@apollo-annotation/shared 0.3.1 → 0.3.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/GFF3/annotationFeatureToGFF3.js +1 -1
- package/dist/GFF3/annotationFeatureToGFF3.js.map +1 -1
- package/dist/GFF3/gff3ToAnnotationFeature.js +150 -3
- package/dist/GFF3/gff3ToAnnotationFeature.js.map +1 -1
- package/dist/GFF3/gff3ToAnnotationFeature.test.js +46 -0
- package/dist/GFF3/gff3ToAnnotationFeature.test.js.map +1 -1
- package/dist/tsconfig.tsbuildinfo +1 -1
- package/package.json +6 -6
- package/src/GFF3/annotationFeatureToGFF3.ts +1 -1
- package/src/GFF3/gff3ToAnnotationFeature.test.ts +58 -0
- package/src/GFF3/gff3ToAnnotationFeature.ts +174 -4
- package/test_data/cds_without_exon.gff +12 -0
- package/test_data/cds_without_exon.json +74 -0
- package/test_data/cds_without_exon_spliced_utr.gff +14 -0
- package/test_data/cds_without_exon_spliced_utr.json +73 -0
- package/test_data/gene_representations.gff3 +5 -4
- package/test_data/onecds_without_exon_spliced_utr.gff +6 -0
- package/test_data/onecds_without_exon_spliced_utr.json +55 -0
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@@ -4,7 +4,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
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4
4
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exports.annotationFeatureToGFF3 = annotationFeatureToGFF3;
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5
5
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const util_1 = require("@jbrowse/core/util");
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6
6
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function annotationFeatureToGFF3(feature, parentId, refSeqNames) {
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7
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-
const attributes = JSON.parse(JSON.stringify(feature.attributes));
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7
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+
const attributes = JSON.parse(JSON.stringify(feature.attributes ?? {}));
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8
8
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const ontologyTerms = [];
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9
9
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const source = feature.attributes?.gff_source?.[0] ?? null;
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10
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delete attributes.gff_source;
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"annotationFeatureToGFF3.js","sourceRoot":"","sources":["../../src/GFF3/annotationFeatureToGFF3.ts"],"names":[],"mappings":";AAAA,4DAA4D;;AAU5D,0DAoGC;AAtGD,6CAAkD;AAElD,SAAgB,uBAAuB,CACrC,OAAkC,EAClC,QAAiB,EACjB,WAAgD;IAEhD,MAAM,UAAU,GAAyC,IAAI,CAAC,KAAK,CACjE,IAAI,CAAC,SAAS,CAAC,OAAO,CAAC,UAAU,CAAC,
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1
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+
