interpros[0].protein_domains diff --git a/imports/startup/server/fixtures/addDefaultAttributes.js b/imports/startup/server/fixtures/addDefaultAttributes.js index 04c59d6b..bf2e3f72 100644 --- a/imports/startup/server/fixtures/addDefaultAttributes.js +++ b/imports/startup/server/fixtures/addDefaultAttributes.js @@ -6,40 +6,48 @@ const PERMANENT_ATTRIBUTES = [ { name: 'Note', query: 'attributes.Note', + display: false }, { name: 'Dbxref', query: 'attributes.Dbxref', + display: false }, { name: 'Ontology Term', query: 'attributes.Ontology_term', + display: false }, { name: 'Orthogroup', query: 'orthogroup.name', + display: false }, { name: 'Gene ID', query: 'ID', + display: true }, { name: 'Has changes', query: 'changed', + display: false }, { name: 'Genome', query: 'genomeId', + display: true }, { name: 'Annotation', query: 'annotationName', + display: true }, ]; export default function addDefaultAttributes() { // add some default attributes to filter on - PERMANENT_ATTRIBUTES.forEach(({ name, query }) => { + PERMANENT_ATTRIBUTES.forEach(({ name, query, display }) => { const existingAttribute = attributeCollection.findOne({ name }); if (typeof existingAttribute === 'undefined') { logger.log(`Adding default filter option: ${name}`); @@ -51,8 +59,8 @@ export default function addDefaultAttributes() { $setOnInsert: { name, query, - defaultShow: false, - defaultSearch: false, + defaultShow: display, + defaultSearch: display, allGenomes: true, }, }, diff --git a/imports/startup/server/fixtures/addTestData.js b/imports/startup/server/fixtures/addTestData.js index 70924a1d..2e7812d4 100644 --- a/imports/startup/server/fixtures/addTestData.js +++ b/imports/startup/server/fixtures/addTestData.js @@ -49,7 +49,7 @@ export function addTestUsers() { return { adminId, newUserId, curatorId } } -export function addTestGenome(annot=false) { +export function addTestGenome(annot=false, multiple=false) { const annotObj = annot ? [{ name: 'myfilename.gff'}] : undefined @@ -93,6 +93,24 @@ export function addTestGenome(annot=false) { seq: 'AAAA', attributes: {"myNewAttribute": 1} }) + + if (multiple){ + Genes.insert({ + ID: 'BniB01g000010.2N', + seqid: 'B1', + source: 'AAFC_GIFS', + strand: '-', + type: 'gene', + start: 13640, + end: 15401, + genomeId: genomeId, + annotationName: "Annotation name 2", + score: '.', + subfeatures: [subfeature, cds], + seq: 'AAAA', + attributes: {"myNewAttribute": 1} + }) + } } return { genomeId, genomeSeqId, geneId: "BniB01g000010.2N" } From d4c2a30e16a714fdd4c31618115b27dc6d87d1c1 Mon Sep 17 00:00:00 2001 From: mboudet <mateo.boudet@gmail.com> Date: Fri, 13 Oct 2023 16:36:42 +0000 Subject: [PATCH 16/36] actually fix tests --- imports/api/genes/alignment/parser/pairwiseParser.js | 10 +++++----- imports/api/genes/eggnog/eggnog.test.js | 6 +++--- imports/api/genes/hectar/hectar.test.js | 8 ++++---- 3 files changed, 12 insertions(+), 12 deletions(-) diff --git a/imports/api/genes/alignment/parser/pairwiseParser.js b/imports/api/genes/alignment/parser/pairwiseParser.js index c8fe618b..b9d62c3f 100644 --- a/imports/api/genes/alignment/parser/pairwiseParser.js +++ b/imports/api/genes/alignment/parser/pairwiseParser.js @@ -85,7 +85,7 @@ class PairwiseProcessor { && this.pairWise.iteration_query !== queryClean) { /** Update or insert pairwise. */ this.similarSeqBulkOp.find({ - iteration_query: this.pairWise.iteration_query, + iteration_query: this.currentGene.ID, protein_id: this.pairWise.iteration_query, annotationName: this.currentGene.annotationName, }).upsert().update( @@ -95,7 +95,7 @@ class PairwiseProcessor { algorithm_ref: this.algorithm, matrix_ref: this.matrix, database_ref: this.database, - iteration_query: this.pairWise.iteration_query, + iteration_query: this.currentGene.ID, annotationName: this.currentGene.annotationName, protein_id: this.pairWise.iteration_query, query_len: this.pairWise.query_length, @@ -384,12 +384,12 @@ class PairwiseProcessor { */ lastPairwise = () => { - if (typeof this.currentGene !== "undefined") { + if (typeof this.currentGene === "undefined") { return { ok:"", writeErrors:"", nInserted:0, nUpserted: 0 } } this.similarSeqBulkOp.find({ - iteration_query: this.pairWise.iteration_query, + iteration_query: this.currentGene.ID, protein_id: this.pairWise.iteration_query, annotationName: this.currentGene.annotationName, }).upsert().update( @@ -399,7 +399,7 @@ class PairwiseProcessor { algorithm_ref: this.algorithm, matrix_ref: this.matrix, database_ref: this.database, - iteration_query: this.pairWise.iteration_query, + iteration_query: this.currentGene.ID, annotationName: this.currentGene.annotationName, protein_id: this.pairWise.iteration_query, query_len: this.pairWise.query_length, diff --git a/imports/api/genes/eggnog/eggnog.test.js b/imports/api/genes/eggnog/eggnog.test.js index ac47bd2d..29ec7d57 100644 --- a/imports/api/genes/eggnog/eggnog.test.js +++ b/imports/api/genes/eggnog/eggnog.test.js @@ -64,10 +64,10 @@ describe('eggnog', function testEggnog() { chai.assert.lengthOf(egg.GOs, 18); chai.assert.equal(egg.Description, 'UDP-glucuronic acid decarboxylase'); - const gene1 = Genes.findOne({ID: 'BniB01g000010.2N.1', annotationName: 'Annotation name'}) - const gene2 = Genes.findOne({ID: 'BniB01g000010.2N.1', annotationName: 'Annotation name 2'}) + const gene1 = Genes.findOne({ID: 'BniB01g000010.2N', annotationName: 'Annotation name'}) + const gene2 = Genes.findOne({ID: 'BniB01g000010.2N', annotationName: 'Annotation name 2'}) - chai.assert.isDefined(gene2.eggnogId, "eggNodeId is not defined for the correct annotation") + chai.assert.isDefined(gene1.eggnogId, "eggNodeId is not defined for the correct annotation") chai.assert.isUndefined(gene2.eggnogId, "eggNodeId is defined for the wrong annotation") diff --git a/imports/api/genes/hectar/hectar.test.js b/imports/api/genes/hectar/hectar.test.js index 9dbae5eb..b9a5312b 100644 --- a/imports/api/genes/hectar/hectar.test.js +++ b/imports/api/genes/hectar/hectar.test.js @@ -63,10 +63,10 @@ describe('hectar', function testHectar() { chai.assert.equal(hec.mitochondrion_score, '0.1032'); chai.assert.equal(hec.other_score, '0.8968'); - const gene1 = Genes.findOne({ID: 'BniB01g000010.2N.1', annotationName: 'Annotation name'}) - const gene2 = Genes.findOne({ID: 'BniB01g000010.2N.1', annotationName: 'Annotation name 2'}) + const gene1 = Genes.findOne({ID: 'BniB01g000010.2N', annotationName: 'Annotation name'}) + const gene2 = Genes.findOne({ID: 'BniB01g000010.2N', annotationName: 'Annotation name 2'}) - chai.assert.isDefined(gene2.eggnogId, "eggNodeId is not defined for the correct annotation") - chai.assert.isUndefined(gene2.eggnogId, "eggNodeId is defined for the wrong annotation") + chai.assert.isDefined(gene1.hectarId, "eggNodeId is not defined for the correct annotation") + chai.assert.isUndefined(gene2.hectarId, "eggNodeId is defined for the wrong annotation") }); }); From 947d12bbd20726163752a6539f49b10f8043b638 Mon Sep 17 00:00:00 2001 From: mboudet <mateo.boudet@gmail.com> Date: Fri, 13 Oct 2023 18:38:37 +0200 Subject: [PATCH 17/36] Index more stuff --- imports/api/genes/alignment/similarSequenceCollection.js | 3 +++ imports/api/genes/interproscan/interproscanCollection.js | 1 + 2 files changed, 4 insertions(+) diff --git a/imports/api/genes/alignment/similarSequenceCollection.js b/imports/api/genes/alignment/similarSequenceCollection.js index b902b752..a4e13d3f 100644 --- a/imports/api/genes/alignment/similarSequenceCollection.js +++ b/imports/api/genes/alignment/similarSequenceCollection.js @@ -20,14 +20,17 @@ const similarSequencesSchema = new SimpleSchema({ }, iteration_query: { type: String, + index: true, label: 'Query sequence name.', }, protein_id: { type: String, + index: true, label: 'Protein_id', }, annotationName: { type: String, + index: true, label: 'Annotation name', }, iteration_hits: { diff --git a/imports/api/genes/interproscan/interproscanCollection.js b/imports/api/genes/interproscan/interproscanCollection.js index 7628ad86..1a175aed 100644 --- a/imports/api/genes/interproscan/interproscanCollection.js +++ b/imports/api/genes/interproscan/interproscanCollection.js @@ -9,6 +9,7 @@ const interproscanSchema = new SimpleSchema({ }, protein_id: { type: String, + index: true, label: 'Linked protein ID', }, annotationName: { From 6efabdb954cdc1d21260ad0d1c5a814d71c73f49 Mon Sep 17 00:00:00 2001 From: mboudet <mateo.boudet@gmail.com> Date: Fri, 13 Oct 2023 18:41:06 +0200 Subject: [PATCH 18/36] Add annot name to UI --- imports/ui/singleGenePage/GeneralInfo.jsx | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/imports/ui/singleGenePage/GeneralInfo.jsx b/imports/ui/singleGenePage/GeneralInfo.jsx index 1982f7f1..bcda3cdf 100644 --- a/imports/ui/singleGenePage/GeneralInfo.jsx +++ b/imports/ui/singleGenePage/GeneralInfo.jsx @@ -364,6 +364,12 @@ function GeneInfo({ </small> </td> </tr> + <tr> + <td>Annotation name</td> + <td> + {`${gene.annotationName} `} + </td> + </tr> <tr> <td>Genome coordinates</td> <td> From 0c0b56455eed1d2511173c8e0f353552352e0b51 Mon Sep 17 00:00:00 2001 From: mboudet <mateo.boudet@gmail.com> Date: Fri, 13 Oct 2023 17:06:07 +0000 Subject: [PATCH 19/36] fixes --- .../geneExpression/SampleSelection.jsx | 26 ++++++++++++++++++- 1 file changed, 25 insertions(+), 1 deletion(-) diff --git a/imports/ui/singleGenePage/geneExpression/SampleSelection.jsx b/imports/ui/singleGenePage/geneExpression/SampleSelection.jsx index e6cbe4bf..bc3d4f8d 100644 --- a/imports/ui/singleGenePage/geneExpression/SampleSelection.jsx +++ b/imports/ui/singleGenePage/geneExpression/SampleSelection.jsx @@ -10,6 +10,10 @@ import { ExperimentInfo } from '/imports/api/transcriptomes/transcriptome_collec import { Dropdown, DropdownMenu, DropdownButton } from '/imports/ui/util/Dropdown.jsx'; +import { + branch, compose, round, /* ErrorBoundary, */ +} from '/imports/ui/util/uiUtil.jsx'; + import './sampleSelection.scss'; function dataTracker({ gene, showHeader, children }) { @@ -27,6 +31,23 @@ function dataTracker({ gene, showHeader, children }) { }; } + +function hasNoExpression({ experiments }) { + return experiments.length === 0; +} + +function NoExpression() { + return ( + <div className="card expression-plot"> + <article className="message no-protein-domains" role="alert"> + <div className="message-body"> + <p className="has-text-grey">No expression data found</p> + </div> + </article> + </div> + ); +} + const customStyles = { control: (provided) => ({ ...provided, @@ -197,4 +218,7 @@ function SampleSelection({ ); } -export default withTracker(dataTracker)(SampleSelection); +export default compose( + withTracker(dataTracker), + branch(hasNoExpression, NoExpression), +)(SampleSelection); From a461e52c2f9dd0e43770aa6533058bcd6a665a47 Mon Sep 17 00:00:00 2001 From: mboudet <mateo.boudet@gmail.com> Date: Mon, 16 Oct 2023 09:59:41 +0200 Subject: [PATCH 20/36] Test gene selection --- imports/ui/singleGenePage/SingleGenePage.jsx | 38 +++++++++++++++----- 1 file changed, 29 insertions(+), 9 deletions(-) diff --git a/imports/ui/singleGenePage/SingleGenePage.jsx b/imports/ui/singleGenePage/SingleGenePage.jsx index 042d1f40..73578b57 100644 --- a/imports/ui/singleGenePage/SingleGenePage.jsx +++ b/imports/ui/singleGenePage/SingleGenePage.jsx @@ -2,6 +2,7 @@ import { Meteor } from 'meteor/meteor'; import { withTracker } from 'meteor/react-meteor-data'; import React from 'react'; +import { Link } from 'react-router-dom'; import hash from 'object-hash'; import { Genes } from '/imports/api/genes/geneCollection.js'; @@ -36,16 +37,34 @@ function isLoading({ loading }) { return loading; } -function isNotFound({ gene }) { - return typeof gene === 'undefined'; +function isNotFound({ genes }) { + return gene.length === 0; } -function isMultiple({ gene }) { +function isMultiple({ genes }) { return gene.length > 1; } -function Multiple( {gene} ){ - return <div>Multiple annotation</div>; +function Multiple( {genes} ){ + let content = genes.map(gene => { + const query = new URLSearchParams(); + query.set("annotation", gene.annotationName); + const url = `/gene/${gene.ID}?${query.toString()}` + return ( + <Link to={url} className="genelink" title={geneId}> + { geneId } + </Link> + ); + }) + + return ( + <div> + <p>This gene has several available versions. Please select one:</p> + <div> + {content} + </div> + </div> + ); } function geneDataTracker({ match, genomeDataCache, location }) { @@ -54,20 +73,21 @@ function geneDataTracker({ match, genomeDataCache, location }) { const geneSub = Meteor.subscribe('singleGene', { geneId }); let gene if (annotation) { - gene = Genes.findOne({ ID: geneId, annotationName: annotation }); + gene = Genes.find{ ID: geneId, annotationName: annotation }).fetch(); } else { - gene = Genes.findOne({ ID: geneId }); + gene = Genes.findOne({ ID: geneId }).fetch(); } const loading = !geneSub.ready(); return { loading, - gene, + genes, genomeDataCache, }; } -function genomeDataTracker({ gene, genomeDataCache }) { +function genomeDataTracker({ genes, genomeDataCache }) { // const genomeSub = Meteor.subscribe('genomes'); + let gene = genes[0] const { genomeId } = gene; let genome; let genomeSub; From c82c2e850fba886d099057f45dc4ace9099dd6ec Mon Sep 17 00:00:00 2001 From: mboudet <mateo.boudet@gmail.com> Date: Mon, 16 Oct 2023 14:49:41 +0000 Subject: [PATCH 21/36] fix ui --- imports/ui/singleGenePage/SingleGenePage.jsx | 37 +++++++++++++------- 1 file changed, 25 insertions(+), 12 deletions(-) diff --git a/imports/ui/singleGenePage/SingleGenePage.jsx b/imports/ui/singleGenePage/SingleGenePage.jsx index 73578b57..39e91f62 100644 --- a/imports/ui/singleGenePage/SingleGenePage.jsx +++ b/imports/ui/singleGenePage/SingleGenePage.jsx @@ -38,30 +38,41 @@ function isLoading({ loading }) { } function isNotFound({ genes }) { - return gene.length === 0; + return genes.length === 0; } function isMultiple({ genes }) { - return gene.length > 1; + return genes.length > 1; } function Multiple( {genes} ){ + let gene = genes[0] + let content = genes.map(gene => { const query = new URLSearchParams(); query.set("annotation", gene.annotationName); const url = `/gene/${gene.ID}?