@apollo-annotation/shared 0.3.7 → 0.3.9
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/Changes/AddAssemblyAndFeaturesFromFileChange.d.ts +3 -0
- package/dist/Changes/AddAssemblyAndFeaturesFromFileChange.js +6 -5
- package/dist/Changes/AddAssemblyAndFeaturesFromFileChange.js.map +1 -1
- package/dist/Changes/AddAssemblyFromFileChange.js +1 -1
- package/dist/Changes/AddAssemblyFromFileChange.js.map +1 -1
- package/dist/Changes/AddFeatureChange.js +14 -2
- package/dist/Changes/AddFeatureChange.js.map +1 -1
- package/dist/Changes/AddFeaturesFromFileChange.d.ts +3 -0
- package/dist/Changes/AddFeaturesFromFileChange.js +5 -2
- package/dist/Changes/AddFeaturesFromFileChange.js.map +1 -1
- package/dist/Changes/AddRefSeqAliasesChange.js +2 -7
- package/dist/Changes/AddRefSeqAliasesChange.js.map +1 -1
- package/dist/Changes/FromFileBaseChange.js +6 -6
- package/dist/Changes/FromFileBaseChange.js.map +1 -1
- package/dist/Changes/ImportJBrowseConfigChange.js +1 -1
- package/dist/Changes/ImportJBrowseConfigChange.js.map +1 -1
- package/dist/Changes/MergeExonsChange.d.ts +0 -1
- package/dist/Changes/MergeExonsChange.js +14 -30
- package/dist/Changes/MergeExonsChange.js.map +1 -1
- package/dist/Changes/MergeTranscriptsChange.d.ts +1 -3
- package/dist/Changes/MergeTranscriptsChange.js +55 -56
- package/dist/Changes/MergeTranscriptsChange.js.map +1 -1
- package/dist/Checks/CDSCheck.d.ts +1 -1
- package/dist/Checks/CDSCheck.js +12 -12
- package/dist/Checks/CDSCheck.js.map +1 -1
- package/dist/Checks/TranscriptCheck.d.ts +9 -0
- package/dist/Checks/TranscriptCheck.js +109 -0
- package/dist/Checks/TranscriptCheck.js.map +1 -0
- package/dist/Checks/index.d.ts +1 -0
- package/dist/Checks/index.js +1 -0
- package/dist/Checks/index.js.map +1 -1
- package/dist/Checks/util.d.ts +2 -0
- package/dist/Checks/util.js +15 -0
- package/dist/Checks/util.js.map +1 -0
- package/dist/GFF3/annotationFeatureToGFF3.js +3 -1
- package/dist/GFF3/annotationFeatureToGFF3.js.map +1 -1
- package/dist/GFF3/gff3ToAnnotationFeature.js +1 -1
- package/dist/GFF3/gff3ToAnnotationFeature.js.map +1 -1
- package/dist/GFF3/gff3ToAnnotationFeature.test.js +4 -4
- package/dist/GFF3/gff3ToAnnotationFeature.test.js.map +1 -1
- package/dist/tsconfig.tsbuildinfo +1 -1
- package/dist/util.d.ts +3 -0
- package/dist/util.js +33 -0
- package/dist/util.js.map +1 -1
- package/package.json +9 -9
- package/src/Changes/AddAssemblyAndFeaturesFromFileChange.ts +8 -6
- package/src/Changes/AddAssemblyFromFileChange.ts +1 -1
- package/src/Changes/AddFeatureChange.ts +16 -2
- package/src/Changes/AddFeaturesFromFileChange.ts +6 -1
- package/src/Changes/AddRefSeqAliasesChange.ts +2 -8
- package/src/Changes/FromFileBaseChange.ts +6 -6
- package/src/Changes/ImportJBrowseConfigChange.ts +1 -1
- package/src/Changes/MergeExonsChange.ts +52 -36
- package/src/Changes/MergeTranscriptsChange.ts +82 -67
- package/src/Checks/CDSCheck.ts +15 -13
- package/src/Checks/TranscriptCheck.ts +138 -0
- package/src/Checks/index.ts +1 -0
- package/src/Checks/util.ts +13 -0
- package/src/GFF3/annotationFeatureToGFF3.ts +4 -1
- package/src/GFF3/gff3ToAnnotationFeature.test.ts +4 -4
- package/src/GFF3/gff3ToAnnotationFeature.ts +1 -1
- package/src/util.ts +37 -0
- package/test_data/example01.json +20 -20
- package/test_data/example02.json +38 -38
- package/test_data/example04.json +57 -57
- package/test_data/gene_representations.gff3 +1054 -276
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1
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+
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@@ -5,7 +5,7 @@ const tslib_1 = require("tslib");
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5
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/* eslint-disable @typescript-eslint/no-floating-promises */
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6
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const node_fs_1 = require("node:fs");
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const node_test_1 = require("node:test");
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8
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-
const gff_1 =
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8
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+
const gff_1 = require("@gmod/gff");
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const chai_1 = require("chai");
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const chai_exclude_1 = tslib_1.__importDefault(require("chai-exclude"));
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11
11
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const gff3ToAnnotationFeature_1 = require("./gff3ToAnnotationFeature");
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@@ -96,14 +96,14 @@ function readFeatureFile(fn) {
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96
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feature.push(line);
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97
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}
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}
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-
const inGff = gff_1.
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+
const inGff = (0, gff_1.parseStringSync)(feature.join('\n'));
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return inGff;
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}
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|
function readAnnotationFeatureSnapshot(fn) {
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103
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const lines = (0, node_fs_1.readFileSync)(fn).toString();
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return JSON.parse(lines);
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105
105
|
}
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|
106
|
-
const [ex1, ex2, ex3, ex4] = readFeatureFile('test_data/gene_representations.gff3');
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|
106
|
+
const [ex1, , ex2, , ex3, , ex4] = readFeatureFile('test_data/gene_representations.gff3');
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107
107
|
(0, node_test_1.describe)('gff3ToAnnotationFeature examples', () => {
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108
108
|
(0, node_test_1.it)('Convert one CDS', () => {
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|
109
109
|
const actual = (0, gff3ToAnnotationFeature_1.gff3ToAnnotationFeature)(readFeatureFile('test_data/one_cds.gff3')[0]);
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@@ -184,7 +184,7 @@ const [ex1, ex2, ex3, ex4] = readFeatureFile('test_data/gene_representations.gff
|
|
|
184
184
|
for (const testCase of testCases) {
|
|
185
185
|
const [description, featureLine, convertedFeature] = testCase;
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|
186
186
|
(0, node_test_1.it)(`converts ${description}`, () => {
|
|
187
|
-
const gff3Feature = gff_1.
|
|
187
|
+
const gff3Feature = (0, gff_1.parseStringSync)(featureLine, {
|
|
188
188
|
parseSequences: false,
|
|
189
189
|
});
|
|
190
190
|
const feature = (0, gff3ToAnnotationFeature_1.gff3ToAnnotationFeature)(gff3Feature[0]);
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|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"gff3ToAnnotationFeature.test.js","sourceRoot":"","sources":["../../src/GFF3/gff3ToAnnotationFeature.test.ts"],"names":[],"mappings":";;AA0HA,sEAKC;;AA/HD,4DAA4D;AAC5D,qCAAsC;AACtC,yCAAwC;AAGxC,
|
|
1
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+
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