@apollo-annotation/shared 0.2.1 → 0.2.2
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/Checks/CDSCheck.js +1 -1
- package/dist/Checks/CDSCheck.js.map +1 -1
- package/dist/GFF3/annotationFeatureToGFF3.d.ts +3 -0
- package/dist/GFF3/annotationFeatureToGFF3.js +209 -0
- package/dist/GFF3/annotationFeatureToGFF3.js.map +1 -0
- package/dist/GFF3/annotationFeatureToGFF3.test.d.ts +1 -0
- package/dist/GFF3/annotationFeatureToGFF3.test.js +156 -0
- package/dist/GFF3/annotationFeatureToGFF3.test.js.map +1 -0
- package/dist/GFF3/gff3ToAnnotationFeature.test.d.ts +2 -1
- package/dist/GFF3/gff3ToAnnotationFeature.test.js +1 -0
- package/dist/GFF3/gff3ToAnnotationFeature.test.js.map +1 -1
- package/dist/GFF3/index.d.ts +1 -0
- package/dist/GFF3/index.js +1 -0
- package/dist/GFF3/index.js.map +1 -1
- package/dist/tsconfig.tsbuildinfo +1 -1
- package/dist/util.d.ts +0 -3
- package/dist/util.js +0 -90
- package/dist/util.js.map +1 -1
- package/package.json +6 -6
- package/src/Checks/CDSCheck.ts +1 -1
- package/src/GFF3/annotationFeatureToGFF3.test.ts +170 -0
- package/src/GFF3/annotationFeatureToGFF3.ts +257 -0
- package/src/GFF3/gff3ToAnnotationFeature.test.ts +3 -1
- package/src/GFF3/index.ts +1 -0
- package/src/util.ts +0 -102
- package/test_data/gene.json +117 -0
package/dist/Checks/CDSCheck.js
CHANGED
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@@ -1 +1 @@
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1
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-
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import { AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
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import { GFF3Feature } from '@gmod/gff';
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export declare function annotationFeatureToGFF3(feature: AnnotationFeatureSnapshot, parentId?: string, refSeqNames?: Record<string, string | undefined>): GFF3Feature;
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"use strict";
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/* eslint-disable @typescript-eslint/no-unsafe-assignment */
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Object.defineProperty(exports, "__esModule", { value: true });
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exports.annotationFeatureToGFF3 = annotationFeatureToGFF3;
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const util_1 = require("@jbrowse/core/util");
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function annotationFeatureToGFF3(feature, parentId, refSeqNames) {
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7
|
+
const attributes = JSON.parse(JSON.stringify(feature.attributes));
|
|
8
|
+
const ontologyTerms = [];
|
|
9
|
+
const source = feature.attributes?.gff_source?.[0] ?? null;
|
|
10
|
+
delete attributes.gff_source;
|
|
11
|
+
if (parentId) {
|
|
12
|
+
attributes.Parent = [parentId];
|
|
13
|
+
}
|
|
14
|
+
if (attributes.gff_id) {
|
|
15
|
+
attributes.ID = attributes.gff_id;
|
|
16
|
+
delete attributes.gff_id;
|
|
17
|
+
}
|
|
18
|
+
else if (feature.children) {
|
|
19
|
+
attributes.ID = [feature._id];
|
|
20
|
+
}
|
|
21
|
+
if (attributes.gff_name) {
|
|
22
|
+
attributes.Name = attributes.gff_name;
|
|
23
|
+
delete attributes.gff_name;
|
|
24
|
+
}
|
|
25
|
+
if (attributes.gff_alias) {
|
|
26
|
+
attributes.Alias = attributes.gff_alias;