${query.toString()}` return ( - <Link to={url} className="genelink" title={geneId}> - { geneId } - </Link> + <p><Link to={url} className="genelink" title={gene.annotationName}> + { gene.annotationName } + </Link></p> ); }) return ( - <div> - <p>This gene has several available versions. Please select one:</p> - <div> - {content} + <div className="container"> + <div className="card single-gene-page"> + <header className="has-background-light"> + <h4 className="title is-size-4 has-text-weight-light"> + {`${gene.ID} `} + </h4> + <div className="box"> + <p>This gene is defined in several annotations. Please select one:</p> + <article className="message is-light"> + {content} + </article> + </div> + </header> </div> </div> ); @@ -71,12 +82,13 @@ function geneDataTracker({ match, genomeDataCache, location }) { const { geneId } = match.params; const annotation = new URLSearchParams(location.search).get("annotation"); const geneSub = Meteor.subscribe('singleGene', { geneId }); - let gene + let genes if (annotation) { - gene = Genes.find{ ID: geneId, annotationName: annotation }).fetch(); + genes = Genes.find({ ID: geneId, annotationName: annotation }).fetch(); } else { - gene = Genes.findOne({ ID: geneId }).fetch(); + genes = Genes.find({ ID: geneId }).fetch(); } + const loading = !geneSub.ready(); return { loading, @@ -211,6 +223,7 @@ export default compose( withTracker(geneDataTracker), branch(isLoading, Loading), branch(isNotFound, NotFound), + branch(isMultiple, Multiple), withTracker(genomeDataTracker), branch(isLoading, Loading), )(SingleGenePage); From f32d42763f06be075ba8ad1d01525043fb69207c Mon Sep 17 00:00:00 2001 From: mboudet <mateo.boudet@gmail.com> Date: Mon, 16 Oct 2023 17:12:23 +0200 Subject: [PATCH 22/36] Test annotation selector in UI --- .../genetable/filteroptions/GenomeSelect.jsx | 99 ++++++++++++++++++- 1 file changed, 95 insertions(+), 4 deletions(-) diff --git a/imports/ui/genetable/filteroptions/GenomeSelect.jsx b/imports/ui/genetable/filteroptions/GenomeSelect.jsx index 638598b3..9584256f 100644 --- a/imports/ui/genetable/filteroptions/GenomeSelect.jsx +++ b/imports/ui/genetable/filteroptions/GenomeSelect.jsx @@ -38,6 +38,16 @@ function GenomeSelect({ new Set(genomes.map((genome) => genome._id)), ); + const [selectedAnnotations, setselectedAnnotations] = useState( + new Set(genomes.map((genome) => { + genome.annotationTrack.map((annotation) => annotation.name) + })).flat()), + ); + + let annotations = new Set(genomes.map((genome) => { + genome.annotationTrack.map((annotation) => annotation.name) + })).flat()) + function toggleGenomeSelect(genomeId) { const newSelection = cloneDeep(selectedGenomes); const newQuery = cloneDeep(query); @@ -57,7 +67,26 @@ function GenomeSelect({ updateQuery(newQuery); } - function selectAll() { + function toggleAnnotationSelect(annotationName) { + const newSelection = cloneDeep(selectedAnnotations); + const newQuery = cloneDeep(query); + + if (newSelection.has(annotationName)) { + newSelection.delete(annotationName); + } else { + newSelection.add(annotationName); + } + setSelectedAnnotations(newSelection); + + if (newSelection.size < annotations.length) { + newQuery.annotationName = { $in: [...newSelection] }; + } else if (hasOwnProperty(query, 'annotationName')) { + delete newQuery.annotationName; + } + updateQuery(newQuery); + } + + function selectAllGenomes() { const newSelection = new Set(genomes.map((genome) => genome._id)); setSelectedGenomes(newSelection); @@ -66,7 +95,7 @@ function GenomeSelect({ updateQuery(newQuery); } - function unselectAll() { + function unselectAllGenomes() { const newSelection = new Set(); setSelectedGenomes(newSelection); @@ -75,6 +104,26 @@ function GenomeSelect({ updateQuery(newQuery); } + function selectAllAnnotations() { + const newSelection = new Set(genomes.map((genome) => { + genome.annotationTrack.map((annotation) => annotation.name) + })).flat()); + setSelectedAnnotations(newSelection); + + const newQuery = cloneDeep(query); + newQuery.annotationName = { $in: [...newSelection] }; + updateQuery(newQuery); + } + + function unselectAllAnnotations() { + const newSelection = new Set(); + setSelectedAnnotations(newSelection); + + const newQuery = cloneDeep(query); + newQuery.annotationName = { $in: [...newSelection] }; + updateQuery(newQuery); + } + return ( <div className="dropdown is-hoverable genomeselect"> <div className="dropdown-trigger"> @@ -108,10 +157,52 @@ function GenomeSelect({ ); })} <div className="buttons has-addons is-centered multiple-select" role="group"> - <button type="button" className="button is-small" onClick={selectAll}> + <button type="button" className="button is-small" onClick={selectAllGenomes}> + Select all + </button> + <button type="button" className="button is-small" onClick={unselectAllGenomes}> + Unselect all + </button> + </div> + </div> + </div> + </div> + <div className="dropdown is-hoverable genomeselect"> + <div className="dropdown-trigger"> + <button type="button" className="button is-small"> + Annotations + <span className="icon-down" /> + </button> + </div> + <div className="dropdown-menu" role="menu"> + <div className="dropdown-content"> + <h6 className="is-h6 dropdown-item dropdown-header"> + Select annotations + </h6> + {annotations.map(({name}) => { + const checked = selectedAnnotations.has(name); + return ( + <div key={`${name}-${checked}`} className="dropdown-item"> + <label className="checkbox"> + <input + type="checkbox" + className="dropdown-checkbox is-small" + id={name} + checked={checked} + onChange={() => { + toggleAnnotationSelect(name); + }} + /> + { name } + </label> + </div> + ); + })} + <div className="buttons has-addons is-centered multiple-select" role="group"> + <button type="button" className="button is-small" onClick={selectAllAnnotations}> Select all </button> - <button type="button" className="button is-small" onClick={unselectAll}> + <button type="button" className="button is-small" onClick={unselectAllAnnotations}> Unselect all </button> </div> From 3e3407e58b3c54ac240ebe21abd432d34487bef7 Mon Sep 17 00:00:00 2001 From: mboudet <mateo.boudet@gmail.com> Date: Mon, 16 Oct 2023 16:02:51 +0000 Subject: [PATCH 23/36] ui --- .../genetable/filteroptions/GenomeSelect.jsx | 23 +++++++++++-------- 1 file changed, 13 insertions(+), 10 deletions(-) diff --git a/imports/ui/genetable/filteroptions/GenomeSelect.jsx b/imports/ui/genetable/filteroptions/GenomeSelect.jsx index 9584256f..a5be7727 100644 --- a/imports/ui/genetable/filteroptions/GenomeSelect.jsx +++ b/imports/ui/genetable/filteroptions/GenomeSelect.jsx @@ -24,6 +24,7 @@ function genomeDataTracker({ ...props }) { annotationTrack: { $exists: true }, }) .fetch(); + return { loading, genomes, @@ -38,15 +39,15 @@ function GenomeSelect({ new Set(genomes.map((genome) => genome._id)), ); - const [selectedAnnotations, setselectedAnnotations] = useState( - new Set(genomes.map((genome) => { - genome.annotationTrack.map((annotation) => annotation.name) - })).flat()), + const [selectedAnnotations, setSelectedAnnotations] = useState( + new Set(genomes.flatMap((genome) => { + return genome.annotationTrack.map((annotation) => annotation.name); + })), ); - let annotations = new Set(genomes.map((genome) => { - genome.annotationTrack.map((annotation) => annotation.name) - })).flat()) + let annotations = genomes.flatMap((genome) => { + return genome.annotationTrack.map((annotation) => annotation.name) + }) function toggleGenomeSelect(genomeId) { const newSelection = cloneDeep(selectedGenomes); @@ -105,9 +106,9 @@ function GenomeSelect({ } function selectAllAnnotations() { - const newSelection = new Set(genomes.map((genome) => { + const newSelection = new Set(genomes.flatMap((genome) => { genome.annotationTrack.map((annotation) => annotation.name) - })).flat()); + })); setSelectedAnnotations(newSelection); const newQuery = cloneDeep(query); @@ -125,6 +126,7 @@ function GenomeSelect({ } return ( + <> <div className="dropdown is-hoverable genomeselect"> <div className="dropdown-trigger"> <button type="button" className="button is-small"> @@ -179,7 +181,7 @@ function GenomeSelect({ <h6 className="is-h6 dropdown-item dropdown-header"> Select annotations </h6> - {annotations.map(({name}) => { + {annotations.map((name) => { const checked = selectedAnnotations.has(name); return ( <div key={`${name}-${checked}`} className="dropdown-item"> @@ -209,6 +211,7 @@ function GenomeSelect({ </div> </div> </div> + </> ); } From 468afd2b9225ca23091d24d93b4424af13de1fe4 Mon Sep 17 00:00:00 2001 From: mboudet <mateo.boudet@gmail.com> Date: Tue, 17 Oct 2023 10:39:31 +0200 Subject: [PATCH 24/36] Add annot to transcriptome --- imports/api/publications.js | 3 +- imports/api/transcriptomes/addExpression.js | 37 ++++++++++++++----- .../addKallistoTranscriptome.js | 35 +++++++++++++----- .../transcriptome_collection.js | 4 ++ .../api/transcriptomes/transcriptomes.test.js | 24 ++++++++---- .../geneExpression/SampleSelection.jsx | 4 +- 6 files changed, 79 insertions(+), 28 deletions(-) diff --git a/imports/api/publications.js b/imports/api/publications.js index eed47fe7..16a3e58b 100644 --- a/imports/api/publications.js +++ b/imports/api/publications.js @@ -154,7 +154,7 @@ Meteor.publish({ $or: [{ genomes: { $in: genomeIds } }, { allGenomes: true }], }); }, - geneExpression(geneId) { + geneExpression(geneId, annotationName) { const publication = this; const roles = Roles.getRolesForUser(publication.userId); const permission = { $in: roles }; @@ -168,6 +168,7 @@ Meteor.publish({ return Transcriptomes.find({ geneId, + annotationName, experimentId: { $in: experimentIds, }, diff --git a/imports/api/transcriptomes/addExpression.js b/imports/api/transcriptomes/addExpression.js index e4ed1b3d..76e86c7e 100644 --- a/imports/api/transcriptomes/addExpression.js +++ b/imports/api/transcriptomes/addExpression.js @@ -12,15 +12,23 @@ import { } from '/imports/api/transcriptomes/transcriptome_collection.js'; import logger from '/imports/api/util/logger.js'; -const getGenomeId = (data) => { +const getGenomeId = (data, annot) => { const firstTranscripts = data.slice(0, 10).map((line) => line.gene); logger.debug(firstTranscripts); - const gene = Genes.findOne({ + + let geneQuery = { $or: [ { ID: { $in: firstTranscripts } }, { 'subfeatures.ID': { $in: firstTranscripts } }, ], - }); + } + + if (annot){ + geneQuery['annotationName'] = annot + } + + const gene = Genes.findOne(geneQuery); + if (typeof gene === "undefined"){ return undefined } @@ -29,7 +37,7 @@ const getGenomeId = (data) => { }; const parseExpressionTsv = ({ - fileName, description, replicas = [], replicaNames = [], permission = 'admin', isPublic = false, + fileName, description, annot, replicas = [], replicaNames = [], permission = 'admin', isPublic = false, }) => new Promise((resolve, reject) => { const fileHandle = fs.readFileSync(fileName, { encoding: 'binary' }); const bulkOp = Transcriptomes.rawCollection().initializeUnorderedBulkOp(); @@ -80,7 +88,7 @@ const parseExpressionTsv = ({ } let firstColumn = replicaGroups.shift(); - const genomeId = getGenomeId(data); + const genomeId = getGenomeId(data, annot); if (typeof genomeId === 'undefined') { reject(new Meteor.Error('Could not find genomeId for first transcript')); @@ -100,12 +108,18 @@ const parseExpressionTsv = ({ }); data.forEach((row) => { - const gene = Genes.findOne({ + let geneQuery = { $or: [ { ID: row[firstColumn] }, { 'subfeatures.ID': row[firstColumn] }, ], - }); + } + + if (annot){ + geneQuery['annotationName'] = annot + } + + const gene = Genes.findOne(geneQuery); if (typeof gene === 'undefined') { logger.warn(`${target_id} not found`); @@ -114,6 +128,7 @@ const parseExpressionTsv = ({ replicaGroups.forEach((replicaGroup) => { bulkOp.insert({ geneId: gene.ID, + annotationName: gene.annotationName, tpm: row[replicaGroup], experimentId: experiments[replicaGroup] }); @@ -136,6 +151,10 @@ const addExpression = new ValidatedMethod({ validate: new SimpleSchema({ fileName: String, description: String, + annot: { + type: String, + optional: true, + }, replicas: { type: Array, optional: true, @@ -158,7 +177,7 @@ const addExpression = new ValidatedMethod({ noRetry: true, }, run({ - fileName, description, replicas, replicaNames, isPublic + fileName, description, annot, replicas, replicaNames, isPublic }) { if (!this.userId) { throw new Meteor.Error('not-authorized'); @@ -167,7 +186,7 @@ const addExpression = new ValidatedMethod({ throw new Meteor.Error('not-authorized'); } return parseExpressionTsv({ - fileName, description, replicas, replicaNames, isPublic + fileName, description, annot, replicas, replicaNames, isPublic }) .catch((error) => { logger.warn(error); diff --git a/imports/api/transcriptomes/addKallistoTranscriptome.js b/imports/api/transcriptomes/addKallistoTranscriptome.js index d6a4ff62..2237910a 100644 --- a/imports/api/transcriptomes/addKallistoTranscriptome.js +++ b/imports/api/transcriptomes/addKallistoTranscriptome.js @@ -12,21 +12,28 @@ import { } from '/imports/api/transcriptomes/transcriptome_collection.js'; import logger from '/imports/api/util/logger.js'; -const getGenomeId = (data) => { +const getGenomeId = (data, annot) => { const firstTranscipts = data.slice(0, 10).map((line) => line.target_id); logger.debug(firstTranscipts); - const { genomeId } = Genes.findOne({ + + let geneQuery = { $or: [ { ID: { $in: firstTranscipts } }, { 'subfeatures.ID': { $in: firstTranscipts } }, ], - }); + } + + if (annot){ + geneQuery['annotationName'] = annot + } + + const { genomeId } = Genes.findOne(geneQuery); logger.debug(genomeId); return genomeId; }; const parseKallistoTsv = ({ - fileName, sampleName, replicaGroup, + fileName, annot, sampleName, replicaGroup, description, permission = 'admin', isPublic = false, }) => new Promise((resolve, reject) => { const fileHandle = fs.readFileSync(fileName, { encoding: 'binary' }); @@ -43,7 +50,7 @@ const parseKallistoTsv = ({ complete({ data }, _file) { let nInserted = 0; - const genomeId = getGenomeId(data); + const genomeId = getGenomeId(data, annot); if (typeof genomeId === 'undefined') { reject(new Meteor.Error('Could not find genomeId for first transcript')); @@ -62,12 +69,18 @@ const parseKallistoTsv = ({ }); data.forEach(({ target_id, tpm, est_counts }) => { - const gene = Genes.findOne({ + let geneQuery = { $or: [ { ID: target_id }, { 'subfeatures.ID': target_id }, ], - }); + } + + if (annot){ + geneQuery['annotationName'] = annot + } + + const gene = Genes.findOne(geneQuery); if (typeof gene === 'undefined') { logger.warn(`${target_id} not found`); @@ -96,6 +109,10 @@ const addKallistoTranscriptome = new ValidatedMethod({ name: 'addKallistoTranscriptome', validate: new SimpleSchema({ fileName: String, + annot: { + type: String, + optional: true, + }, sampleName: String, replicaGroup: String, description: String, @@ -105,7 +122,7 @@ const addKallistoTranscriptome = new ValidatedMethod({ noRetry: true, }, run({ - fileName, sampleName, replicaGroup, description, isPublic + fileName, annot, sampleName, replicaGroup, description, isPublic }) { if (!this.userId) { throw new Meteor.Error('not-authorized'); @@ -114,7 +131,7 @@ const