{"version":3,"file":"annotationFeatureToGFF3.js","sourceRoot":"","sources":["../../src/GFF3/annotationFeatureToGFF3.ts"],"names":[],"mappings":";AAAA,4DAA4D;;AAU5D,0DAoGC;AAtGD,6CAAkD;AAElD,SAAgB,uBAAuB,CACrC,OAAkC,EAClC,QAAiB,EACjB,WAAgD;IAEhD,MAAM,UAAU,GAAyC,IAAI,CAAC,KAAK,CACjE,IAAI,CAAC,SAAS,CAAC,OAAO,CAAC,UAAU,IAAI,EAAE,CAAC,CACzC,CAAA;IACD,MAAM,aAAa,GAAa,EAAE,CAAA;IAClC,MAAM,MAAM,GAAG,OAAO,CAAC,UAAU,EAAE,UAAU,EAAE,CAAC,CAAC,CAAC,IAAI,IAAI,CAAA;IAE1D,OAAO,UAAU,CAAC,UAAU,CAAA;IAC5B,IAAI,QAAQ,EAAE,CAAC;QACb,UAAU,CAAC,MAAM,GAAG,CAAC,QAAQ,CAAC,CAAA;IAChC,CAAC;IACD,IAAI,UAAU,CAAC,MAAM,EAAE,CAAC;QACtB,UAAU,CAAC,EAAE,GAAG,UAAU,CAAC,MAAM,CAAA;QACjC,OAAO,UAAU,CAAC,MAAM,CAAA;IAC1B,CAAC;SAAM,IAAI,OAAO,CAAC,QAAQ,EAAE,CAAC;QAC5B,UAAU,CAAC,EAAE,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;IAC/B,CAAC;IACD,IAAI,UAAU,CAAC,QAAQ,EAAE,CAAC;QACxB,UAAU,CAAC,IAAI,GAAG,UAAU,CAAC,QAAQ,CAAA;QACrC,OAAO,UAAU,CAAC,QAAQ,CAAA;IAC5B,CAAC;IACD,IAAI,UAAU,CAAC,SAAS,EAAE,CAAC;QACzB,UAAU,CAAC,KAAK,GAAG,UAAU,CAAC,SAAS,CAAA;QACvC,OAAO,UAAU,CAAC,SAAS,CAAA;IAC7B,CAAC;IACD,IAAI,UAAU,CAAC,UAAU,EAAE,CAAC;QAC1B,UAAU,CAAC,MAAM,GAAG,UAAU,CAAC,UAAU,CAAA;QACzC,OAAO,UAAU,CAAC,UAAU,CAAA;IAC9B,CAAC;IACD,IAAI,UAAU,CAAC,OAAO,EAAE,CAAC;QACvB,UAAU,CAAC,GAAG,GAAG,UAAU,CAAC,OAAO,CAAA;QACnC,OAAO,UAAU,CAAC,OAAO,CAAA;IAC3B,CAAC;IACD,IAAI,UAAU,CAAC,gBAAgB,EAAE,CAAC;QAChC,UAAU,CAAC,YAAY,GAAG,UAAU,CAAC,gBAAgB,CAAA;QACrD,OAAO,UAAU,CAAC,gBAAgB,CAAA;IACpC,CAAC;IACD,IAAI,UAAU,CAAC,QAAQ,EAAE,CAAC;QACxB,UAAU,CAAC,IAAI,GAAG,UAAU,CAAC,QAAQ,CAAA;QACrC,OAAO,UAAU,CAAC,QAAQ,CAAA;IAC5B,CAAC;IACD,IAAI,UAAU,CAAC,UAAU,EAAE,CAAC;QAC1B,UAAU,CAAC,MAAM,GAAG,UAAU,CAAC,UAAU,CAAA;QACzC,OAAO,UAAU,CAAC,UAAU,CAAA;IAC9B,CAAC;IACD,IAAI,UAAU,CAAC,eAAe,EAAE,CAAC;QAC/B,UAAU,CAAC,WAAW,GAAG,UAAU,CAAC,eAAe,CAAA;QACnD,OAAO,UAAU,CAAC,eAAe,CAAA;IACnC,CAAC;IACD,IAAI,UAAU,CAAC,iBAAiB,EAAE,CAAC;QACjC,aAAa,CAAC,IAAI,CAAC,GAAG,UAAU,CAAC,iBAAiB,CAAC,CAAA;QACnD,OAAO,UAAU,CAAC,iBAAiB,CAAA;IACrC,CAAC;IACD,IAAI,UAAU,CAAC,eAAe,CAAC,EAAE,CAAC;QAChC,aAAa,CAAC,IAAI,CAAC,GAAG,UAAU,CAAC,eAAe,CAAC,CAAC,CAAA;QAClD,OAAO,UAAU,CAAC,eAAe,CAAC,CAAA;IACpC,CAAC;IACD,IAAI,UAAU,CAAC,mBAAmB,CAAC,EAAE,CAAC;QACpC,aAAa,CAAC,IAAI,CAAC,GAAG,UAAU,CAAC,mBAAmB,CAAC,CAAC,CAAA;QACtD,OAAO,UAAU,CAAC,mBAAmB,CAAC,CAAA;IACxC,CAAC;IACD,IAAI,aAAa,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QAC7B,UAAU,CAAC,aAAa,GAAG,aAAa,CAAA;IAC1C,CAAC;IAED,MAAM,SAAS,GAAG,OAAO,CAAC,UAAU,EAAE,SAAS,CAAA;IAC/C,IAAI,KAAK,GAAkB,IAAI,CAAA;IAC/B,IAAI,SAAS,IAAI,SAAS,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACtC,IAAI,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC;YACjB,KAAK,GAAG,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,CAAA;YAC5B,IAAI,MAAM,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC;gBACxB,KAAK,GAAG,IAAI,CAAA;YACd,CAAC;QACH,CAAC;QACD,OAAO,UAAU,CAAC,SAAS,CAAA;IAC7B,CAAC;IAED,MAAM,SAAS,GAAG,CAAC,EAAE,KAAK,EAAE,OAAO,CAAC,GAAG,EAAE,GAAG,EAAE,OAAO,CAAC,GAAG,EAAE,CAAC,CAAA;IAE5D,OAAO,SAAS,CAAC,GAAG,CAAC,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAC;QAClC,KAAK,EAAE,MAAM,CAAC,QAAQ,CAAC,KAAK,CAAC,GAAG,CAAC;QACjC,GAAG,EAAE,MAAM,CAAC,QAAQ,CAAC,GAAG,CAAC;QACzB,MAAM,EAAE,WAAW,CAAC,CAAC,CAAC,WAAW,CAAC,OAAO,CAAC,MAAM,CAAC,IAAI,IAAI,CAAC,CAAC,CAAC,OAAO,CAAC,MAAM;QAC1E,MAAM;QACN,IAAI,EAAE,OAAO,CAAC,IAAI;QAClB,KAAK;QACL,MAAM,EAAE,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI;QAClE,KAAK,EAAE,IAAI;QACX,UAAU,EAAE,MAAM,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,IAAI;QAClE,gBAAgB,EAAE,EAAE;QACpB,cAAc,EAAE,oBAAoB,CAClC,OAAO,EACP,UAAU,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,EAClB,WAAW,CACZ;KACF,CAAC,CAAC,CAAA;AACL,CAAC;AAED,SAAS,oBAAoB,CAC3B,OAAkC,EAClC,QAAiB,EACjB,WAAgD;IAEhD,IAAI,CAAC,OAAO,CAAC,QAAQ,EAAE,CAAC;QACtB,OAAO,EAAE,CAAA;IACX,CAAC;IACD,IAAI,OAAO,CAAC,IAAI,KAAK,MAAM,EAAE,CAAC;QAC5B,MAAM,cAAc,GAAkB,EAAE,CAAA;QACxC,MAAM,YAAY,GAAG,eAAe,CAAC,OAAO,CAAC,CAAA;QAC7C,IAAI,OAAO,GAAG,CAAC,CAAA;QACf,KAAK,MAAM,KAAK,IAAI,MAAM,CAAC,MAAM,CAAC,OAAO,CAAC,QAAQ,CAAC,EAAE,CAAC;YACpD,MAAM,QAAQ,GAAG,uBAAuB,CAAC,KAAK,EAAE,QAAQ,EAAE,WAAW,CAAC,CAAA;YACtE,IAAI,KAAK,CAAC,IAAI,KAAK,KAAK,EAAE,CAAC;gBACzB,KAAK,MAAM,GAAG,IAAI,YAAY,CAAC,OAAO,CAAC,EAAE,CAAC;oBACxC,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,CAAgB,CAAA;oBAClE,IAAI,MAAM,CAAC,MAAM,IAAI,CAAC,EAAE,CAAC;wBACvB,yBAAyB;wBACzB,MAAM,IAAI,KAAK,CACb,mBAAmB,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,EAAE,CACrD,CAAA;oBACH,CAAC;oBACD,MAAM,CAAC,CAAC,CAAC,CAAC,KAAK,GAAG,GAAG,CAAC,GAAG,GAAG,CAAC,CAAA;oBAC7B,MAAM,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG,GAAG,CAAC,GAAG,CAAA;oBACvB,MAAM,CAAC,CAAC,CAAC,CAAC,KAAK,GAAG,GAAG,CAAC,KAAK,CAAC,QAAQ,EAAE,CAAA;oBACtC,MAAM,CAAC,CAAC,CAAC,CAAC,IAAI,GAAG,GAAG,CAAC,IAAI,CAAA,CAAC,mBAAmB;oBAC7C,cAAc,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;gBAC7B,CAAC;gBACD,OAAO,EAAE,CAAA;YACX,CAAC;iBAAM,CAAC;gBACN,cAAc,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;YAC/B,CAAC;QACH,CAAC;QACD,OAAO,cAAc,CAAA;IACvB,CAAC;IACD,OAAO,MAAM,CAAC,MAAM,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC,GAAG,CAAC,CAAC,KAAK,EAAE,EAAE,CACnD,uBAAuB,CAAC,KAAK,EAAE,QAAQ,EAAE,WAAW,CAAC,CACtD,CAAA;AACH,CAAC;AASD,SAAS,kBAAkB,CACzB,OAAkC;IAElC,IAAI,OAAO,CAAC,IAAI,KAAK,MAAM,EAAE,CAAC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@@ -99,6 +99,9 @@ function convertFeatureAttributes(gff3Feature) {
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const newKey = (0, gffReservedKeys_1.isGFFReservedAttribute)(key) ? gffReservedKeys_1.gffToInternal[key] : key;
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const existingVal = convertedAttributes[newKey];
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if (existingVal) {
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// if (JSON.stringify(existingVal) === JSON.stringify(val)) {
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// continue
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// }
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const valSet = new Set([...existingVal, ...val]);
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convertedAttributes[newKey] = [...valSet];
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}
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@@ -125,8 +128,17 @@ function convertChildren(gff3Feature, refSeq, featureIds) {
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const [firstFeature] = locationsWithChildren;
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const { child_features: childFeatures } = firstFeature;
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const cdsFeatures = [];
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const exonFeatures = [];
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const utrFeatures = [];
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for (const childFeature of childFeatures) {
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const [firstChildFeatureLocation] = childFeature;
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if (firstChildFeatureLocation.type === 'exon') {
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exonFeatures.push(childFeature);