|
|
27
|
+
delete attributes.gff_alias;
|
|
28
|
+
}
|
|
29
|
+
if (attributes.gff_target) {
|
|
30
|
+
attributes.Target = attributes.gff_target;
|
|
31
|
+
delete attributes.gff_target;
|
|
32
|
+
}
|
|
33
|
+
if (attributes.gff_gap) {
|
|
34
|
+
attributes.Gap = attributes.gff_gap;
|
|
35
|
+
delete attributes.gff_gap;
|
|
36
|
+
}
|
|
37
|
+
if (attributes.gff_derives_from) {
|
|
38
|
+
attributes.Derives_from = attributes.gff_derives_from;
|
|
39
|
+
delete attributes.gff_derives_from;
|
|
40
|
+
}
|
|
41
|
+
if (attributes.gff_note) {
|
|
42
|
+
attributes.Note = attributes.gff_note;
|
|
43
|
+
delete attributes.gff_note;
|
|
44
|
+
}
|
|
45
|
+
if (attributes.gff_dbxref) {
|
|
46
|
+
attributes.Dbxref = attributes.gff_dbxref;
|
|
47
|
+
delete attributes.gff_dbxref;
|
|
48
|
+
}
|
|
49
|
+
if (attributes.gff_is_circular) {
|
|
50
|
+
attributes.Is_circular = attributes.gff_is_circular;
|
|
51
|
+
delete attributes.gff_is_circular;
|
|
52
|
+
}
|
|
53
|
+
if (attributes.gff_ontology_term) {
|
|
54
|
+
ontologyTerms.push(...attributes.gff_ontology_term);
|
|
55
|
+
delete attributes.gff_ontology_term;
|
|
56
|
+
}
|
|
57
|
+
if (attributes['Gene Ontology']) {
|
|
58
|
+
ontologyTerms.push(...attributes['Gene Ontology']);
|
|
59
|
+
delete attributes['Gene Ontology'];
|
|
60
|
+
}
|
|
61
|
+
if (attributes['Sequence Ontology']) {
|
|
62
|
+
ontologyTerms.push(...attributes['Sequence Ontology']);
|
|
63
|
+
delete attributes['Sequence Ontology'];
|
|
64
|
+
}
|
|
65
|
+
if (ontologyTerms.length > 0) {
|
|
66
|
+
attributes.Ontology_term = ontologyTerms;
|
|
67
|
+
}
|
|
68
|
+
const gff_score = feature.attributes?.gff_score;
|
|
69
|
+
let score = null;
|
|
70
|
+
if (gff_score && gff_score.length > 0) {
|
|
71
|
+
if (gff_score[0]) {
|
|
72
|
+
score = Number(gff_score[0]);
|
|
73
|
+
if (Number.isNaN(score)) {
|
|
74
|
+
score = null;
|
|
75
|
+
}
|
|
76
|
+
}
|
|
77
|
+
delete attributes.gff_score;
|
|
78
|
+
}
|
|
79
|
+
const locations = [{ start: feature.min, end: feature.max }];
|
|
80
|
+
return locations.map((location) => ({
|
|
81
|
+
start: Number(location.start) + 1,
|
|
82
|
+
end: Number(location.end),
|
|
83
|
+
seq_id: refSeqNames ? refSeqNames[feature.refSeq] ?? null : feature.refSeq,
|
|
84
|
+
source,
|
|
85
|
+
type: feature.type,
|
|
86
|
+
score,
|
|
87
|
+
strand: feature.strand ? (feature.strand === 1 ? '+' : '-') : null,
|
|
88
|
+
phase: null,
|
|
89
|
+
attributes: Object.keys(attributes).length > 0 ? attributes : null,
|
|
90
|
+
derived_features: [],
|
|
91
|
+
child_features: prepareChildFeatures(feature, attributes.ID?.[0], refSeqNames),
|
|
92
|
+
}));
|
|
93
|
+
}
|
|
94
|
+
function prepareChildFeatures(feature, parentID, refSeqNames) {
|
|
95
|
+
if (!feature.children) {
|
|
96
|
+
return [];
|
|
97
|
+
}
|
|
98
|
+
if (feature.type === 'mRNA') {
|
|
99
|
+
const child_features = [];
|
|
100
|
+
const cdsLocations = getCdsLocations(feature);
|
|
101
|
+
let cds_idx = 0;
|
|
102
|
+
for (const child of Object.values(feature.children)) {
|
|
103
|
+
const gffChild = annotationFeatureToGFF3(child, parentID, refSeqNames);
|
|
104
|
+
if (child.type === 'CDS') {
|
|
105
|
+
for (const loc of cdsLocations[cds_idx]) {
|
|
106
|
+
const gffCds = JSON.parse(JSON.stringify(gffChild));
|
|
107
|
+
if (gffCds.length != 1) {
|
|
108
|
+
// Do we need this check?