addKallistoTranscriptome = new ValidatedMethod({ throw new Meteor.Error('not-authorized'); } return parseKallistoTsv({ - fileName, sampleName, replicaGroup, description, isPublic + fileName, annot, sampleName, replicaGroup, description, isPublic }) .catch((error) => { logger.warn(error); diff --git a/imports/api/transcriptomes/transcriptome_collection.js b/imports/api/transcriptomes/transcriptome_collection.js index 574256cd..d51527dc 100644 --- a/imports/api/transcriptomes/transcriptome_collection.js +++ b/imports/api/transcriptomes/transcriptome_collection.js @@ -40,6 +40,10 @@ const TranscriptomeSchema = new SimpleSchema({ label: 'Gene ID', index: true, }, + annotationName: { + type: String, + label: 'Annotation name', + }, experimentId: { type: String, label: 'Experiment ID', diff --git a/imports/api/transcriptomes/transcriptomes.test.js b/imports/api/transcriptomes/transcriptomes.test.js index a52a60d9..482535a5 100644 --- a/imports/api/transcriptomes/transcriptomes.test.js +++ b/imports/api/transcriptomes/transcriptomes.test.js @@ -37,10 +37,11 @@ describe('transcriptomes', function testTranscriptomes() { // Increase timeout this.timeout(20000); - const {genomeId, genomeSeqId} = addTestGenome(annot=true) + const {genomeId, genomeSeqId} = addTestGenome(annot=true, multiple=true) const transcriParams = { fileName: 'assets/app/data/Bnigra_kallisto_abundance.tsv', + annot: "Annotation name", sampleName: "mySample", replicaGroup: "replicaGroup", description: "A new description", @@ -77,6 +78,7 @@ describe('transcriptomes', function testTranscriptomes() { const transcriptome = transcriptomes[0] chai.assert.equal(transcriptome.geneId, 'BniB01g000010.2N') + chai.assert.equal(transcriptome.annotationName, "Annotation name") chai.assert.equal(transcriptome.tpm, '1.80368') chai.assert.equal(transcriptome.est_counts, '21') @@ -86,10 +88,11 @@ describe('transcriptomes', function testTranscriptomes() { // Increase timeout this.timeout(20000); - const {genomeId, genomeSeqId} = addTestGenome(annot=true) + const {genomeId, genomeSeqId} = addTestGenome(annot=true, multiple=true) const transcriParams = { fileName: 'assets/app/data/Bnigra_abundance.tsv', + annot: "Annotation name", description: "A new description", isPublic: false }; @@ -128,6 +131,7 @@ describe('transcriptomes', function testTranscriptomes() { const transcriptome = transcriptomes[0] chai.assert.equal(transcriptome.geneId, 'BniB01g000010.2N') + chai.assert.equal(transcriptome.annotationName, "Annotation name") chai.assert.equal(transcriptome.tpm, '40') chai.assert.isUndefined(transcriptome.est_counts) @@ -137,10 +141,11 @@ describe('transcriptomes', function testTranscriptomes() { // Increase timeout this.timeout(20000); - const {genomeId, genomeSeqId} = addTestGenome(annot=true) + const {genomeId, genomeSeqId} = addTestGenome(annot=true, multiple=true) const transcriParams = { fileName: 'assets/app/data/Bnigra_abundance.tsv', + annot: "Annotation name", description: "A new description", replicas: ["1,2"], isPublic: false @@ -184,6 +189,7 @@ describe('transcriptomes', function testTranscriptomes() { const transcriptome = transcriptomes[0] chai.assert.equal(transcriptome.geneId, 'BniB01g000010.2N') + chai.assert.equal(transcriptome.annotationName, "Annotation name") chai.assert.equal(transcriptome.tpm, '40') chai.assert.isUndefined(transcriptome.est_counts) @@ -193,10 +199,11 @@ describe('transcriptomes', function testTranscriptomes() { // Increase timeout this.timeout(20000); - const {genomeId, genomeSeqId} = addTestGenome(annot=true) + const {genomeId, genomeSeqId} = addTestGenome(annot=true, multiple=true) const transcriParams = { fileName: 'assets/app/data/Bnigra_abundance.tsv', + annot: "Annotation name", description: "A new description", replicas: ["1,2"], replicaNames: ["My replica group name", "Another group name"], @@ -245,6 +252,7 @@ describe('transcriptomes', function testTranscriptomes() { const transcriptome = transcriptomes[0] chai.assert.equal(transcriptome.geneId, 'BniB01g000010.2N') + chai.assert.equal(transcriptome.annotationName, "Annotation name") chai.assert.equal(transcriptome.tpm, '40') chai.assert.isUndefined(transcriptome.est_counts) @@ -254,10 +262,11 @@ describe('transcriptomes', function testTranscriptomes() { // Increase timeout this.timeout(20000); - const {genomeId, genomeSeqId} = addTestGenome(annot=true) + const {genomeId, genomeSeqId} = addTestGenome(annot=true, multiple=true) const transcriParams = { fileName: 'assets/app/data/Bnigra_abundance.tsv', + annot: "Annotation name", description: "A new description", replicaNames: ["TestReplica1", "TestReplica2"], isPublic: false @@ -301,6 +310,7 @@ describe('transcriptomes', function testTranscriptomes() { const transcriptome = transcriptomes[0] chai.assert.equal(transcriptome.geneId, 'BniB01g000010.2N') + chai.assert.equal(transcriptome.annotationName, "Annotation name") chai.assert.equal(transcriptome.tpm, '40') chai.assert.isUndefined(transcriptome.est_counts) @@ -311,7 +321,7 @@ describe('transcriptomes', function testTranscriptomes() { // Increase timeout this.timeout(20000); - const {genomeId, genomeSeqId, geneId} = addTestGenome(annot=true) + const {genomeId, genomeSeqId, geneId} = addTestGenome(annot=true, multiple=true) const {expId, transcriptomeId} = addTestTranscriptome(genomeId, geneId) const updateParams = { @@ -347,7 +357,7 @@ describe('transcriptomes', function testTranscriptomes() { // Increase timeout this.timeout(20000); - const {genomeId, genomeSeqId, geneId} = addTestGenome(annot=true) + const {genomeId, genomeSeqId, geneId} = addTestGenome(annot=true, multiple=true) const {expId, transcriptomeId} = addTestTranscriptome(genomeId, geneId) const updateParams = { diff --git a/imports/ui/singleGenePage/geneExpression/SampleSelection.jsx b/imports/ui/singleGenePage/geneExpression/SampleSelection.jsx index bc3d4f8d..b79a8272 100644 --- a/imports/ui/singleGenePage/geneExpression/SampleSelection.jsx +++ b/imports/ui/singleGenePage/geneExpression/SampleSelection.jsx @@ -17,10 +17,10 @@ import { import './sampleSelection.scss'; function dataTracker({ gene, showHeader, children }) { - const { genomeId } = gene; + const { genomeId, annotationName } = gene; const experimentSub = Meteor.subscribe('experimentInfo'); const loading = !experimentSub.ready(); - const experiments = ExperimentInfo.find({ genomeId }).fetch(); + const experiments = ExperimentInfo.find({ genomeId, annotationName }).fetch(); const replicaGroups = groupBy(experiments, 'replicaGroup'); return { showHeader, From 0e3b0607a2998e5a9a323e747bff1662bb08d460 Mon Sep 17 00:00:00 2001 From: mboudet <mateo.boudet@gmail.com> Date: Tue, 17 Oct 2023 14:30:47 +0200 Subject: [PATCH 25/36] Fix tests --- imports/api/transcriptomes/addKallistoTranscriptome.js | 1 + imports/startup/server/fixtures/addTestData.js | 1 + 2 files changed, 2 insertions(+) diff --git a/imports/api/transcriptomes/addKallistoTranscriptome.js b/imports/api/transcriptomes/addKallistoTranscriptome.js index 2237910a..08861bfc 100644 --- a/imports/api/transcriptomes/addKallistoTranscriptome.js +++ b/imports/api/transcriptomes/addKallistoTranscriptome.js @@ -88,6 +88,7 @@ const parseKallistoTsv = ({ nInserted += 1; bulkOp.insert({ geneId: gene.ID, + annotationName: gene.annotationName, tpm, est_counts, experimentId, diff --git a/imports/startup/server/fixtures/addTestData.js b/imports/startup/server/fixtures/addTestData.js index 2e7812d4..973e0e93 100644 --- a/imports/startup/server/fixtures/addTestData.js +++ b/imports/startup/server/fixtures/addTestData.js @@ -129,6 +129,7 @@ export function addTestTranscriptome(genomeId, geneId) { const transcriptomeId = Transcriptomes.insert({ geneId: geneId, + annotationName: "Annotation name", tpm: "60", est_counts: "1000", experimentId: expId From 311557c3cbb13b6dcf74495f8ef3d3af71d10c4b Mon Sep 17 00:00:00 2001 From: mboudet <mateo.boudet@gmail.com> Date: Wed, 18 Oct 2023 08:38:57 +0000 Subject: [PATCH 26/36] Fix --- imports/ui/singleGenePage/geneExpression/SampleSelection.jsx | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/imports/ui/singleGenePage/geneExpression/SampleSelection.jsx b/imports/ui/singleGenePage/geneExpression/SampleSelection.jsx index b79a8272..bc3d4f8d 100644 --- a/imports/ui/singleGenePage/geneExpression/SampleSelection.jsx +++ b/imports/ui/singleGenePage/geneExpression/SampleSelection.jsx @@ -17,10 +17,10 @@ import { import './sampleSelection.scss'; function dataTracker({ gene, showHeader, children }) { - const { genomeId, annotationName } = gene; + const { genomeId } = gene; const experimentSub = Meteor.subscribe('experimentInfo'); const loading = !experimentSub.ready(); - const experiments = ExperimentInfo.find({ genomeId, annotationName }).fetch(); + const experiments = ExperimentInfo.find({ genomeId }).fetch(); const replicaGroups = groupBy(experiments, 'replicaGroup'); return { showHeader, From 7c18735b926f8c9f225dc9d5456061fe162c2672 Mon Sep 17 00:00:00 2001 From: mboudet <mateo.boudet@gmail.com> Date: Wed, 18 Oct 2023 09:24:20 +0000 Subject: [PATCH 27/36] fix expression ui --- imports/ui/singleGenePage/geneExpression/ExpressionPlot.jsx | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/imports/ui/singleGenePage/geneExpression/ExpressionPlot.jsx b/imports/ui/singleGenePage/geneExpression/ExpressionPlot.jsx index 16db79ef..c84ae4d7 100644 --- a/imports/ui/singleGenePage/geneExpression/ExpressionPlot.jsx +++ b/imports/ui/singleGenePage/geneExpression/ExpressionPlot.jsx @@ -29,13 +29,14 @@ import './expressionPlot.scss'; function expressionDataTracker({ gene, samples, loading, }) { - const transcriptomeSub = Meteor.subscribe('geneExpression', gene.ID); + const transcriptomeSub = Meteor.subscribe('geneExpression', gene.ID, gene.annotationName); const sampleInfo = groupBy(samples, '_id'); const sampleIds = samples.map((sample) => sample._id); const values = Transcriptomes.find({ geneId: gene.ID, + annotationName: gene.annotationName, experimentId: { $in: sampleIds, }, From 16545e656d0b201c018a910157b7bf0d49e816af Mon Sep 17 00:00:00 2001 From: mboudet <mateo.boudet@gmail.com> Date: Wed, 18 Oct 2023 14:43:22 +0200 Subject: [PATCH 28/36] Add annotationName to experiment document to pre-filter in geneList --- imports/api/transcriptomes/addExpression.js | 7 +++--- .../addKallistoTranscriptome.js | 23 +++++++++++-------- .../transcriptome_collection.js | 4 ++++ .../api/transcriptomes/transcriptomes.test.js | 23 +++++++++++++++---- .../geneExpression/SampleSelection.jsx | 4 ++-- 5 files changed, 42 insertions(+), 19 deletions(-) diff --git a/imports/api/transcriptomes/addExpression.js b/imports/api/transcriptomes/addExpression.js index 76e86c7e..cf738578 100644 --- a/imports/api/transcriptomes/addExpression.js +++ b/imports/api/transcriptomes/addExpression.js @@ -33,7 +33,7 @@ const getGenomeId = (data, annot) => { return undefined } logger.debug(gene.genomeId); - return gene.genomeId + return {genomeId: gene.genomeId, annotationName: gene.annotationName} }; const parseExpressionTsv = ({ @@ -88,7 +88,7 @@ const parseExpressionTsv = ({ } let firstColumn = replicaGroups.shift(); - const genomeId = getGenomeId(data, annot); + const {genomeId, annotationName} = getGenomeId(data, annot); if (typeof genomeId === 'undefined') { reject(new Meteor.Error('Could not find genomeId for first transcript')); @@ -99,6 +99,7 @@ const parseExpressionTsv = ({ const replicaGroup = replicaIndex + 1 in replicaNamesDict ? replicaNamesDict[replicaIndex + 1] : sampleName experiments[sampleName] = ExperimentInfo.insert({ genomeId, + annotationName, sampleName, replicaGroup, description, @@ -128,7 +129,7 @@ const parseExpressionTsv = ({ replicaGroups.forEach((replicaGroup) => { bulkOp.insert({ geneId: gene.ID, - annotationName: gene.annotationName, + annotationName, tpm: row[replicaGroup], experimentId: experiments[replicaGroup] }); diff --git a/imports/api/transcriptomes/addKallistoTranscriptome.js b/imports/api/transcriptomes/addKallistoTranscriptome.js index 08861bfc..e79ab933 100644 --- a/imports/api/transcriptomes/addKallistoTranscriptome.js +++ b/imports/api/transcriptomes/addKallistoTranscriptome.js @@ -13,13 +13,13 @@ import { import logger from '/imports/api/util/logger.js'; const getGenomeId = (data, annot) => { - const firstTranscipts = data.slice(0, 10).map((line) => line.target_id); - logger.debug(firstTranscipts); + const firstTranscripts = data.slice(0, 10).map((line) => line.gene); + logger.debug(firstTranscripts); let geneQuery = { $or: [ - { ID: { $in: firstTranscipts } }, - { 'subfeatures.ID': { $in: firstTranscipts } }, + { ID: { $in: firstTranscripts } }, + { 'subfeatures.ID': { $in: firstTranscripts } }, ], } @@ -27,9 +27,13 @@ const getGenomeId = (data, annot) => { geneQuery['annotationName'] = annot } - const { genomeId } = Genes.findOne(geneQuery); - logger.debug(genomeId); - return genomeId; + const gene = Genes.findOne(geneQuery); + + if (typeof gene === "undefined"){ + return undefined + } + logger.debug(gene.genomeId); + return {genomeId: gene.genomeId, annotationName: gene.annotationName} }; const parseKallistoTsv = ({ @@ -50,7 +54,7 @@ const parseKallistoTsv = ({ complete({ data }, _file) { let nInserted = 0; - const genomeId = getGenomeId(data, annot); + const {genomeId, annotationName} = getGenomeId(data, annot); if (typeof genomeId === 'undefined') { reject(new Meteor.Error('Could not find genomeId for first transcript')); @@ -60,6 +64,7 @@ const parseKallistoTsv = ({ const experimentId = ExperimentInfo.insert({ genomeId, + annotationName, sampleName, replicaGroup, description, @@ -88,7 +93,7 @@ const parseKallistoTsv = ({ nInserted += 1; bulkOp.insert({ geneId: gene.ID, - annotationName: gene.annotationName, + annotationName, tpm, est_counts, experimentId, diff --git a/imports/api/transcriptomes/transcriptome_collection.js b/imports/api/transcriptomes/transcriptome_collection.js index d51527dc..3ce2fc15 100644 --- a/imports/api/transcriptomes/transcriptome_collection.js +++ b/imports/api/transcriptomes/transcriptome_collection.js @@ -8,6 +8,10 @@ const ExperimentInfoSchema = new SimpleSchema({ type: String, label: 'Genome ID', }, + annotationName: { + type: String, + label: 'Annotation name', + }, sampleName: { type: String, label: 'Short name for the sample', diff --git a/imports/api/transcriptomes/transcriptomes.test.js b/imports/api/transcriptomes/transcriptomes.test.js index 482535a5..72db2997 100644 --- a/imports/api/transcriptomes/transcriptomes.test.js +++ b/imports/api/transcriptomes/transcriptomes.test.js @@ -70,6 +70,7 @@ describe('transcriptomes', function testTranscriptomes() { chai.assert.equal(exp.sampleName, 