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}
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if (firstChildFeatureLocation.type === 'three_prime_UTR' ||
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firstChildFeatureLocation.type === 'five_prime_UTR') {
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utrFeatures.push(childFeature);
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}
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if (firstChildFeatureLocation.type === 'three_prime_UTR' ||
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firstChildFeatureLocation.type === 'five_prime_UTR' ||
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firstChildFeatureLocation.type === 'intron' ||
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@@ -142,15 +154,150 @@ function convertChildren(gff3Feature, refSeq, featureIds) {
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convertedChildren[child._id] = child;
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}
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}
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-
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-
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147
|
-
|
|
157
|
+
if (cdsFeatures.length > 0) {
|
|
158
|
+
const processedCDS = processCDS(cdsFeatures, refSeq, featureIds);
|
|
159
|
+
for (const cds of processedCDS) {
|
|
160
|
+
convertedChildren[cds._id] = cds;
|
|
161
|
+
}
|
|
162
|
+
const missingExons = inferMissingExons(cdsFeatures, exonFeatures, utrFeatures, processedCDS[0].refSeq);
|
|
163
|
+
for (const exon of missingExons) {
|
|
164
|
+
convertedChildren[exon._id] = exon;
|
|
165
|
+
}
|
|
148
166
|
}
|
|
149
167
|
if (Object.keys(convertedChildren).length > 0) {
|
|
150
168
|
return convertedChildren;
|
|
151
169
|
}
|
|
152
170
|
return;
|
|
153
171
|
}
|
|
172
|
+
function inferMissingExons(cdsFeatures, existingExons, utrFeatures, refSeq) {
|
|
173
|
+
// Convert utrFeatures from GFF3Feature to AnnotationFeatureSnapshot
|
|
174
|
+
const utrExons = [];
|
|
175
|
+
for (const utrs of utrFeatures) {
|
|
176
|
+
for (const utr of utrs) {
|
|
177
|
+
if (!utr.start || !utr.end) {
|
|
178
|
+
throw new Error(`UTR has undefined start and/or end\n: ${JSON.stringify(utr, null, 2)}`);
|
|
179
|
+
}
|
|
180
|
+
let strand = undefined;
|
|
181
|
+
if (utr.strand === '+') {
|
|
182
|
+
strand = 1;
|
|
183
|
+
}
|
|
184
|
+
else if (utr.strand === '-') {
|
|
185
|
+
strand = -1;
|
|
186
|
+
}
|
|
187
|
+
utrExons.push({
|
|
188
|
+
_id: new bson_objectid_1.default().toHexString(),
|
|
189
|
+
refSeq,
|
|
190
|
+
type: 'exon',
|
|
191
|
+
min: utr.start - 1,
|
|
192
|
+
max: utr.end,
|
|
193
|
+
strand,
|
|
194
|
+
});
|
|
195
|
+
}
|
|
196
|
+
}
|
|
197
|
+
utrExons.sort((a, b) => a.min - b.min);
|
|
198
|
+
const missingExons = [];
|
|
199
|
+
for (const protein of cdsFeatures) {
|
|
200
|
+
protein.sort((a, b) => {
|
|
201
|
+
if (!a.start || !b.start) {
|
|
202
|
+
throw new Error('CDS has undefined start');
|
|
203
|
+
}
|
|
204
|
+
return a.start - b.start;
|
|
205
|
+
});
|
|
206
|
+
for (let cdsIdx = 0; cdsIdx < protein.length; cdsIdx++) {
|
|
207
|
+
const cds = protein[cdsIdx];
|
|
208
|
+
// For CDS check if there is an exon containing it. If not, create an exon with same coords as the CDS.
