@apollo-annotation/shared 0.3.7 → 0.3.8

package/dist/Checks/TranscriptCheck.js

@@ -0,0 +1,109 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.TranscriptCheck = void 0;
+const tslib_1 = require("tslib");
+const common_1 = require("@apollo-annotation/common");
+const util_1 = require("@jbrowse/core/util");
+const bson_objectid_1 = tslib_1.__importDefault(require("bson-objectid"));
+var CAUSES;
+(function (CAUSES) {
+    CAUSES[CAUSES["NonCanonicalSpliceSiteAtFivePrime"] = 0] = "NonCanonicalSpliceSiteAtFivePrime";
+    CAUSES[CAUSES["NonCanonicalSpliceSiteAtThreePrime"] = 1] = "NonCanonicalSpliceSiteAtThreePrime";
+})(CAUSES || (CAUSES = {}));
+const CHECK_NAME = 'TranscriptCheck';
+async function getSpliceSequences(transcript, getSequence) {
+    if (!transcript.children) {
+        return [];
+    }
+    const exons = [];
+    for (const [, child] of Object.entries(transcript.children)) {
+        if (child.type === 'exon') {
+            exons.push(child);
+        }
+    }
+    if (exons.length < 2) {
+        return [];
+    }
+    const spliceSeq = [];
+    for (let i = 0; i < exons.length - 1; i++) {
+        let fivePrimeMin = exons[i].max;
+        let threePrimeMin = exons[i + 1].min - 2;
+        if (transcript.strand === -1) {
+            const _fivePrimeMin = fivePrimeMin;
+            fivePrimeMin = threePrimeMin;
+            threePrimeMin = _fivePrimeMin;
+        }
+        let fivePrimeSeq = await getSequence(fivePrimeMin, fivePrimeMin + 2);
+        let threePrimeSeq = await getSequence(threePrimeMin, threePrimeMin + 2);
+        if (transcript.strand === -1) {
+            threePrimeSeq = (0, util_1.revcom)(threePrimeSeq);
+            fivePrimeSeq = (0, util_1.revcom)(fivePrimeSeq);
+        }
+        spliceSeq.push({
+            fivePrimeSeq,
+            fivePrimeMin,
+            threePrimeSeq,
+            threePrimeMin,
+        });
+    }
+    return spliceSeq;
+}
+async function checkTranscript(feature, getSequence) {
+    const checkResults = [];
+    const VALID_FIVE_PRIME_SEQ = new Set(['GT']);
+    const VALID_THREE_PRIME_SEQ = new Set(['AG']);
+    const spliceSequences = await getSpliceSequences(feature, getSequence);
+    for (const spliceSequence of spliceSequences) {
+        if (!VALID_FIVE_PRIME_SEQ.has(spliceSequence.fivePrimeSeq.toUpperCase())) {
+            checkResults.push({
+                _id: new bson_objectid_1.default().toHexString(),
+                name: CHECK_NAME,
+                cause: CAUSES[CAUSES.NonCanonicalSpliceSiteAtFivePrime],
+                ids: [feature._id],
+                refSeq: feature.refSeq.toString(),
+                start: spliceSequence.fivePrimeMin,
+                end: spliceSequence.fivePrimeMin + 2,
+                message: `Unexpected 5' splice site in "${feature._id}". Expected: ${[...VALID_FIVE_PRIME_SEQ].join('|')}, got: ${spliceSequence.fivePrimeSeq}`,
+            });
+        }
+        if (!VALID_THREE_PRIME_SEQ.has(spliceSequence.threePrimeSeq.toUpperCase())) {
+            checkResults.push({
+                _id: new bson_objectid_1.default().toHexString(),
+                name: CHECK_NAME,
+                cause: CAUSES[CAUSES.NonCanonicalSpliceSiteAtThreePrime],
+                ids: [feature._id],
+                refSeq: feature.refSeq.toString(),
+                start: spliceSequence.threePrimeMin,
+                end: spliceSequence.threePrimeMin + 2,
+                message: `Unexpected 3' splice site in "${feature._id}". Expected: ${[...VALID_THREE_PRIME_SEQ].join('|')}, got: ${spliceSequence.threePrimeSeq}`,
+            });
+        }
+    }
+    return checkResults;
+}
+function getCauses() {
+    return Object.values(CAUSES).filter((x) => Number.isNaN(Number(x)));
+}
+class TranscriptCheck extends common_1.Check {
+    name = 'TranscriptCheck';
+    causes = getCauses();
+    version = 1;
+    isDefault = true;
+    async checkFeature(feature, getSequence) {
+        if (feature.type === 'mRNA' ||
+            feature.type === 'transcript' ||
+            feature.type === 'pseudogenic_transcript') {
+            return checkTranscript(feature, getSequence);
+        }
+        if (!feature.children) {
+            return [];
+        }
+        const checkResults = [];
+        for (const child of Object.values(feature.children)) {
+            checkResults.push(...(await this.checkFeature(child, getSequence)));
+        }
+        return checkResults;
+    }
+}
+exports.TranscriptCheck = TranscriptCheck;
+//# sourceMappingURL=TranscriptCheck.js.map

package/dist/Checks/TranscriptCheck.js.map

@@ -0,0 +1 @@
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package/dist/Checks/index.d.ts

@@ -1 +1,2 @@
 export * from './CDSCheck';
+export * from './TranscriptCheck';

package/dist/Checks/index.js

@@ -2,4 +2,5 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 const tslib_1 = require("tslib");
 tslib_1.__exportStar(require("./CDSCheck"), exports);
+tslib_1.__exportStar(require("./TranscriptCheck"), exports);
 //# sourceMappingURL=index.js.map

package/dist/Checks/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/Checks/index.ts"],"names":[],"mappings":";;;AAAA,qDAA0B"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/Checks/index.ts"],"names":[],"mappings":";;;AAAA,qDAA0B;AAC1B,4DAAiC"}

package/dist/GFF3/gff3ToAnnotationFeature.test.js

@@ -103,7 +103,7 @@ function readAnnotationFeatureSnapshot(fn) {
     const lines = (0, node_fs_1.readFileSync)(fn).toString();
     return JSON.parse(lines);
 }
-const [ex1, ex2, ex3, ex4] = readFeatureFile('test_data/gene_representations.gff3');
+const [ex1, , ex2, , ex3, , ex4] = readFeatureFile('test_data/gene_representations.gff3');
 (0, node_test_1.describe)('gff3ToAnnotationFeature examples', () => {
     (0, node_test_1.it)('Convert one CDS', () => {
         const actual = (0, gff3ToAnnotationFeature_1.gff3ToAnnotationFeature)(readFeatureFile('test_data/one_cds.gff3')[0]);

package/dist/GFF3/gff3ToAnnotationFeature.test.js.map

@@ -1 +1 @@
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