'mySample') chai.assert.equal(exp.replicaGroup, 'replicaGroup') chai.assert.equal(exp.description, 'A new description') + chai.assert.equal(exp.annotationName, "Annotation name") const transcriptomes = Transcriptomes.find({experimentId: exp._id}).fetch() @@ -78,8 +79,8 @@ describe('transcriptomes', function testTranscriptomes() { const transcriptome = transcriptomes[0] chai.assert.equal(transcriptome.geneId, 'BniB01g000010.2N') - chai.assert.equal(transcriptome.annotationName, "Annotation name") chai.assert.equal(transcriptome.tpm, '1.80368') + chai.assert.equal(transcriptome.annotationName, "Annotation name") chai.assert.equal(transcriptome.est_counts, '21') }) @@ -119,10 +120,12 @@ describe('transcriptomes', function testTranscriptomes() { chai.assert.equal(exp.sampleName, 'sample1') chai.assert.equal(exp.replicaGroup, 'sample1') chai.assert.equal(exp.description, 'A new description') + chai.assert.equal(exp.annotationName, "Annotation name") chai.assert.equal(exps[1].sampleName, 'sample2') chai.assert.equal(exps[1].replicaGroup, 'sample2') chai.assert.equal(exps[1].description, 'A new description') + chai.assert.equal(exps[1].annotationName, "Annotation name") const transcriptomes = Transcriptomes.find({experimentId: exp._id}).fetch() @@ -131,8 +134,8 @@ describe('transcriptomes', function testTranscriptomes() { const transcriptome = transcriptomes[0] chai.assert.equal(transcriptome.geneId, 'BniB01g000010.2N') - chai.assert.equal(transcriptome.annotationName, "Annotation name") chai.assert.equal(transcriptome.tpm, '40') + chai.assert.equal(transcriptome.annotationName, "Annotation name") chai.assert.isUndefined(transcriptome.est_counts) }) @@ -173,14 +176,17 @@ describe('transcriptomes', function testTranscriptomes() { chai.assert.equal(exp.sampleName, 'sample1') chai.assert.equal(exp.replicaGroup, 'sample1') chai.assert.equal(exp.description, 'A new description') + chai.assert.equal(exp.annotationName, "Annotation name") chai.assert.equal(exps[1].sampleName, 'sample2') chai.assert.equal(exps[1].replicaGroup, 'sample1') chai.assert.equal(exps[1].description, 'A new description') + chai.assert.equal(exps[1].annotationName, "Annotation name") chai.assert.equal(exps[2].sampleName, 'sample3') chai.assert.equal(exps[2].replicaGroup, 'sample3') chai.assert.equal(exps[2].description, 'A new description') + chai.assert.equal(exps[2].annotationName, "Annotation name") const transcriptomes = Transcriptomes.find({experimentId: exp._id}).fetch() @@ -189,8 +195,8 @@ describe('transcriptomes', function testTranscriptomes() { const transcriptome = transcriptomes[0] chai.assert.equal(transcriptome.geneId, 'BniB01g000010.2N') - chai.assert.equal(transcriptome.annotationName, "Annotation name") chai.assert.equal(transcriptome.tpm, '40') + chai.assert.equal(transcriptome.annotationName, "Annotation name") chai.assert.isUndefined(transcriptome.est_counts) }) @@ -232,18 +238,22 @@ describe('transcriptomes', function testTranscriptomes() { chai.assert.equal(exp.sampleName, 'sample1') chai.assert.equal(exp.replicaGroup, 'My replica group name') chai.assert.equal(exp.description, 'A new description') + chai.assert.equal(exp.annotationName, "Annotation name") chai.assert.equal(exps[1].sampleName, 'sample2') chai.assert.equal(exps[1].replicaGroup, 'My replica group name') chai.assert.equal(exps[1].description, 'A new description') + chai.assert.equal(exps[1].annotationName, "Annotation name") chai.assert.equal(exps[2].sampleName, 'sample3') chai.assert.equal(exps[2].replicaGroup, 'Another group name') chai.assert.equal(exps[2].description, 'A new description') + chai.assert.equal(exps[2].annotationName, "Annotation name") chai.assert.equal(exps[3].sampleName, 'sample4') chai.assert.equal(exps[3].replicaGroup, 'sample4') chai.assert.equal(exps[3].description, 'A new description') + chai.assert.equal(exps[3].annotationName, "Annotation name") const transcriptomes = Transcriptomes.find({experimentId: exp._id}).fetch() @@ -252,9 +262,9 @@ describe('transcriptomes', function testTranscriptomes() { const transcriptome = transcriptomes[0] chai.assert.equal(transcriptome.geneId, 'BniB01g000010.2N') - chai.assert.equal(transcriptome.annotationName, "Annotation name") chai.assert.equal(transcriptome.tpm, '40') chai.assert.isUndefined(transcriptome.est_counts) + chai.assert.equal(transcriptome.annotationName, "Annotation name") }) @@ -294,14 +304,17 @@ describe('transcriptomes', function testTranscriptomes() { chai.assert.equal(exp.sampleName, 'sample1') chai.assert.equal(exp.replicaGroup, 'TestReplica1') chai.assert.equal(exp.description, 'A new description') + chai.assert.equal(exp.annotationName, "Annotation name") chai.assert.equal(exps[1].sampleName, 'sample2') chai.assert.equal(exps[1].replicaGroup, 'TestReplica2') chai.assert.equal(exps[1].description, 'A new description') + chai.assert.equal(exps[1].annotationName, "Annotation name") chai.assert.equal(exps[2].sampleName, 'sample3') chai.assert.equal(exps[2].replicaGroup, 'sample3') chai.assert.equal(exps[2].description, 'A new description') + chai.assert.equal(exps[2].annotationName, "Annotation name") const transcriptomes = Transcriptomes.find({experimentId: exp._id}).fetch() @@ -310,8 +323,8 @@ describe('transcriptomes', function testTranscriptomes() { const transcriptome = transcriptomes[0] chai.assert.equal(transcriptome.geneId, 'BniB01g000010.2N') - chai.assert.equal(transcriptome.annotationName, "Annotation name") chai.assert.equal(transcriptome.tpm, '40') + chai.assert.equal(transcriptome.annotationName, "Annotation name") chai.assert.isUndefined(transcriptome.est_counts) }) diff --git a/imports/ui/singleGenePage/geneExpression/SampleSelection.jsx b/imports/ui/singleGenePage/geneExpression/SampleSelection.jsx index bc3d4f8d..b79a8272 100644 --- a/imports/ui/singleGenePage/geneExpression/SampleSelection.jsx +++ b/imports/ui/singleGenePage/geneExpression/SampleSelection.jsx @@ -17,10 +17,10 @@ import { import './sampleSelection.scss'; function dataTracker({ gene, showHeader, children }) { - const { genomeId } = gene; + const { genomeId, annotationName } = gene; const experimentSub = Meteor.subscribe('experimentInfo'); const loading = !experimentSub.ready(); - const experiments = ExperimentInfo.find({ genomeId }).fetch(); + const experiments = ExperimentInfo.find({ genomeId, annotationName }).fetch(); const replicaGroups = groupBy(experiments, 'replicaGroup'); return { showHeader, From 47003c8fb9cf4493084f3ab95e8b60d32d50fa82 Mon Sep 17 00:00:00 2001 From: mboudet <mateo.boudet@gmail.com> Date: Wed, 18 Oct 2023 15:12:28 +0000 Subject: [PATCH 29/36] fix test & ui --- imports/api/transcriptomes/addExpression.js | 8 ++++---- .../transcriptomes/addKallistoTranscriptome.js | 4 ++-- imports/startup/server/fixtures/addTestData.js | 1 + .../geneExpression/ExpressionPlot.jsx | 18 ++++++++++++++++++ .../geneExpression/SampleSelection.jsx | 7 +++++-- 5 files changed, 30 insertions(+), 8 deletions(-) diff --git a/imports/api/transcriptomes/addExpression.js b/imports/api/transcriptomes/addExpression.js index cf738578..75b0dabc 100644 --- a/imports/api/transcriptomes/addExpression.js +++ b/imports/api/transcriptomes/addExpression.js @@ -12,8 +12,8 @@ import { } from '/imports/api/transcriptomes/transcriptome_collection.js'; import logger from '/imports/api/util/logger.js'; -const getGenomeId = (data, annot) => { - const firstTranscripts = data.slice(0, 10).map((line) => line.gene); +const getGenomeId = (data, firstColumn, annot) => { + const firstTranscripts = data.slice(0, 10).map((line) => line[firstColumn]); logger.debug(firstTranscripts); let geneQuery = { @@ -30,7 +30,7 @@ const getGenomeId = (data, annot) => { const gene = Genes.findOne(geneQuery); if (typeof gene === "undefined"){ - return undefined + return {genomeId: undefined, annotationName: undefined} } logger.debug(gene.genomeId); return {genomeId: gene.genomeId, annotationName: gene.annotationName} @@ -88,7 +88,7 @@ const parseExpressionTsv = ({ } let firstColumn = replicaGroups.shift(); - const {genomeId, annotationName} = getGenomeId(data, annot); + const {genomeId, annotationName} = getGenomeId(data, firstColumn, annot); if (typeof genomeId === 'undefined') { reject(new Meteor.Error('Could not find genomeId for first transcript')); diff --git a/imports/api/transcriptomes/addKallistoTranscriptome.js b/imports/api/transcriptomes/addKallistoTranscriptome.js index e79ab933..64547317 100644 --- a/imports/api/transcriptomes/addKallistoTranscriptome.js +++ b/imports/api/transcriptomes/addKallistoTranscriptome.js @@ -13,7 +13,7 @@ import { import logger from '/imports/api/util/logger.js'; const getGenomeId = (data, annot) => { - const firstTranscripts = data.slice(0, 10).map((line) => line.gene); + const firstTranscripts = data.slice(0, 10).map((line) => line.target_id); logger.debug(firstTranscripts); let geneQuery = { @@ -30,7 +30,7 @@ const getGenomeId = (data, annot) => { const gene = Genes.findOne(geneQuery); if (typeof gene === "undefined"){ - return undefined + return {genomeId: undefined, annotationName: undefined} } logger.debug(gene.genomeId); return {genomeId: gene.genomeId, annotationName: gene.annotationName} diff --git a/imports/startup/server/fixtures/addTestData.js b/imports/startup/server/fixtures/addTestData.js index 973e0e93..9001129f 100644 --- a/imports/startup/server/fixtures/addTestData.js +++ b/imports/startup/server/fixtures/addTestData.js @@ -121,6 +121,7 @@ export function addTestTranscriptome(genomeId, geneId) { const expId = ExperimentInfo.insert({ genomeId: genomeId, sampleName: "sampleName", + annotationName: "Annotation name", replicaGroup: "replicaGroup", description: 'description', permission: 'admin', diff --git a/imports/ui/singleGenePage/geneExpression/ExpressionPlot.jsx b/imports/ui/singleGenePage/geneExpression/ExpressionPlot.jsx index c84ae4d7..6bddb97c 100644 --- a/imports/ui/singleGenePage/geneExpression/ExpressionPlot.jsx +++ b/imports/ui/singleGenePage/geneExpression/ExpressionPlot.jsx @@ -83,6 +83,23 @@ function Loading() { ); } +function hasNoExpression({ values }) { + return values.length == 0; +} + +function NoExpression() { + return( + <div className="card expression-plot"> + <article className="message no-protein-domains" role="alert"> + <div className="message-body"> + <p className="has-text-grey">No expression data for the selected samples</p> + </div> + </article> + </div> + ) +} + + function YAxis({ scale, numTicks }) { const range = scale.range(); const [start, end] = scale.domain(); @@ -407,4 +424,5 @@ export default compose( branch(hasNoSamples, NoSamples), withTracker(expressionDataTracker), branch(isLoading, Loading), + branch(hasNoExpression, NoExpression) )(ExpressionPlot); diff --git a/imports/ui/singleGenePage/geneExpression/SampleSelection.jsx b/imports/ui/singleGenePage/geneExpression/SampleSelection.jsx index b79a8272..6fc4a990 100644 --- a/imports/ui/singleGenePage/geneExpression/SampleSelection.jsx +++ b/imports/ui/singleGenePage/geneExpression/SampleSelection.jsx @@ -41,7 +41,7 @@ function NoExpression() { <div className="card expression-plot"> <article className="message no-protein-domains" role="alert"> <div className="message-body"> - <p className="has-text-grey">No expression data found</p> + <p className="has-text-grey">No samples found</p> </div> </article> </div> @@ -91,10 +91,13 @@ function SampleSelection({ })); } + let className = showHeader ? "is-pulled-right" : "" + let style = showHeader ? {} : {"text-align": "right"} + return ( <> { showHeader && <hr /> } - <div className="is-pulled-right"> + <div className={className} style={style}> <div className="dropdown is-right is-hoverable"> <div className="dropdown-trigger"> <button type="button" className="button is-small"> From 395dc1980b030684ae8a6658669f135a4fe5e4bc Mon Sep 17 00:00:00 2001 From: mboudet <mateo.boudet@gmail.com> Date: Thu, 19 Oct 2023 09:49:56 +0200 Subject: [PATCH 30/36] Add character to decode and decoding before annot funct --- imports/api/genes/alignment/alignment.test.js | 8 +++--- .../genes/alignment/parser/pairwiseParser.js | 4 +-- .../api/genes/alignment/parser/xmlParser.js | 2 +- imports/api/genes/download/download.test.js | 14 +++++----- imports/api/genes/eggnog/addEggnog.js | 2 ++ imports/api/genes/eggnog/eggnog.test.js | 6 ++-- imports/api/genes/hectar/addHectar.js | 2 ++ imports/api/genes/hectar/hectar.test.js | 6 ++-- .../genes/interproscan/interproscan.test.js | 6 ++-- .../api/genes/orthogroup/orthogroups.test.js | 4 +-- .../orthogroup/parser/treeNewickParser.js | 2 +- imports/api/genes/parseGff3Interproscan.js | 2 ++ imports/api/genes/parseTsvInterproscan.js | 2 ++ .../genomes/annotation/addAnnotation.test.js | 6 ++-- imports/api/methods/methods.test.js | 2 +- imports/api/transcriptomes/addExpression.js | 6 ++-- .../addKallistoTranscriptome.js | 6 ++-- .../api/transcriptomes/transcriptomes.test.js | 10 +++---- imports/api/util/util.test.js | 4 +-- .../startup/server/fixtures/addTestData.js | 10 +++---- private/data/BLAST_blastx_bnigra.txt | 4 +-- private/data/Bnigra.gff3 | 28 +++++++++---------- private/data/Bnigra_abundance.tsv | 2 +- private/data/Bnigra_eggnog.tsv | 2 +- private/data/Bnigra_hectar.tab | 2 +- private/data/Bnigra_interproscan.gff | 4 +-- private/data/Bnigra_interproscan.tsv | 4 +-- private/data/Bnigra_kallisto_abundance.tsv | 2 +- private/data/Bnigra_min.gff3 | 6 ++-- private/data/Diamond_blastp_bnigra.xml | 4 +-- private/data/Diamond_blastx_bnigra.txt | 2 +- private/data/orthogroups/OG0000001_tree.txt | 2 +- 32 files changed, 87 insertions(+), 79 deletions(-) diff --git a/imports/api/genes/alignment/alignment.test.js b/imports/api/genes/alignment/alignment.test.js index 4420bb47..58f1751a 100644 --- a/imports/api/genes/alignment/alignment.test.js +++ b/imports/api/genes/alignment/alignment.test.js @@ -60,13 +60,13 @@ describe('alignment', function testAlignment() { let result = addSimilarSequence._execute(adminContext, diamondParams); - const simSeq = similarSequencesCollection.find({iteration_query: "BniB01g000010.2N", annotationName: "Annotation name"}).fetch(); + const simSeq = similarSequencesCollection.find({iteration_query: "Bni|B01g000010.2N", annotationName: "Annotation name"}).fetch(); chai.assert.lengthOf(simSeq, 1, "No similar sequence found") const seq = simSeq[0] chai.assert.equal(seq.algorithm_ref, 'blastx') - chai.assert.equal(seq.protein_id, 'BniB01g000010.2N.1-P') + chai.assert.equal(seq.protein_id, 'Bni|B01g000010.2N.1-P') chai.assert.equal(seq.database_ref, 'nr') chai.assert.equal(seq.program_ref, 'diamond') chai.assert.equal(seq.query_len, 