|
|
209
|
+
let exonFound = false;
|
|
210
|
+
for (const x of existingExons) {
|
|
211
|
+
if (x.length != 1) {
|
|
212
|
+
throw new Error('Unexpected number of exons');
|
|
213
|
+
}
|
|
214
|
+
const [exon] = x;
|
|
215
|
+
if (exon.start &&
|
|
216
|
+
exon.end &&
|
|
217
|
+
cds.start &&
|
|
218
|
+
cds.end &&
|
|
219
|
+
exon.start <= cds.start &&
|
|
220
|
+
exon.end >= cds.end) {
|
|
221
|
+
exonFound = true;
|
|
222
|
+
break;
|
|
223
|
+
}
|
|
224
|
+
}
|
|
225
|
+
if (!exonFound) {
|
|
226
|
+
if (!cds.start || !cds.end) {
|
|
227
|
+
throw new Error(`CDS has undefined start and/or end: ${JSON.stringify(cds, null, 2)}`);
|
|
228
|
+
}
|
|
229
|
+
let strand = undefined;
|
|
230
|
+
if (cds.strand === '+') {
|
|
231
|
+
strand = 1;
|
|
232
|
+
}
|
|
233
|
+
else if (cds.strand === '-') {
|
|
234
|
+
strand = -1;
|
|
235
|
+
}
|
|
236
|
+
const newExon = {
|
|
237
|
+
_id: new bson_objectid_1.default().toHexString(),
|
|
238
|
+
refSeq,
|
|
239
|
+
type: 'exon',
|
|
240
|
+
min: cds.start - 1,
|
|
241
|
+
max: cds.end,
|
|
242
|
+
strand,
|
|
243
|
+
};
|
|
244
|
+
if (cdsIdx === 0) {
|
|
245
|
+
// If this CDS is the leftmost (or the only CDS in this protein), check if we need to add UTRs before it
|
|
246
|
+
for (const utr of utrExons) {
|
|
247
|
+
if (utr.max > newExon.min) {
|
|
248
|
+
break;
|
|
249
|
+
}
|
|
250
|
+
if (utr.max === newExon.min) {
|
|
251
|
+
// UTR ends where exon begins: Extend the exon to include this UTR
|
|
252
|
+
newExon.min = utr.min;
|
|
253
|
+
}
|
|
254
|
+
else {
|
|
255
|
+
missingExons.push(utr);
|
|
256
|
+
}
|
|
257
|
+
}
|
|
258
|
+
}
|
|
259
|
+
if (cdsIdx === protein.length - 1) {
|
|
260
|
+
// If this CDS is the rightmost (or the only CDS in this protein), check if we need to add UTRs after it
|
|
261
|
+
for (const utr of utrExons) {
|
|
262
|
+
if (utr.min < newExon.max) {
|
|
263
|
+
continue;
|
|
264
|
+
}
|
|
265
|
+
if (utr.min === newExon.max) {
|
|
266
|
+
// UTR begins where exon end: Extend the exon to include this UTR
|
|
267
|
+
newExon.max = utr.max;
|
|
268
|
+
}
|
|
269
|
+
else {
|
|
270
|
+
missingExons.push(utr);
|
|
271
|
+
}
|
|
272
|
+
}
|
|
273
|
+
}
|
|
274
|
+
missingExons.push(newExon);
|
|
275
|
+
}
|
|
276
|
+
}
|
|
277
|
+
}
|
|
278
|
+
const mergedExons = mergeAnnotationFeatures(missingExons);
|
|
279
|
+
return mergedExons;
|
|
280
|
+
}
|
|
281
|
+
function mergeAnnotationFeatures(features) {
|
|
282
|
+
if (features.length === 0) {
|
|
283
|
+
return [];
|
|
284
|
+
}
|
|
285
|
+
features.sort((a, b) => a.min - b.min);
|
|
286
|
+
const res = [];
|
|
287
|
+
res.push(features[0]);
|
|
288
|
+
for (let i = 1; i < features.length; i++) {
|
|
289
|
+
const last = res.at(-1);
|
|
290
|
+
const curr = features[i];
|
|
291
|
+
// If current interval overlaps with the last merged interval, merge them
|
|
292
|
+
if (last && curr.min <= last.max) {
|
|
293
|
+
last.max = Math.max(last.max, curr.max);
|
|
294
|
+
}
|
|
295
|
+
else {
|
|
296
|
+
res.push(curr);
|
|
297
|
+
}
|
|
298
|
+
}
|
|
299
|
+
return res;
|
|
300
|
+
}
|
|
154
301
|
/**
|
|
155
302
|
* If a GFF3 file has CDS features that either (1) don't have an ID or (2) have
|
|
156
303
|
* different IDs for each CDS, we have to do a bit of guessing about how they