420) @@ -105,7 +105,7 @@ describe('alignment', function testAlignment() { //Meteor._sleepForMs(10000); - const simSeq = similarSequencesCollection.find({iteration_query: "BniB01g000010.2N", annotationName: "Annotation name"}).fetch(); + const simSeq = similarSequencesCollection.find({iteration_query: "Bni|B01g000010.2N", annotationName: "Annotation name"}).fetch(); chai.assert.lengthOf(simSeq, 1, "No similar sequence found") @@ -147,7 +147,7 @@ describe('alignment', function testAlignment() { let result = addSimilarSequence._execute(adminContext, diamondParams); - const simSeq = similarSequencesCollection.find({iteration_query: "BniB01g000010.2N", annotationName: "Annotation name"}).fetch(); + const simSeq = similarSequencesCollection.find({iteration_query: "Bni|B01g000010.2N", annotationName: "Annotation name"}).fetch(); chai.assert.lengthOf(simSeq, 1, "No similar sequence found") const seq = simSeq[0] diff --git a/imports/api/genes/alignment/parser/pairwiseParser.js b/imports/api/genes/alignment/parser/pairwiseParser.js index b9d62c3f..663f05db 100644 --- a/imports/api/genes/alignment/parser/pairwiseParser.js +++ b/imports/api/genes/alignment/parser/pairwiseParser.js @@ -61,7 +61,7 @@ class PairwiseProcessor { /** In the event that it is the first element of the collection to be created. */ if (typeof this.pairWise.iteration_query === 'undefined') { - this.pairWise.iteration_query = queryClean; + this.pairWise.iteration_query = decodeURIComponent(queryClean); } let geneQuery = { @@ -111,7 +111,7 @@ class PairwiseProcessor { /** Initializes a new pairwise. */ this.pairWise = new Pairwise({}); - this.pairWise.iteration_query = queryClean; + this.pairWise.iteration_query = decodeURIComponent(queryClean); this.pairWise.iteration_hits = []; } diff --git a/imports/api/genes/alignment/parser/xmlParser.js b/imports/api/genes/alignment/parser/xmlParser.js index c88147de..9d713c0a 100644 --- a/imports/api/genes/alignment/parser/xmlParser.js +++ b/imports/api/genes/alignment/parser/xmlParser.js @@ -103,7 +103,7 @@ class XmlProcessor { await Promise.all(splitIterationQuery.map(async (iter) => { /** Chek if the queries exist in the genes collection. */ - let geneQuery = { $or: [{'subfeatures.ID': iter}, {'subfeatures.protein_id': iter}] } + let geneQuery = { $or: [{'subfeatures.ID': decodeURIComponent(iter)}, {'subfeatures.protein_id': decodeURIComponent(iter)}] } if (typeof this.annot !== "undefined"){ geneQuery['annotationName'] = this.annot } diff --git a/imports/api/genes/download/download.test.js b/imports/api/genes/download/download.test.js index 8652f59e..5437a74c 100644 --- a/imports/api/genes/download/download.test.js +++ b/imports/api/genes/download/download.test.js @@ -64,7 +64,7 @@ describe('download', function testDownload() { addTestGenome(annot=true) const dlParams = { - query: {ID: "BniB01g000010.2N"}, + query: {ID: "Bni|B01g000010.2N"}, dataType: 'Annotation', options: {}, async: false @@ -79,8 +79,8 @@ describe('download', function testDownload() { const expected = [ '##gff-version 3', 'B1\tAAFC_GIFS\tgene\t13640\t15401\t.\t-\t-\tmyNewAttribute=1', - 'B1\tAAFC_GIFS\tmRNA\t13641\t15400\t.\t-\t.\tParent=BniB01g000010.2N', - 'B1\tAAFC_GIFS\tCDS\t13641\t13653\t.\t-\t.\tParent=BniB01g000010.2N.1' + 'B1\tAAFC_GIFS\tmRNA\t13641\t15400\t.\t-\t.\tParent=Bni|B01g000010.2N', + 'B1\tAAFC_GIFS\tCDS\t13641\t13653\t.\t-\t.\tParent=Bni|B01g000010.2N.1' ] const data = await readFile(dataFile) @@ -95,7 +95,7 @@ describe('download', function testDownload() { addTestGenome(annot=true) const dlParams = { - query: {ID: "BniB01g000010.2N"}, + query: {ID: "Bni|B01g000010.2N"}, dataType: 'Sequence', options: {seqType: "nucl", primaryTranscriptOnly: false}, async: false @@ -108,7 +108,7 @@ describe('download', function testDownload() { chai.assert.equal(stat.size, 51) const expected = [ - ">BniB01g000010.2N.1", + ">Bni|B01g000010.2N.1", "AGTTTAGAATAC" ] const data = await readFile(dataFile) @@ -124,7 +124,7 @@ describe('download', function testDownload() { const {expId, transcriptomeId} = addTestTranscriptome(genomeId, geneId) const dlParams = { - query: {ID: "BniB01g000010.2N"}, + query: {ID: "Bni|B01g000010.2N"}, dataType: 'Expression', options: {selectedSamples: ["replicaGroup"]}, async: false @@ -138,7 +138,7 @@ describe('download', function testDownload() { const expected = [ "gene_id\treplicaGroup", - "BniB01g000010.2N\t60" + "Bni|B01g000010.2N\t60" ] const data = await readFile(dataFile) diff --git a/imports/api/genes/eggnog/addEggnog.js b/imports/api/genes/eggnog/addEggnog.js index a6a2f1ab..26b2ad2a 100644 --- a/imports/api/genes/eggnog/addEggnog.js +++ b/imports/api/genes/eggnog/addEggnog.js @@ -53,6 +53,8 @@ class EggnogProcessor { pfams, ] = line.split('\t'); + queryName = decodeURIComponent(queryName) + // Organize data in a dictionary. const annotations = { query_name: queryName, diff --git a/imports/api/genes/eggnog/eggnog.test.js b/imports/api/genes/eggnog/eggnog.test.js index 29ec7d57..fe8bd98a 100644 --- a/imports/api/genes/eggnog/eggnog.test.js +++ b/imports/api/genes/eggnog/eggnog.test.js @@ -51,7 +51,7 @@ describe('eggnog', function testEggnog() { chai.assert.equal(result.nInserted, 1) - const eggs = eggnogCollection.find({ query_name: 'BniB01g000010.2N.1-P', annotationName: "Annotation name" }).fetch(); + const eggs = eggnogCollection.find({ query_name: 'Bni|B01g000010.2N.1-P', annotationName: "Annotation name" }).fetch(); chai.assert.lengthOf(eggs, 1, 'No eggnog data found'); @@ -64,8 +64,8 @@ describe('eggnog', function testEggnog() { chai.assert.lengthOf(egg.GOs, 18); chai.assert.equal(egg.Description, 'UDP-glucuronic acid decarboxylase'); - const gene1 = Genes.findOne({ID: 'BniB01g000010.2N', annotationName: 'Annotation name'}) - const gene2 = Genes.findOne({ID: 'BniB01g000010.2N', annotationName: 'Annotation name 2'}) + const gene1 = Genes.findOne({ID: 'Bni|B01g000010.2N', annotationName: 'Annotation name'}) + const gene2 = Genes.findOne({ID: 'Bni|B01g000010.2N', annotationName: 'Annotation name 2'}) chai.assert.isDefined(gene1.eggnogId, "eggNodeId is not defined for the correct annotation") chai.assert.isUndefined(gene2.eggnogId, "eggNodeId is defined for the wrong annotation") diff --git a/imports/api/genes/hectar/addHectar.js b/imports/api/genes/hectar/addHectar.js index 9981c443..4fb024ed 100644 --- a/imports/api/genes/hectar/addHectar.js +++ b/imports/api/genes/hectar/addHectar.js @@ -40,6 +40,8 @@ class HectarProcessor { otherScore, ] = line.split('\t'); + proteinId = decodeURIComponent(proteinId) + // Organize data in a dictionary. const annotations = { protein_id: proteinId, diff --git a/imports/api/genes/hectar/hectar.test.js b/imports/api/genes/hectar/hectar.test.js index b9a5312b..b1f6d702 100644 --- a/imports/api/genes/hectar/hectar.test.js +++ b/imports/api/genes/hectar/hectar.test.js @@ -51,7 +51,7 @@ describe('hectar', function testHectar() { chai.assert.equal(result.nInserted, 1) - const hecs = hectarCollection.find({ protein_id: 'BniB01g000010.2N.1', annotationName: "Annotation name" }).fetch(); + const hecs = hectarCollection.find({ protein_id: 'Bni|B01g000010.2N.1', annotationName: "Annotation name" }).fetch(); chai.assert.lengthOf(hecs, 1, 'No hectar data found'); @@ -63,8 +63,8 @@ describe('hectar', function testHectar() { chai.assert.equal(hec.mitochondrion_score, '0.1032'); chai.assert.equal(hec.other_score, '0.8968'); - const gene1 = Genes.findOne({ID: 'BniB01g000010.2N', annotationName: 'Annotation name'}) - const gene2 = Genes.findOne({ID: 'BniB01g000010.2N', annotationName: 'Annotation name 2'}) + const gene1 = Genes.findOne({ID: 'Bni|B01g000010.2N', annotationName: 'Annotation name'}) + const gene2 = Genes.findOne({ID: 'Bni|B01g000010.2N', annotationName: 'Annotation name 2'}) chai.assert.isDefined(gene1.hectarId, "eggNodeId is not defined for the correct annotation") chai.assert.isUndefined(gene2.hectarId, "eggNodeId is defined for the wrong annotation") diff --git a/imports/api/genes/interproscan/interproscan.test.js b/imports/api/genes/interproscan/interproscan.test.js index 58fb26ab..a4e91233 100644 --- a/imports/api/genes/interproscan/interproscan.test.js +++ b/imports/api/genes/interproscan/interproscan.test.js @@ -58,12 +58,12 @@ describe('interproscan', function testInterproscan() { let result = addInterproscan._execute(adminContext, interproParams); - const gene = Genes.findOne({ID: "BniB01g000010.2N"}) + const gene = Genes.findOne({ID: "Bni|B01g000010.2N"}) chai.assert.deepEqual(gene.attributes.Dbxref, [ 'InterPro:1236' ]) chai.assert.deepEqual(gene.attributes.Ontology_term, [ 'GO:1238' ]) - const interpros = interproscanCollection.find({gene_id: "BniB01g000010.2N", annotationName: "Annotation name"}).fetch(); + const interpros = interproscanCollection.find({gene_id: "Bni|B01g000010.2N", annotationName: "Annotation name"}).fetch(); chai.assert.lengthOf(interpros, 1, "No Interpro document found") const protein_domains = interpros[0].protein_domains @@ -107,7 +107,7 @@ describe('interproscan', function testInterproscan() { let result = addInterproscan._execute(adminContext, interproParams); - const interpros = interproscanCollection.find({gene_id: "BniB01g000010.2N", annotationName: "Annotation name"}).fetch(); + const interpros = interproscanCollection.find({gene_id: "Bni|B01g000010.2N", annotationName: "Annotation name"}).fetch(); chai.assert.lengthOf(interpros, 1, "No Interpro document found") const protein_domains = interpros[0].protein_domains diff --git a/imports/api/genes/orthogroup/orthogroups.test.js b/imports/api/genes/orthogroup/orthogroups.test.js index 26d5ea8e..812cba7d 100644 --- a/imports/api/genes/orthogroup/orthogroups.test.js +++ b/imports/api/genes/orthogroup/orthogroups.test.js @@ -58,7 +58,7 @@ describe('orthogroups', function testOrthogroups() { let result = addOrthogroupTrees._execute(adminContext, orthoGroupsParams); - const gene = Genes.findOne({ID: "BniB01g000010.2N"}) + const gene = Genes.findOne({ID: "Bni|B01g000010.2N"}) chai.assert.isDefined(gene.orthogroup, 'orthogroup key is undefined') @@ -73,7 +73,7 @@ describe('orthogroups', function testOrthogroups() { chai.assert.deepEqual(ortho.genomes["unknown"], { name: 'unknown', count: 56 }) chai.assert.deepEqual(ortho.genomes[genomeId], { name: 'Test Genome', count: 1 }) - chai.assert.sameMembers(ortho.geneIds, ['BniB01g000010.2N']) + chai.assert.sameMembers(ortho.geneIds, ['Bni|B01g000010.2N']) chai.assert.equal(ortho.size, 84.5) chai.assert.equal(ortho.name, 'OG0000001') }); diff --git a/imports/api/genes/orthogroup/parser/treeNewickParser.js b/imports/api/genes/orthogroup/parser/treeNewickParser.js index df0edc65..add12fb2 100644 --- a/imports/api/genes/orthogroup/parser/treeNewickParser.js +++ b/imports/api/genes/orthogroup/parser/treeNewickParser.js @@ -117,7 +117,7 @@ class NewickProcessor { getGeneId = async (prefixes, geneid) => { return new Promise((resolve, reject) => { - let geneName = geneid + let geneName = decodeURIComponent(geneid) try { if (prefixes){ for (const i in prefixes) { diff --git a/imports/api/genes/parseGff3Interproscan.js b/imports/api/genes/parseGff3Interproscan.js index 4f3a23ee..51cfde75 100644 --- a/imports/api/genes/parseGff3Interproscan.js +++ b/imports/api/genes/parseGff3Interproscan.js @@ -45,6 +45,8 @@ class ParseGff3File extends InterproscanProcessor { if (!(line[0] === '#' || line.split('\t').length <= 1)) { const [seqId, source, type, start, end, score, , , attributeString, ] = line.split('\t'); + seqId = decodeURIComponent(seqId) + if (this.isProteinMatch(type)) { const attributes = this.parseAllAttributes(attributeString); if (attributes) { diff --git a/imports/api/genes/parseTsvInterproscan.js b/imports/api/genes/parseTsvInterproscan.js index 6043e037..d96c22b1 100644 --- a/imports/api/genes/parseTsvInterproscan.js +++ b/imports/api/genes/parseTsvInterproscan.js @@ -22,6 +22,8 @@ class ParseTsvFile extends InterproscanProcessor { pathwaysAnnotations, // Dbxref (gff3) ] = line.split('\t'); + seqId = decodeURIComponent(seqId) + // Add to bulk if protein changes if (seqId !== this.currentProt){ if (seqId !== ""){ diff --git a/imports/api/genomes/annotation/addAnnotation.test.js b/imports/api/genomes/annotation/addAnnotation.test.js index 66c14718..1acaa66d 100644 --- a/imports/api/genomes/annotation/addAnnotation.test.js +++ b/imports/api/genomes/annotation/addAnnotation.test.js @@ -54,7 +54,7 @@ describe('AddAnnotation', function testAnnotation() { const gene = genes[0]; - chai.assert.equal(gene.ID, 'BniB01g000010.2N'); + chai.assert.equal(gene.ID, 'Bni|B01g000010.2N'); chai.assert.equal(gene.annotationName, 'Test annotation'); chai.assert.equal(gene.seqid, 'B1'); chai.assert.equal(gene.source, 'AAFC_GIFS'); @@ -170,7 +170,7 @@ describe('AddAnnotation', function testAnnotation() { const genes = Genes.find({ genomeId: genomeId }).fetch(); const mRNA = genes[0].subfeatures[0] - chai.assert.equal("BniB01g000010.2N.1-protattr", mRNA.protein_id) + chai.assert.equal("Bni|B01g000010.2N.1-protattr", mRNA.protein_id) }); @@ -192,7 +192,7 @@ describe('AddAnnotation', function testAnnotation() { const genes = Genes.find({ genomeId: genomeId }).fetch(); const mRNA = genes[0].subfeatures[0] - chai.assert.equal("BniB01g000010.2N.1-protattr", mRNA.protein_id) + chai.assert.equal("Bni|B01g000010.2N.1-protattr", mRNA.protein_id) }); }); diff --git a/imports/api/methods/methods.test.js b/imports/api/methods/methods.test.js index d3c1f345..17507021 100644 --- a/imports/api/methods/methods.test.js +++ b/imports/api/methods/methods.test.js @@ -29,7 +29,7 @@ describe('methods', function testMethods() { it('Should get the genes query count', function testGetQueryCount() { addTestGenome(annot=true) - const queryParams = {query: {ID: "BniB01g000010.2N"}} + const queryParams = {query: {ID: "Bni|B01g000010.2N"}} const count = getQueryCount._execute({}, queryParams) chai.assert.equal(count, 1) diff --git a/imports/api/transcriptomes/addExpression.js b/imports/api/transcriptomes/addExpression.js index 75b0dabc..d345b07f 100644 --- a/imports/api/transcriptomes/addExpression.js +++ b/imports/api/transcriptomes/addExpression.js @@ -13,7 +13,7 @@ import { import logger from '/imports/api/util/logger.js'; const getGenomeId = (data, firstColumn, annot) => { - const firstTranscripts = data.slice(0, 10).map((line) => line[firstColumn]); + const firstTranscripts = data.slice(0, 10).map((line) => decodeURIComponent(line[firstColumn])); logger.debug(firstTranscripts); let geneQuery = { @@ -111,8 +111,8 @@ const parseExpressionTsv = ({ data.forEach((row) => { let geneQuery = { $or: [ - { ID: row[firstColumn] }, - { 'subfeatures.ID': row[firstColumn] }, + { ID: decodeURIComponent(row[firstColumn]) }, + { 'subfeatures.ID': decodeURIComponent(row[firstColumn]) }, ], } diff --git a/imports/api/transcriptomes/addKallistoTranscriptome.js b/imports/api/transcriptomes/addKallistoTranscriptome.js index 64547317..202414ba 100644 --- a/imports/api/transcriptomes/addKallistoTranscriptome.js +++ b/imports/api/transcriptomes/addKallistoTranscriptome.js @@ -13,7 +13,7 @@ import { import logger from '/imports/api/util/logger.js'; const getGenomeId = (data, annot) => { - const firstTranscripts = data.slice(0, 10).map((line) => line.target_id); + const firstTranscripts = data.slice(0, 10).map((line) => decodeURIComponent(line.target_id)); logger.debug(firstTranscripts); let geneQuery = { @@ -76,8 +76,8 @@ const parseKallistoTsv = ({ data.forEach(({ target_id, tpm, est_counts }) => { let geneQuery = { $or: [ - { ID: target_id }, - { 'subfeatures.ID': target_id }, + { ID: decodeURIComponent(target_id) }, + { 'subfeatures.ID': decodeURIComponent(target_id) }, ], } diff --git a/imports/api/transcriptomes/transcriptomes.test.js b/imports/api/transcriptomes/transcriptomes.test.js index 72db2997..43228ef6 100644 --- a/imports/api/transcriptomes/transcriptomes.test.js +++ b/imports/api/transcriptomes/transcriptomes.test.js @@ -78,7 +78,7 @@ describe('transcriptomes', function testTranscriptomes() { const transcriptome = transcriptomes[0] - chai.assert.equal(transcriptome.geneId, 'BniB01g000010.2N') + chai.assert.equal(transcriptome.geneId, 'Bni|B01g000010.2N') chai.assert.equal(transcriptome.tpm, '1.80368') chai.assert.equal(transcriptome.annotationName, "Annotation name") chai.assert.equal(transcriptome.est_counts, '21') @@ -133,7 +133,7 @@ describe('transcriptomes', function testTranscriptomes() { const transcriptome = transcriptomes[0] - chai.assert.equal(transcriptome.geneId, 'BniB01g000010.2N') + chai.assert.equal(transcriptome.geneId, 'Bni|B01g000010.2N') chai.assert.equal(transcriptome.tpm, '40') chai.assert.equal(transcriptome.annotationName, "Annotation name") chai.assert.isUndefined(transcriptome.est_counts) @@ -194,7 +194,7 @@ describe('transcriptomes', function testTranscriptomes() { const transcriptome = transcriptomes[0] - chai.assert.equal(transcriptome.geneId, 'BniB01g000010.2N') + chai.assert.equal(transcriptome.geneId, 'Bni|B01g000010.2N') chai.assert.equal(transcriptome.tpm, '40') chai.assert.equal(transcriptome.annotationName, "Annotation name") chai.assert.isUndefined(transcriptome.est_counts) @@ -261,7 +261,7 @@ describe('transcriptomes', function testTranscriptomes() { const transcriptome = transcriptomes[0] - chai.assert.equal(transcriptome.geneId, 'BniB01g000010.2N') + chai.assert.equal(transcriptome.geneId, 'Bni|B01g000010.2N') chai.assert.equal(transcriptome.tpm, '40') chai.assert.isUndefined(transcriptome.est_counts) chai.assert.equal(transcriptome.annotationName, "Annotation name") @@ -322,7 +322,7 @@ describe('transcriptomes', function testTranscriptomes() { const transcriptome = transcriptomes[0] - chai.assert.equal(transcriptome.geneId, 'BniB01g000010.2N') + chai.assert.equal(transcriptome.geneId, 'Bni|B01g000010.2N') chai.assert.equal(transcriptome.tpm, '40') chai.assert.equal(transcriptome.annotationName, "Annotation name") chai.assert.isUndefined(transcriptome.est_counts) diff --git a/imports/api/util/util.test.js b/imports/api/util/util.test.js index b7af9cad..973c2f5e 100644 --- a/imports/api/util/util.test.js +++ b/imports/api/util/util.test.js @@ -42,8 +42,8 @@ describe('util', function testUtils() { const gene = Genes.findOne({ID: geneId}) const seq = getGeneSequences(gene) const expected = [{ - ID: "BniB01g000010.2N.1", - protein_id: "BniB01g000010.2N.1-P", + ID: "Bni|B01g000010.2N.1", + protein_id: "Bni|B01g000010.2N.1-P", nucl: "AGTTTAGAATAC", prot: "SLEY" }] diff --git a/imports/startup/server/fixtures/addTestData.js b/imports/startup/server/fixtures/addTestData.js index 9001129f..e55b810a 100644 --- a/imports/startup/server/fixtures/addTestData.js +++ b/imports/startup/server/fixtures/addTestData.js @@ -75,11 +75,11 @@ export function addTestGenome(annot=false, multiple=false) { let geneId if (annot) { - const subfeature = {ID: "BniB01g000010.2N.1", phase: '.', protein_id: "BniB01g000010.2N.1-P", type: 'mRNA', parents: ['BniB01g000010.2N'], seq: 'GTATTCTAAACT', start:13641, end:15400, score: '.', attributes: {}} - const cds = {ID: "BniB01g000010.2N.1.cds1", phase: '.', type: 'CDS', parents: ['BniB01g000010.2N.1'], seq: 'GTATTCTAAACT', start:13641, end:13653, score: '.', attributes: {}} + const subfeature = {ID: "Bni|B01g000010.2N.1", phase: '.', protein_id: "Bni|B01g000010.2N.1-P", type: 'mRNA', parents: ['Bni|B01g000010.2N'], seq: 'GTATTCTAAACT', start:13641, end:15400, score: '.', attributes: {}} + const cds = {ID: "Bni|B01g000010.2N.1.cds1", phase: '.', type: 'CDS', parents: ['Bni|B01g000010.2N.1'], seq: 'GTATTCTAAACT', start:13641, end:13653, score: '.', attributes: {}} Genes.insert({ - ID: 'BniB01g000010.2N', + ID: 'Bni|B01g000010.2N', seqid: 'B1', source: 'AAFC_GIFS', strand: '-', @@ -96,7 +96,7 @@ export function addTestGenome(annot=false, multiple=false) { if (multiple){ Genes.insert({ - ID: 'BniB01g000010.2N', + ID: 'Bni|B01g000010.2N', seqid: 'B1', source: 'AAFC_GIFS', strand: '-', @@ -113,7 +113,7 @@ export function addTestGenome(annot=false, multiple=false) { } } - return { genomeId, genomeSeqId, geneId: "BniB01g000010.2N" } + return { genomeId, genomeSeqId, geneId: "Bni|B01g000010.2N" } } export function addTestTranscriptome(genomeId, geneId) { diff --git a/private/data/BLAST_blastx_bnigra.txt b/private/data/BLAST_blastx_bnigra.txt index 118e49fb..d07935e0 100644 --- a/private/data/BLAST_blastx_bnigra.txt +++ b/private/data/BLAST_blastx_bnigra.txt @@ -1,8 +1,8 @@ RID: G78X34UU01R -Job Title:2 sequences (BniB01g000010.2Nq) +Job Title:2 sequences (Bni%7CB01g000010.2Nq) Program: BLASTX Database: nr All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF excluding environmental samples from WGS projects -Query #1: BniB01g000010.2N.1-P Query ID: Query_1 Length: 420 +Query #1: Bni%7CB01g000010.2N.1-P Query ID: Query_1 Length: 420 Alignments: diff --git a/private/data/Bnigra.gff3 b/private/data/Bnigra.gff3 index f86e3a9c..26a88232 100644 --- a/private/data/Bnigra.gff3 +++ b/private/data/Bnigra.gff3 @@ -1,18 +1,18 @@ ##gff-version 3 -B1 AAFC_GIFS gene 13640 15401 . - . ID=BniB01g000010.2N;Name=BniB01g000010.2N -B1 AAFC_GIFS mRNA 13640 15401 . - . ID=BniB01g000010.2N.1;Name=BniB01g000010.2N.1;Parent=BniB01g000010.2N -B1 AAFC_GIFS exon 14702 15401 . - . ID=BniB01g000010.2N.1.exon1;Parent=BniB01g000010.2N.1 -B1 AAFC_GIFS exon 14557 14636 . - . ID=BniB01g000010.2N.1.exon2;Parent=BniB01g000010.2N.1 -B1 AAFC_GIFS exon 14403 14486 . - . ID=BniB01g000010.2N.1.exon3;Parent=BniB01g000010.2N.1 -B1 AAFC_GIFS exon 14210 14284 . - . ID=BniB01g000010.2N.1.exon4;Parent=BniB01g000010.2N.1 -B1 AAFC_GIFS exon 13970 14062 . - . ID=BniB01g000010.2N.1.exon5;Parent=BniB01g000010.2N.1 -B1 AAFC_GIFS exon 13640 13870 . - . ID=BniB01g000010.2N.1.exon6;Parent=BniB01g000010.2N.1 -B1 AAFC_GIFS CDS 14702 15401 . - 0 ID=BniB01g000010.2N.1.cds1;Parent=BniB01g000010.2N.1 -B1 AAFC_GIFS CDS 14557 14636 . - 2 ID=BniB01g000010.2N.1.cds2;Parent=BniB01g000010.2N.1 -B1 AAFC_GIFS CDS 14403 14486 . - 0 ID=BniB01g000010.2N.1.cds3;Parent=BniB01g000010.2N.1 -B1 AAFC_GIFS CDS 14210 14284 . - 0 ID=BniB01g000010.2N.1.cds4;Parent=BniB01g000010.2N.1 -B1 AAFC_GIFS CDS 13970 14062 . - 0 ID=BniB01g000010.2N.1.cds5;Parent=BniB01g000010.2N.1 -B1 AAFC_GIFS CDS 13640 13870 . - 0 ID=BniB01g000010.2N.1.cds6;Parent=BniB01g000010.2N.1 +B1 AAFC_GIFS gene 13640 15401 . - . ID=Bni%7CB01g000010.2N;Name=Bni%7CB01g000010.2N +B1 AAFC_GIFS mRNA 13640 15401 . - . ID=Bni%7CB01g000010.2N.1;Name=Bni%7CB01g000010.2N.1;Parent=Bni%7CB01g000010.2N +B1 AAFC_GIFS exon 14702 15401 . - . ID=Bni%7CB01g000010.2N.1.exon1;Parent=Bni%7CB01g000010.2N.1 +B1 AAFC_GIFS exon 14557 14636 . - . ID=Bni%7CB01g000010.2N.1.exon2;Parent=Bni%7CB01g000010.2N.1 +B1 AAFC_GIFS exon 14403 14486 . - . ID=Bni%7CB01g000010.2N.1.exon3;Parent=Bni%7CB01g000010.2N.1 +B1 AAFC_GIFS exon 14210 14284 . - . ID=Bni%7CB01g000010.2N.1.exon4;Parent=Bni%7CB01g000010.2N.1 +B1 AAFC_GIFS exon 13970 14062 . - . ID=Bni%7CB01g000010.2N.1.exon5;Parent=Bni%7CB01g000010.2N.1 +B1 AAFC_GIFS exon 13640 13870 . - . ID=Bni%7CB01g000010.2N.1.exon6;Parent=Bni%7CB01g000010.2N.1 +B1 AAFC_GIFS CDS 14702 15401 . - 0 ID=Bni%7CB01g000010.2N.1.cds1;Parent=Bni%7CB01g000010.2N.1 +B1 AAFC_GIFS CDS 14557 14636 . - 2 ID=Bni%7CB01g000010.2N.1.cds2;Parent=Bni%7CB01g000010.2N.1 +B1 AAFC_GIFS CDS 14403 14486 . - 0 ID=Bni%7CB01g000010.2N.1.cds3;Parent=Bni%7CB01g000010.2N.1 +B1 AAFC_GIFS CDS 14210 14284 . - 0 ID=Bni%7CB01g000010.2N.1.cds4;Parent=Bni%7CB01g000010.2N.1 +B1 AAFC_GIFS CDS 13970 14062 . - 0 ID=Bni%7CB01g000010.2N.1.cds5;Parent=Bni%7CB01g000010.2N.1 +B1 AAFC_GIFS CDS 13640 13870 . - 0 ID=Bni%7CB01g000010.2N.1.cds6;Parent=Bni%7CB01g000010.2N.1 B1 AAFC_GIFS gene 17243 18722 . - . ID=BniB01g000020.2N;Name=BniB01g000020.2N B1 AAFC_GIFS mRNA 17243 18722 . - . ID=BniB01g000020.2N.1;Name=BniB01g000020.2N.1;Parent=BniB01g000020.2N B1 AAFC_GIFS exon 18670 18722 . - . ID=BniB01g000020.2N.1.exon1;Parent=BniB01g000020.2N.1 diff --git a/private/data/Bnigra_abundance.tsv b/private/data/Bnigra_abundance.tsv index 50b1229e..07761e95 100644 --- a/private/data/Bnigra_abundance.tsv +++ b/private/data/Bnigra_abundance.tsv @@ -1,2 +1,2 @@ gene sample1 sample2 sample3 sample4 -BniB01g000010.2N 40 60 80 90 +Bni%7CB01g000010.2N 40 60 80 90 diff --git a/private/data/Bnigra_eggnog.tsv b/private/data/Bnigra_eggnog.tsv index c8e97337..6910e0f1 100644 --- a/private/data/Bnigra_eggnog.tsv +++ b/private/data/Bnigra_eggnog.tsv @@ -2,4 +2,4 @@ ## emapper-2.1.6 ## #query seed_ortholog evalue score eggNOG_OGs max_annot_lvl COG_category Description Preferred_name GOs EC KEGG_ko KEGG_Pathway KEGG_Module KEGG_Reaction KEGG_rclass BRITE KEGG_TC CAZy BiGG_Reaction PFAMs -BniB01g000010.2N.1-P 3711.Bra000457.1 1.01e-260 720.0 COG0451@1|root,KOG1429@2759|Eukaryota,37K7R@33090|Viridiplantae,3GH1V@35493|Streptophyta,3HMJX@3699|Brassicales 35493|Streptophyta GM UDP-glucuronic acid decarboxylase - GO:0000166,GO:0003674,GO:0003824,GO:0005488,GO:0016829,GO:0016830,GO:0016831,GO:0036094,GO:0043167,GO:0043168,GO:0048037,GO:0048040,GO:0050662,GO:0051287,GO:0070403,GO:0097159,GO:1901265,GO:1901363 4.1.1.35 ko:K08678 ko00520,ko01100,map00520,map01100 M00361 R01384 RC00508 ko00000,ko00001,ko00002,ko01000 - - - GDP_Man_Dehyd +Bni%7CB01g000010.2N.1-P 3711.Bra000457.1 1.01e-260 720.0 COG0451@1|root,KOG1429@2759|Eukaryota,37K7R@33090|Viridiplantae,3GH1V@35493|Streptophyta,3HMJX@3699|Brassicales 35493|Streptophyta GM UDP-glucuronic acid decarboxylase - GO:0000166,GO:0003674,GO:0003824,GO:0005488,GO:0016829,GO:0016830,GO:0016831,GO:0036094,GO:0043167,GO:0043168,GO:0048037,GO:0048040,GO:0050662,GO:0051287,GO:0070403,GO:0097159,GO:1901265,GO:1901363 4.1.1.35 ko:K08678 ko00520,ko01100,map00520,map01100 M00361 R01384 RC00508 ko00000,ko00001,ko00002,ko01000 - - - GDP_Man_Dehyd diff --git a/private/data/Bnigra_hectar.tab b/private/data/Bnigra_hectar.tab index 3926ca41..a9f89247 100644 --- a/private/data/Bnigra_hectar.tab +++ b/private/data/Bnigra_hectar.tab @@ -1,2 +1,2 @@ protein id predicted targeting category signal peptide score signal peptide cleavage site type II signal anchor score chloroplast score mitochondrion score other score -BniB01g000010.2N.1 other localisation 0.0583 - 0.0228 - 0.1032 0.8968 +Bni%7CB01g000010.2N.1 other localisation 0.0583 - 0.0228 - 0.1032 0.8968 diff --git a/private/data/Bnigra_interproscan.gff b/private/data/Bnigra_interproscan.gff index 65c68940..7392a35e 100644 --- a/private/data/Bnigra_interproscan.gff +++ b/private/data/Bnigra_interproscan.gff @@ -2,5 +2,5 @@ ##interproscan-version 5.26-65.0 ##sequence-region AACH01000027 1 1347 ##seqid|source|type|start|end|score|strand|phase|attributes -BniB01g000010.2N.1-P Gene3D protein_match 212 401 1.2E-59 + . Name=G3DSA:1.10.510.10; -BniB01g000010.2N.1-P getorf protein_match 1 1347 . + . Name=AACH01000027.2_21;Target=pep_AACH01000027_1_1347 1 449;md5=b2a7416cb92565c004becb7510f46840;ID=orf_AACH01000027_1_1347 +Bni%7CB01g000010.2N.1-P Gene3D protein_match 212 401 1.2E-59 + . Name=G3DSA:1.10.510.10; +Bni%7CB01g000010.2N.1-P getorf protein_match 1 1347 . + . Name=AACH01000027.2_21;Target=pep_AACH01000027_1_1347 1 449;md5=b2a7416cb92565c004becb7510f46840;ID=orf_AACH01000027_1_1347 diff --git a/private/data/Bnigra_interproscan.tsv b/private/data/Bnigra_interproscan.tsv index 56514977..854ef0c4 100644 --- a/private/data/Bnigra_interproscan.tsv +++ b/private/data/Bnigra_interproscan.tsv @@ -1,2 +1,2 @@ -BniB01g000010.2N.1 8e1d37cac64c27778e5988f5d12e5bc0 409 Gene3D G3DSA:1.10.510.10 Transferase(Phosphotransferase) domain 1 212 401 1.2E-59 T 25-08-2022 1236 - GO:1238 -BniB01g000010.2N.1 8e1d37cac64c27778e5988f5d12e5bc0 409 PANTHER PTHR23257 SERINE-THREONINE PROTEIN KINASE 1 400 9.5E-250 T 25-08-2022 - - +Bni%7CB01g000010.2N.1 8e1d37cac64c27778e5988f5d12e5bc0 409 Gene3D G3DSA:1.10.510.10 Transferase(Phosphotransferase) domain 1 212 401 1.2E-59 T 25-08-2022 1236 - GO:1238 +Bni%7CB01g000010.2N.1 8e1d37cac64c27778e5988f5d12e5bc0 409 PANTHER PTHR23257 SERINE-THREONINE PROTEIN KINASE 1 400 9.5E-250 T 25-08-2022 - - diff --git a/private/data/Bnigra_kallisto_abundance.tsv b/private/data/Bnigra_kallisto_abundance.tsv index a70549a7..3f9f9d79 100644 --- a/private/data/Bnigra_kallisto_abundance.tsv +++ b/private/data/Bnigra_kallisto_abundance.tsv @@ -1,2 +1,2 @@ target_id length eff_length est_counts tpm -BniB01g000010.2N 1221 1021.99 21 1.80368 +Bni%7CB01g000010.2N 1221 1021.99 21 1.80368 diff --git a/private/data/Bnigra_min.gff3 b/private/data/Bnigra_min.gff3 index d36a394a..21b80d98 100644 --- a/private/data/Bnigra_min.gff3 +++ b/private/data/Bnigra_min.gff3 @@ -1,4 +1,4 @@ ##gff-version 3 -B1 AAFC_GIFS gene 13640 15401 . - . ID=BniB01g000010.2N;Name=BniB01g000010.2N -B1 AAFC_GIFS mRNA 13640 15401 . - . ID=BniB01g000010.2N.1;Name=BniB01g000010.2N.1;Parent=BniB01g000010.2N;protid=BniB01g000010.2N.1-protattr -B1 AAFC_GIFS CDS 14702 15401 . - 0 ID=BniB01g000010.2N.1.cds1;Parent=BniB01g000010.2N.1;protid2=BniB01g000010.2N.1-protattr +B1 AAFC_GIFS gene 13640 15401 . - . ID=Bni%7CB01g000010.2N;Name=Bni%7CB01g000010.2N +B1 AAFC_GIFS mRNA 13640 15401 . - . ID=Bni%7CB01g000010.2N.1;Name=Bni%7CB01g000010.2N.1;Parent=Bni%7CB01g000010.2N;protid=Bni%7CB01g000010.2N.1-protattr +B1 AAFC_GIFS CDS 14702 15401 . - 0 ID=Bni%7CB01g000010.2N.1.cds1;Parent=Bni%7CB01g000010.2N.1;protid2=Bni%7CB01g000010.2N.1-protattr diff --git a/private/data/Diamond_blastp_bnigra.xml b/private/data/Diamond_blastp_bnigra.xml index 42a273bd..793028df 100644 --- a/private/data/Diamond_blastp_bnigra.xml +++ b/private/data/Diamond_blastp_bnigra.xml @@ -6,7 +6,7 @@ <BlastOutput_reference>Benjamin Buchfink, Xie Chao, and Daniel Huson (2015), "Fast and sensitive protein alignment using DIAMOND", Nature Methods 12:59-60.