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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@@ -160,6 +160,26 @@ const [ex1, ex2, ex3, ex4] = readFeatureFile('test_data/gene_representations.gff
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160
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chai_1.assert.equal(txt.match(/_codon/g), null);
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161
161
|
});
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162
162
|
});
|
|
163
|
+
(0, node_test_1.describe)('CDS without exons', () => {
|
|
164
|
+
(0, node_test_1.it)('Convert mRNA with CDS but without exon', () => {
|
|
165
|
+
const [gffFeature] = readFeatureFile('test_data/cds_without_exon.gff');
|
|
166
|
+
const actual = (0, gff3ToAnnotationFeature_1.gff3ToAnnotationFeature)(gffFeature);
|
|
167
|
+
const expected = readAnnotationFeatureSnapshot('test_data/cds_without_exon.json');
|
|
168
|
+
compareFeatures(actual, expected);
|
|
169
|
+
});
|
|
170
|
+
(0, node_test_1.it)('Convert mRNA with CDS but without exon and spliced UTR', () => {
|
|
171
|
+
const [gffFeature] = readFeatureFile('test_data/cds_without_exon_spliced_utr.gff');
|
|
172
|
+
const actual = (0, gff3ToAnnotationFeature_1.gff3ToAnnotationFeature)(gffFeature);
|
|
173
|
+
const expected = readAnnotationFeatureSnapshot('test_data/cds_without_exon_spliced_utr.json');
|
|
174
|
+
compareFeatures(actual, expected);
|
|
175
|
+
});
|
|
176
|
+
(0, node_test_1.it)('Convert mRNA with one CDS, without exons non-adjacent UTR', () => {
|
|
177
|
+
const [gffFeature] = readFeatureFile('test_data/onecds_without_exon_spliced_utr.gff');
|
|
178
|
+
const actual = (0, gff3ToAnnotationFeature_1.gff3ToAnnotationFeature)(gffFeature);
|
|
179
|
+
const expected = readAnnotationFeatureSnapshot('test_data/onecds_without_exon_spliced_utr.json');
|
|
180
|
+
compareFeatures(actual, expected);
|
|
181
|
+
});
|
|
182
|
+
});
|
|
163
183
|
(0, node_test_1.describe)('gff3ToAnnotationFeature', () => {
|
|
164
184
|
for (const testCase of testCases) {
|
|
165
185
|
const [description, featureLine, convertedFeature] = testCase;
|
|
@@ -172,4 +192,30 @@ const [ex1, ex2, ex3, ex4] = readFeatureFile('test_data/gene_representations.gff
|
|
|
172
192
|
});
|
|
173
193
|
}
|
|
174
194
|
});
|
|
195
|
+
(0, node_test_1.describe)('Source and score', () => {
|
|
196
|
+
(0, node_test_1.it)('Convert score and source', () => {
|
|
197
|
+
const gffFeature = [
|
|
198
|
+
{
|
|
199
|
+
seq_id: 'chr1',
|
|
200
|
+
source: 'mySource',
|
|
201
|
+
type: 'gene',
|
|
202
|
+
start: 1000,
|
|
203
|
+
end: 9000,
|
|
204
|
+
score: 0,
|
|
205
|
+
strand: '+',
|
|
206
|
+
phase: null,
|
|
207
|
+
attributes: {
|
|
208
|
+
ID: ['gene10001'],
|
|
209
|
+
Name: ['EDEN'],
|
|
210
|
+
testid: ['t003'],
|
|
211
|
+
},
|
|
212
|
+
child_features: [],
|
|
213
|
+
derived_features: [],
|
|
214
|
+
},
|
|
215
|
+
];
|
|
216
|
+
const actual = (0, gff3ToAnnotationFeature_1.gff3ToAnnotationFeature)(gffFeature);
|
|
217
|
+
chai_1.assert.deepStrictEqual(actual.attributes?.gff_source?.at(0), 'mySource');
|
|
218
|
+
chai_1.assert.deepStrictEqual(actual.attributes?.gff_score?.at(0), '0');
|
|
219
|
+
});
|
|
220
|
+
});
|
|
175
221
|
//# sourceMappingURL=gff3ToAnnotationFeature.test.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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