</BlastOutput_reference> <BlastOutput_db>/db/nr/NR_2021-6-16/diamond/nr.dmnd</BlastOutput_db> <BlastOutput_query-ID>Query_1</BlastOutput_query-ID> - <BlastOutput_query-def>BniB01g000010.2N.1-P</BlastOutput_query-def> + <BlastOutput_query-def>Bni%7CB01g000010.2N.1-P</BlastOutput_query-def> <BlastOutput_query-len>420</BlastOutput_query-len> <BlastOutput_param> <Parameters> @@ -21,7 +21,7 @@ <Iteration> <Iteration_iter-num>1</Iteration_iter-num> <Iteration_query-ID>Query_1</Iteration_query-ID> - <Iteration_query-def>BniB01g000010.2N.1-P</Iteration_query-def> + <Iteration_query-def>Bni%7CB01g000010.2N.1-P</Iteration_query-def> <Iteration_query-len>420</Iteration_query-len> <Iteration_hits> <Hit> diff --git a/private/data/Diamond_blastx_bnigra.txt b/private/data/Diamond_blastx_bnigra.txt index bf8678db..6a4c2f04 100644 --- a/private/data/Diamond_blastx_bnigra.txt +++ b/private/data/Diamond_blastx_bnigra.txt @@ -1,7 +1,7 @@ BLASTP 2.3.0+ -Query= BniB01g000010.2N.1-P 900 bp +Query= Bni%7CB01g000010.2N.1-P 900 bp Length=420 diff --git a/private/data/orthogroups/OG0000001_tree.txt b/private/data/orthogroups/OG0000001_tree.txt index 48070beb..d962c1ad 100644 --- a/private/data/orthogroups/OG0000001_tree.txt +++ b/private/data/orthogroups/OG0000001_tree.txt @@ -1 +1 @@ -(Brassica_nigra_BniB01g000010.2N:2.67279e-05,(Brassica_nigra_orange1.1g036683m.v1.1:0.939183,((Brassica_nigra_orange1.1g048302m.v1.1:0.829171,((((((Brassica_nigra_orange1.1g035904m.v1.1:0.142101,(Brassica_nigra_orange1.1g041953m.v1.1:0.106727,Brassica_nigra_orange1.1g023644m.v1.1:0.282697):0.242572):0.0804454,Brassica_nigra_orange1.1g047196m.v1.1:0.659561):0.179646,(Brassica_nigra_orange1.1g043006m.v1.1:0.238673,Brassica_nigra_orange1.1g042885m.v1.1:0.398667):0.379625):0.0998815,(((((Brassica_nigra_orange1.1g040833m.v1.1:0.132268,(Brassica_nigra_orange1.1g041938m.v1.1:0.0547695,(Brassica_nigra_orange1.1g048125m.v1.1:0.354786,Brassica_nigra_orange1.1g043372m.v1.1:0.187525):0.0506125):0.0132697):0.203976,((Brassica_nigra_orange1.1g042573m.v1.1:0.327281,Brassica_nigra_orange1.1g046340m.v1.1:0.0254404):0.223387,Brassica_nigra_orange1.1g040849m.v1.1:0.0621755):0.216996):0.211494,Brassica_nigra_orange1.1g036656m.v1.1:0.300618):0.194936,((Brassica_nigra_orange1.1g037951m.v1.1:0.443269,Brassica_nigra_orange1.1g042446m.v1.1:0.18526):0.402016,(Brassica_nigra_orange1.1g038776m.v1.1:0.310625,Brassica_nigra_orange1.1g037538m.v1.1:0.731269):0.0500583):0.045443):0.0372386,((Brassica_nigra_orange1.1g041497m.v1.1:0.624805,Brassica_nigra_orange1.1g040195m.v1.1:0.527528):0.120536,(Brassica_nigra_orange1.1g038612m.v1.1:0.828945,Brassica_nigra_orange1.1g041374m.v1.1:0.49884):0.134113):0.153193):0.108356):0.0531267,(((Brassica_nigra_orange1.1g040301m.v1.1:0.561397,Brassica_nigra_orange1.1g036593m.v1.1:0.526869):0.197955,((Brassica_nigra_orange1.1g045304m.v1.1:0.416663,Brassica_nigra_orange1.1g038106m.v1.1:0.241498):0.333555,Brassica_nigra_orange1.1g042802m.v1.1:0.744456):0.100487):0.179528,Brassica_nigra_orange1.1g045504m.v1.1:2.67279e-05):0.0417408):0.0159876,((((((Brassica_nigra_orange1.1g040294m.v1.1:0.408544,(Brassica_nigra_orange1.1g042902m.v1.1:0.225841,Brassica_nigra_orange1.1g047705m.v1.1:0.27893):0.02523):0.0720332,((Brassica_nigra_orange1.1g038098m.v1.1:0.170662,(Brassica_nigra_orange1.1g019843m.v1.1:0.0797284,Brassica_nigra_orange1.1g019568m.v1.1:0.122984):0.0596993):0.0231807,(Brassica_nigra_orange1.1g039799m.v1.1:0.195572,Brassica_nigra_orange1.1g046842m.v1.1:0.447335):0.0370941):0.0943989):0.0512309,Brassica_nigra_orange1.1g042107m.v1.1:0.442217):0.155241,Brassica_nigra_orange1.1g036266m.v1.1:0.720434):0.101417,((Brassica_nigra_orange1.1g039258m.v1.1:0.253561,(Brassica_nigra_orange1.1g043932m.v1.1:0.139827,Brassica_nigra_orange1.1g043388m.v1.1:0.229492):0.0765385):0.193234,((Brassica_nigra_orange1.1g046112m.v1.1:0.440284,(Brassica_nigra_orange1.1g011508m.v1.1:0.14342,Brassica_nigra_orange1.1g042634m.v1.1:0.246287):0.197221):0.0417206,Brassica_nigra_orange1.1g043902m.v1.1:0.455974):0.103205):0.229013):0.150393,((((Brassica_nigra_orange1.1g034256m.v1.1:0.360577,Brassica_nigra_orange1.1g043981m.v1.1:0.266436):0.0886867,(Brassica_nigra_orange1.1g037267m.v1.1:0.222895,(Brassica_nigra_orange1.1g035782m.v1.1:0.115728,Brassica_nigra_orange1.1g043099m.v1.1:0.125937):0.0612782):0.260096):0.251251,(Brassica_nigra_orange1.1g031224m.v1.1:0.448203,Brassica_nigra_orange1.1g042057m.v1.1:0.498641):0.0947461):0.15494,Brassica_nigra_orange1.1g037415m.v1.1:0.58221):0.0326248):0.111369):0.0158713):0.00496014,Brassica_nigra_orange1.1g036666m.v1.1:0.837022):0.0439816):2.67279e-05); +(Brassica_nigra_Bni%7CB01g000010.2N:2.67279e-05,(Brassica_nigra_orange1.1g036683m.v1.1:0.939183,((Brassica_nigra_orange1.1g048302m.v1.1:0.829171,((((((Brassica_nigra_orange1.1g035904m.v1.1:0.142101,(Brassica_nigra_orange1.1g041953m.v1.1:0.106727,Brassica_nigra_orange1.1g023644m.v1.1:0.282697):0.242572):0.0804454,Brassica_nigra_orange1.1g047196m.v1.1:0.659561):0.179646,(Brassica_nigra_orange1.1g043006m.v1.1:0.238673,Brassica_nigra_orange1.1g042885m.v1.1:0.398667):0.379625):0.0998815,(((((Brassica_nigra_orange1.1g040833m.v1.1:0.132268,(Brassica_nigra_orange1.1g041938m.v1.1:0.0547695,(Brassica_nigra_orange1.1g048125m.v1.1:0.354786,Brassica_nigra_orange1.1g043372m.v1.1:0.187525):0.0506125):0.0132697):0.203976,((Brassica_nigra_orange1.1g042573m.v1.1:0.327281,Brassica_nigra_orange1.1g046340m.v1.1:0.0254404):0.223387,Brassica_nigra_orange1.1g040849m.v1.1:0.0621755):0.216996):0.211494,Brassica_nigra_orange1.1g036656m.v1.1:0.300618):0.194936,((Brassica_nigra_orange1.1g037951m.v1.1:0.443269,Brassica_nigra_orange1.1g042446m.v1.1:0.18526):0.402016,(Brassica_nigra_orange1.1g038776m.v1.1:0.310625,Brassica_nigra_orange1.1g037538m.v1.1:0.731269):0.0500583):0.045443):0.0372386,((Brassica_nigra_orange1.1g041497m.v1.1:0.624805,Brassica_nigra_orange1.1g040195m.v1.1:0.527528):0.120536,(Brassica_nigra_orange1.1g038612m.v1.1:0.828945,Brassica_nigra_orange1.1g041374m.v1.1:0.49884):0.134113):0.153193):0.108356):0.0531267,(((Brassica_nigra_orange1.1g040301m.v1.1:0.561397,Brassica_nigra_orange1.1g036593m.v1.1:0.526869):0.197955,((Brassica_nigra_orange1.1g045304m.v1.1:0.416663,Brassica_nigra_orange1.1g038106m.v1.1:0.241498):0.333555,Brassica_nigra_orange1.1g042802m.v1.1:0.744456):0.100487):0.179528,Brassica_nigra_orange1.1g045504m.v1.1:2.67279e-05):0.0417408):0.0159876,((((((Brassica_nigra_orange1.1g040294m.v1.1:0.408544,(Brassica_nigra_orange1.1g042902m.v1.1:0.225841,Brassica_nigra_orange1.1g047705m.v1.1:0.27893):0.02523):0.0720332,((Brassica_nigra_orange1.1g038098m.v1.1:0.170662,(Brassica_nigra_orange1.1g019843m.v1.1:0.0797284,Brassica_nigra_orange1.1g019568m.v1.1:0.122984):0.0596993):0.0231807,(Brassica_nigra_orange1.1g039799m.v1.1:0.195572,Brassica_nigra_orange1.1g046842m.v1.1:0.447335):0.0370941):0.0943989):0.0512309,Brassica_nigra_orange1.1g042107m.v1.1:0.442217):0.155241,Brassica_nigra_orange1.1g036266m.v1.1:0.720434):0.101417,((Brassica_nigra_orange1.1g039258m.v1.1:0.253561,(Brassica_nigra_orange1.1g043932m.v1.1:0.139827,Brassica_nigra_orange1.1g043388m.v1.1:0.229492):0.0765385):0.193234,((Brassica_nigra_orange1.1g046112m.v1.1:0.440284,(Brassica_nigra_orange1.1g011508m.v1.1:0.14342,Brassica_nigra_orange1.1g042634m.v1.1:0.246287):0.197221):0.0417206,Brassica_nigra_orange1.1g043902m.v1.1:0.455974):0.103205):0.229013):0.150393,((((Brassica_nigra_orange1.1g034256m.v1.1:0.360577,Brassica_nigra_orange1.1g043981m.v1.1:0.266436):0.0886867,(Brassica_nigra_orange1.1g037267m.v1.1:0.222895,(Brassica_nigra_orange1.1g035782m.v1.1:0.115728,Brassica_nigra_orange1.1g043099m.v1.1:0.125937):0.0612782):0.260096):0.251251,(Brassica_nigra_orange1.1g031224m.v1.1:0.448203,Brassica_nigra_orange1.1g042057m.v1.1:0.498641):0.0947461):0.15494,Brassica_nigra_orange1.1g037415m.v1.1:0.58221):0.0326248):0.111369):0.0158713):0.00496014,Brassica_nigra_orange1.1g036666m.v1.1:0.837022):0.0439816):2.67279e-05); From 54cc6e262ca08e2cfdf32dc19df1822b048851cd Mon Sep 17 00:00:00 2001 From: mboudet <mateo.boudet@gmail.com> Date: Thu, 19 Oct 2023 14:55:00 +0000 Subject: [PATCH 31/36] Fix tests --- imports/api/genes/alignment/parser/xmlParser.js | 6 ++++-- imports/api/genes/download/download.test.js | 6 +++--- imports/api/genes/eggnog/addEggnog.js | 2 +- imports/api/genes/hectar/addHectar.js | 2 +- imports/api/genes/orthogroup/parser/treeNewickParser.js | 5 +++-- imports/api/genes/parseGff3Interproscan.js | 2 +- imports/api/genes/parseTsvInterproscan.js | 2 +- imports/api/genomes/annotation/addAnnotation.test.js | 2 +- 8 files changed, 15 insertions(+), 12 deletions(-) diff --git a/imports/api/genes/alignment/parser/xmlParser.js b/imports/api/genes/alignment/parser/xmlParser.js index 9d713c0a..0195bfdf 100644 --- a/imports/api/genes/alignment/parser/xmlParser.js +++ b/imports/api/genes/alignment/parser/xmlParser.js @@ -100,10 +100,12 @@ class XmlProcessor { const splitIterationQuery = iterationQuery.split(' '); - await Promise.all(splitIterationQuery.map(async (iter) => { + await Promise.all(splitIterationQuery.map(async (iter_encode) => { /** Chek if the queries exist in the genes collection. */ - let geneQuery = { $or: [{'subfeatures.ID': decodeURIComponent(iter)}, {'subfeatures.protein_id': decodeURIComponent(iter)}] } + const iter = decodeURIComponent(iter_encode) + + let geneQuery = { $or: [{'subfeatures.ID': iter}, {'subfeatures.protein_id': iter}] } if (typeof this.annot !== "undefined"){ geneQuery['annotationName'] = this.annot } diff --git a/imports/api/genes/download/download.test.js b/imports/api/genes/download/download.test.js index 5437a74c..5fd30906 100644 --- a/imports/api/genes/download/download.test.js +++ b/imports/api/genes/download/download.test.js @@ -74,7 +74,7 @@ describe('download', function testDownload() { dataFile = result.value const stat = fs.statSync(dataFile) - chai.assert.equal(stat.size, 140) + chai.assert.equal(stat.size, 141) const expected = [ '##gff-version 3', @@ -105,7 +105,7 @@ describe('download', function testDownload() { dataFile = result.value const stat = fs.statSync(dataFile) - chai.assert.equal(stat.size, 51) + chai.assert.equal(stat.size, 52) const expected = [ ">Bni|B01g000010.2N.1", @@ -134,7 +134,7 @@ describe('download', function testDownload() { dataFile = result.value const stat = fs.statSync(dataFile) - chai.assert.equal(stat.size, 59) + chai.assert.equal(stat.size, 60) const expected = [ "gene_id\treplicaGroup", diff --git a/imports/api/genes/eggnog/addEggnog.js b/imports/api/genes/eggnog/addEggnog.js index 26b2ad2a..1bfe1550 100644 --- a/imports/api/genes/eggnog/addEggnog.js +++ b/imports/api/genes/eggnog/addEggnog.js @@ -29,7 +29,7 @@ class EggnogProcessor { parse = (line) => { if (!(line[0] === '#' || line.split('\t').length <= 1)) { // Get all eggnog informations line by line and separated by tabs. - const [ + let [ queryName, seedEggnogOrtholog, seedOrthologEvalue, diff --git a/imports/api/genes/hectar/addHectar.js b/imports/api/genes/hectar/addHectar.js index 4fb024ed..eaa7bd4e 100644 --- a/imports/api/genes/hectar/addHectar.js +++ b/imports/api/genes/hectar/addHectar.js @@ -29,7 +29,7 @@ class HectarProcessor { parse = (line) => { if (!(line.slice(0,10) === 'protein id' || line.split('\t').length <= 1)) { // Get all hectar informations line by line and separated by tabs. - const [ + let [ proteinId, predictedTargetingCategory, signalPeptideScore, diff --git a/imports/api/genes/orthogroup/parser/treeNewickParser.js b/imports/api/genes/orthogroup/parser/treeNewickParser.js index add12fb2..1a0db693 100644 --- a/imports/api/genes/orthogroup/parser/treeNewickParser.js +++ b/imports/api/genes/orthogroup/parser/treeNewickParser.js @@ -115,9 +115,10 @@ class NewickProcessor { * @return {Array} The list of genes without their prefixes. */ - getGeneId = async (prefixes, geneid) => { + getGeneId = async (prefixes, geneIdEncoded) => { + let geneid = decodeURIComponent(geneIdEncoded) return new Promise((resolve, reject) => { - let geneName = decodeURIComponent(geneid) + let geneName = geneid try { if (prefixes){ for (const i in prefixes) { diff --git a/imports/api/genes/parseGff3Interproscan.js b/imports/api/genes/parseGff3Interproscan.js index 51cfde75..43c753b1 100644 --- a/imports/api/genes/parseGff3Interproscan.js +++ b/imports/api/genes/parseGff3Interproscan.js @@ -43,7 +43,7 @@ class ParseGff3File extends InterproscanProcessor { parse = (line) => { // Check if the line is different of fasta sequence or others indications. if (!(line[0] === '#' || line.split('\t').length <= 1)) { - const [seqId, source, type, start, end, score, , , attributeString, ] = line.split('\t'); + let [seqId, source, type, start, end, score, , , attributeString, ] = line.split('\t'); seqId = decodeURIComponent(seqId) diff --git a/imports/api/genes/parseTsvInterproscan.js b/imports/api/genes/parseTsvInterproscan.js index d96c22b1..fc34390a 100644 --- a/imports/api/genes/parseTsvInterproscan.js +++ b/imports/api/genes/parseTsvInterproscan.js @@ -4,7 +4,7 @@ import logger from '/imports/api/util/logger.js'; class ParseTsvFile extends InterproscanProcessor { parse = async (line) => { - const [ + let [ seqId, md5, length, diff --git a/imports/api/genomes/annotation/addAnnotation.test.js b/imports/api/genomes/annotation/addAnnotation.test.js index 1acaa66d..5350f8ea 100644 --- a/imports/api/genomes/annotation/addAnnotation.test.js +++ b/imports/api/genomes/annotation/addAnnotation.test.js @@ -147,7 +147,7 @@ describe('AddAnnotation', function testAnnotation() { const genes = Genes.find({ genomeId: genomeId }).fetch(); const mRNA = genes[0].subfeatures[0] - chai.assert.equal("testprot-B01g000010.2N.1", mRNA.protein_id) + chai.assert.equal("testprot-|B01g000010.2N.1", mRNA.protein_id) }); From 36f0590b58aec83b59e4dbf5dfc97bf9e6cbfbf3 Mon Sep 17 00:00:00 2001 From: mboudet <mateo.boudet@gmail.com> Date: Thu, 19 Oct 2023 17:36:01 +0200 Subject: [PATCH 32/36] Orthogroups and changelog --- CHANGELOG.md | 11 +++++ cli/genoboo.js | 11 ++++- .../genes/orthogroup/addOrthogroupTrees.js | 11 ++++- .../genes/orthogroup/orthogroupCollection.js | 8 ++++ .../api/genes/orthogroup/orthogroups.test.js | 9 +++- .../orthogroup/parser/treeNewickParser.js | 43 +++++++++++++------ imports/api/jobqueue/process-orthogroup.js | 4 +- 7 files changed, 77 insertions(+), 20 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 84cb52b9..b8d69383 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,6 +18,17 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. - 'query_param' : optional get parameter to use for the query - 'field_param': optional get parameter to use to restrict the results to the gene_field value - 'count_param': optional get parameter to restrict the number of results +- Multiple annotations for the same genome + - When adding an annotation, you must now set the '--annot' to set the annotation name. + - When integrating data afterward, you can use the --annot tag to specify the annotation you are aiming for. + - If you have multiple genes with the same ID, and do not specify '--annot', the results may be variables + - You can specify --annotations multiple time when integrating orthogroups +- Will now decode proteins and genes IDs when integrating data. (It was already done when integrating gffs, so there was some mismatch with IDs) + +## Changed + +- Various UI fixes to better fit multiple annotation versions + - Including an 'annotation' selector in the gene list ## [0.4.7] 2023-09-26 diff --git a/cli/genoboo.js b/cli/genoboo.js index 36f307a3..48f52b35 100755 --- a/cli/genoboo.js +++ b/cli/genoboo.js @@ -323,7 +323,7 @@ addAnnotation 'Reference genome name to which the annotation should be added.', ) .requiredOption( - '--annot <annotation-ame>', + '--annot <annotation-name>', 'Annotation name', ) .option( @@ -920,17 +920,23 @@ addOrthogroups '-f, --force [force]', 'Ignore the use of prefixes.', ) + .option( + '-a, --annotations <annotations...>', + 'Name of the annotation to use for gene matching. Can be set multiple times' + ) .requiredOption('-u, --username <username>', 'GeneNoteBook admin username') .requiredOption('-p, --password <password>', 'GeneNoteBook admin password') .option( '--port [port]', 'Port on which GeneNoteBook is running. Default: 3000' ) - .action((file, { prefixe, list, force, username, password, port = 3000 }) => { + .action((file, { prefixe, list, force, annotations, username, password, port = 3000 }) => { if (typeof file !== 'string') addOrthogroups.help(); const folderName = path.resolve(file); const prefixes = (typeof list !== 'undefined' ? list : path.resolve(prefixe)); + annotations = annotations || [] + if (!(folderName && username && password)) { addOrthogroups.help(); } @@ -941,6 +947,7 @@ addOrthogroups folderName, force, prefixes, + annotations }, ); }) diff --git a/imports/api/genes/orthogroup/addOrthogroupTrees.js b/imports/api/genes/orthogroup/addOrthogroupTrees.js index c00a99e5..f3ed2c1b 100644 --- a/imports/api/genes/orthogroup/addOrthogroupTrees.js +++ b/imports/api/genes/orthogroup/addOrthogroupTrees.js @@ -33,11 +33,19 @@ const addOrthogroupTrees = new ValidatedMethod({ return true; }, }, + annotations: { + type: Array, + optional: true, + defaultValue: [] + }, + 'annotations.$': { + type: String, + }, }).validator(), applyOptions: { noRetry: true, }, - run({ folderName, prefixes }) { + run({ folderName, prefixes, annotations }) { if (!this.userId) { throw new Meteor.Error('not-authorized'); } @@ -51,6 +59,7 @@ const addOrthogroupTrees = new ValidatedMethod({ { folderName, prefixes, + annotations, }, ); const jobId = job.priority('high').save(); diff --git a/imports/api/genes/orthogroup/orthogroupCollection.js b/imports/api/genes/orthogroup/orthogroupCollection.js index 80e88aff..7db7270d 100644 --- a/imports/api/genes/orthogroup/orthogroupCollection.js +++ b/imports/api/genes/orthogroup/orthogroupCollection.js @@ -14,6 +14,14 @@ const orthogroupSchema = new SimpleSchema({ type: String, label: 'Gene ID string', }, + annotations: { + type: Array, + label: 'Array of all annotations names in the orthogroup', + }, + 'annotations.$': { + type: String, + label: 'Annotation name', + }, tree: { type: Object, blackbox: true, diff --git a/imports/api/genes/orthogroup/orthogroups.test.js b/imports/api/genes/orthogroup/orthogroups.test.js index 812cba7d..0e48581e 100644 --- a/imports/api/genes/orthogroup/orthogroups.test.js +++ b/imports/api/genes/orthogroup/orthogroups.test.js @@ -37,12 +37,13 @@ describe('orthogroups', function testOrthogroups() { // Increase timeout this.timeout(20000); - const {genomeId} = addTestGenome(annot=true) + const {genomeId} = addTestGenome(annot=true, multiple=true) const orthoGroupsParams = { folderName: 'assets/app/data/orthogroups/', force: false, prefixes: "Brassica_nigra", + annotations: ["Annotation name"] }; // Should fail for non-logged in @@ -58,7 +59,7 @@ describe('orthogroups', function testOrthogroups() { let result = addOrthogroupTrees._execute(adminContext, orthoGroupsParams); - const gene = Genes.findOne({ID: "Bni|B01g000010.2N"}) + let gene = Genes.findOne({ID: "Bni|B01g000010.2N", annotationName: "Annotation name"}) chai.assert.isDefined(gene.orthogroup, 'orthogroup key is undefined') @@ -76,6 +77,10 @@ describe('orthogroups', function testOrthogroups() { chai.assert.sameMembers(ortho.geneIds, ['Bni|B01g000010.2N']) chai.assert.equal(ortho.size, 84.5) chai.assert.equal(ortho.name, 'OG0000001') + chai.assert.sameMembers(ortho.annotations, ['Annotation name']) + + let gene = Genes.findOne({ID: "Bni|B01g000010.2N", annotationName: "Annotation name 2"}) + chai.assert.isUndefined(gene.orthogroup, 'orthogroup key is undefined') }); }) diff --git a/imports/api/genes/orthogroup/parser/treeNewickParser.js b/imports/api/genes/orthogroup/parser/treeNewickParser.js index add12fb2..c1de2401 100644 --- a/imports/api/genes/orthogroup/parser/treeNewickParser.js +++ b/imports/api/genes/orthogroup/parser/treeNewickParser.js @@ -13,9 +13,10 @@ import path from 'path' * @public */ class NewickProcessor { - constructor() { + constructor(annotations) { this.genesDb = Genes.rawCollection(); this.nOrthogroups = 0; + this.annotations = annotations; } /** @@ -127,16 +128,19 @@ class NewickProcessor { } } } - const gene = Genes - .findOne( - { - $or: [ - { ID: geneName }, - { 'subfeatures.ID': geneName }, - { 'subfeatures.protein_id': geneName }, - ], - }, - ) + let geneQuery = { + $or: [ + { ID: geneName }, + { 'subfeatures.ID': geneName }, + { 'subfeatures.protein_id': geneName }, + ], + } + + if (self.annotations.length > 0){ + geneQuery['annotationName'] = { $in: self.annotations } + } + + const gene = Genes.findOne(geneQuery) resolve({gene, geneName}) } catch (err) { reject(err); @@ -177,15 +181,22 @@ class NewickProcessor { }); } + let geneQuery = { geneIds: { $in: rmDuplicateGeneIDs } } + + if (self.annotations.length > 0){ + geneQuery['annotations'] = { $in: self.annotations } + } + // Add the orthogroups and link them to their genes. if (rmDuplicateGeneIDs.length !== 0) { const documentOrthogroup = await orthogroupCollection.update( - { geneIds: { $in: rmDuplicateGeneIDs } }, // Selector. + geneQuery, // Selector. { $set: // Modifier. { name: name, geneIds: rmDuplicateGeneIDs, + annotations: self.annotations, tree: tree, size: treeSize, genomes: genomeDict @@ -200,9 +211,15 @@ class NewickProcessor { // Increment orthogroups. this.nOrthogroups += documentOrthogroup; + let geneQuery = { ID: { $in: rmDuplicateGeneIDs } } + + if (self.annotations.length > 0){ + geneQuery['annotationName'] = { $in: self.annotations } + } + const orthogroupIdentifiant = orthogroupCollection.findOne({ tree: tree })._id; await this.genesDb.update( - { ID: { $in: rmDuplicateGeneIDs } }, + geneQuery, { $set: // Modifier. { diff --git a/imports/api/jobqueue/process-orthogroup.js b/imports/api/jobqueue/process-orthogroup.js index 688922c0..c3a3889a 100644 --- a/imports/api/jobqueue/process-orthogroup.js +++ b/imports/api/jobqueue/process-orthogroup.js @@ -10,10 +10,10 @@ jobQueue.processJobs( payload: 1, }, async (job, callback) => { - const { folderName, prefixes } = job.data; + const { folderName, prefixes, annotations } = job.data; const orthofinder = new OrthoFinderPrefix(prefixes); - const newickProcessor = new NewickProcessor(); + const newickProcessor = new NewickProcessor(annotations); const listprefixes = (typeof prefixes !== 'undefined' ? await orthofinder.getListPrefixes() : null); From a9c42350ea1adb64c5837d2470c63d81b361335f Mon Sep 17 00:00:00 2001 From: mboudet <mateo.boudet@gmail.com> Date: Fri, 20 Oct 2023 08:25:22 +0000 Subject: [PATCH 33/36] fix test --- imports/api/genes/orthogroup/orthogroups.test.js | 2 +- .../genes/orthogroup/parser/treeNewickParser.js | 16 ++++++++-------- 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/imports/api/genes/orthogroup/orthogroups.test.js b/imports/api/genes/orthogroup/orthogroups.test.js index 0e48581e..9c627360 100644 --- a/imports/api/genes/orthogroup/orthogroups.test.js +++ b/imports/api/genes/orthogroup/orthogroups.test.js @@ -79,7 +79,7 @@ describe('orthogroups', function testOrthogroups() { chai.assert.equal(ortho.name, 'OG0000001') chai.assert.sameMembers(ortho.annotations, ['Annotation name']) - let gene = Genes.findOne({ID: "Bni|B01g000010.2N", annotationName: "Annotation name 2"}) + gene = Genes.findOne({ID: "Bni|B01g000010.2N", annotationName: "Annotation name 2"}) chai.assert.isUndefined(gene.orthogroup, 'orthogroup key is undefined') }); diff --git a/imports/api/genes/orthogroup/parser/treeNewickParser.js b/imports/api/genes/orthogroup/parser/treeNewickParser.js index 5c836a25..c87a093e 100644 --- a/imports/api/genes/orthogroup/parser/treeNewickParser.js +++ b/imports/api/genes/orthogroup/parser/treeNewickParser.js @@ -137,8 +137,8 @@ class NewickProcessor { ], } - if (self.annotations.length > 0){ - geneQuery['annotationName'] = { $in: self.annotations } + if (this.annotations.length > 0){ + geneQuery['annotationName'] = { $in: this.annotations } } const gene = Genes.findOne(geneQuery) @@ -184,8 +184,8 @@ class NewickProcessor { let geneQuery = { geneIds: { $in: rmDuplicateGeneIDs } } - if (self.annotations.length > 0){ - geneQuery['annotations'] = { $in: self.annotations } + if (this.annotations.length > 0){ + geneQuery['annotations'] = { $in: this.annotations } } // Add the orthogroups and link them to their genes. @@ -197,7 +197,7 @@ class NewickProcessor { { name: name, geneIds: rmDuplicateGeneIDs, - annotations: self.annotations, + annotations: this.annotations, tree: tree, size: treeSize, genomes: genomeDict @@ -212,10 +212,10 @@ class NewickProcessor { // Increment orthogroups. this.nOrthogroups += documentOrthogroup; - let geneQuery = { ID: { $in: rmDuplicateGeneIDs } } + geneQuery = { ID: { $in: rmDuplicateGeneIDs } } - if (self.annotations.length > 0){ - geneQuery['annotationName'] = { $in: self.annotations } + if (this.annotations.length > 0){ + geneQuery['annotationName'] = { $in: this.annotations } } const orthogroupIdentifiant = orthogroupCollection.findOne({ tree: tree })._id; From cb8bf07d6cc048442c22200d0580be39ac893f15 Mon Sep 17 00:00:00 2001 From: mboudet <mateo.boudet@gmail.com> Date: Fri, 20 Oct 2023 13:21:57 +0000 Subject: [PATCH 34/36] Fix UI --- .../singleGenePage/geneExpression/SampleSelection.jsx | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/imports/ui/singleGenePage/geneExpression/SampleSelection.jsx b/imports/ui/singleGenePage/geneExpression/SampleSelection.jsx index 6fc4a990..bf09162d 100644 --- a/imports/ui/singleGenePage/geneExpression/SampleSelection.jsx +++ b/imports/ui/singleGenePage/geneExpression/SampleSelection.jsx @@ -36,8 +36,15 @@ function hasNoExpression({ experiments }) { return experiments.length === 0; } -function NoExpression() { +function NoExpression({ showHeader }) { return ( + <> + { showHeader && + <> + <hr / > + <h4 className="subtitle is-4">Gene Expression</h4> + </> + } <div className="card expression-plot"> <article className="message no-protein-domains" role="alert"> <div className="message-body"> @@ -45,6 +52,7 @@ function NoExpression() { </div> </article> </div> + </> ); } From 5dea2a54eb95174c6ce4d9e729549cffc0a63c67 Mon Sep 17 00:00:00 2001 From: mboudet <mateo.boudet@gmail.com> Date: Fri, 20 Oct 2023 15:32:48 +0200 Subject: [PATCH 35/36] Prepare release --- CHANGELOG.md | 2 +- cli/genoboo.js | 2 +- package.json | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b8d69383..7f7745af 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,7 +5,7 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html) -## [0.4.8] Unreleased +## [0.4.8] 2023-10-20 ### Added diff --git a/cli/genoboo.js b/cli/genoboo.js index 48f52b35..8e649981 100755 --- a/cli/genoboo.js +++ b/cli/genoboo.js @@ -513,7 +513,7 @@ file extension is not "xml", "txt"`); Example: genenotebook add diamond mmucedo.xml -u admin -p admin or - genenotebook add diamond mmucedo.txt --format txt --program blastp --matrix BLOSUM90 -db "Non-reundant protein sequences (nr)" -u admin -p admin + genenotebook add diamond mmucedo.txt --format txt --matrix BLOSUM90 -db "Non-reundant protein sequences (nr)" -u admin -p admin `); }) .exitOverride(customExitOverride(addDiamond)); diff --git a/package.json b/package.json index 1807b049..35103876 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "genoboo", - "version": "0.4.7", + "version": "0.4.8", "repository": "https://github.com/gogepp/genoboo", "description": "A portable website for browsing and querying genome sequences and annotations. Forked from genenotebook", "license": "AGPL-3.0", From cb046a2bd2b1bccd85e02bddcc15ff5e8193720c Mon Sep 17 00:00:00 2001 From: mboudet <mateo.boudet@gmail.com> Date: Fri, 20 Oct 2023 13:40:43 +0000 Subject: [PATCH 36/36] update package-lock.json --- package-lock.json | 7342 +++++++++++---------------------------------- 1 file changed, 1724 insertions(+), 5618 deletions(-) diff --git a/package-lock.json b/package-lock.json index 28fc6d08..13321c43 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,12 +1,12 @@ { "name": "genoboo", - "version": "0.4.4", + "version": "0.4.8", "lockfileVersion": 2, "requires": true, "packages": { "": { "name": "genoboo", - "version": "0.4.4", + "version": "0.4.8", "hasInstallScript": true, "license": "AGPL-3.0", "dependencies": { @@ -90,8 +90,7 @@ }, "node_modules/@ampproject/remapping": { "version": "2.2.0", - "resolved": "https://registry.npmjs.org/@ampproject/remapping/-/remapping-2.2.0.tgz", - "integrity": "sha512-qRmjj8nj9qmLTQXXmaR1cck3UXSRMPrbsLJAasZpF+t3riI71BXed5ebIOYwQntykeZuhjsdweEc9BxH5Jc26w==", + "license": "Apache-2.0", "dependencies": { "@jridgewell/gen-mapping": "^0.1.0", "@jridgewell/trace-mapping": "^0.3.9" @@ -102,8 +101,7 @@ }, "node_modules/@babel/code-frame": { "version": "7.18.6", - 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