|
|
109
|
+
throw new Error(`Unexpected CDS: ${JSON.stringify(gffCds, null, 2)}`);
|
|
110
|
+
}
|
|
111
|
+
gffCds[0].start = loc.min + 1;
|
|
112
|
+
gffCds[0].end = loc.max;
|
|
113
|
+
gffCds[0].phase = loc.phase.toString();
|
|
114
|
+
gffCds[0].type = loc.type; // Do we need this?
|
|
115
|
+
child_features.push(gffCds);
|
|
116
|
+
}
|
|
117
|
+
cds_idx++;
|
|
118
|
+
}
|
|
119
|
+
else {
|
|
120
|
+
child_features.push(gffChild);
|
|
121
|
+
}
|
|
122
|
+
}
|
|
123
|
+
return child_features;
|
|
124
|
+
}
|
|
125
|
+
return Object.values(feature.children).map((child) => annotationFeatureToGFF3(child, parentID, refSeqNames));
|
|
126
|
+
}
|
|
127
|
+
function getTranscriptParts(feature) {
|
|
128
|
+
if (feature.type !== 'mRNA') {
|
|
129
|
+
throw new Error('Only features of type "mRNA" or equivalent can calculate CDS locations');
|
|
130
|
+
}
|
|
131
|
+
if (!feature.children) {
|
|
132
|
+
throw new Error('no CDS or exons in mRNA');
|
|
133
|
+
}
|
|
134
|
+
// In AnnotationFeatureModel we have `children.values()`
|
|
135
|
+
const children = Object.values(feature.children);
|
|
136
|
+
const cdsChildren = children.filter((child) => child.type === 'CDS');
|
|
137
|
+
if (cdsChildren.length === 0) {
|
|
138
|
+
throw new Error('no CDS in mRNA');
|
|
139
|
+
}
|
|
140
|
+
const transcriptParts = [];
|
|
141
|
+
for (const cds of cdsChildren) {
|
|
142
|
+
const { max: cdsMax, min: cdsMin } = cds;
|
|
143
|
+
const parts = [];
|
|
144
|
+
let hasIntersected = false;
|
|
145
|
+
const exonLocations = [];
|
|
146
|
+
for (const child of children) {
|
|
147
|
+
if (child.type === 'exon') {
|
|
148
|
+
exonLocations.push({ min: child.min, max: child.max });
|
|
149
|
+
}
|
|
150
|
+
}
|
|
151
|
+
exonLocations.sort(({ min: a }, { min: b }) => a - b);
|
|
152
|
+
for (const child of exonLocations) {
|
|
153
|
+
const lastPart = parts.at(-1);
|
|
154
|
+
if (lastPart) {
|
|
155
|
+
parts.push({ min: lastPart.max, max: child.min, type: 'intron' });
|
|
156
|
+
}
|
|
157
|
+
const [start, end] = (0, util_1.intersection2)(cdsMin, cdsMax, child.min, child.max);
|
|
158
|
+
let utrType;
|
|
159
|
+
if (hasIntersected) {
|
|
160
|
+
utrType = feature.strand === 1 ? 'threePrimeUTR' : 'fivePrimeUTR';
|
|
161
|
+
}
|
|
162
|
+
else {
|
|
163
|
+
utrType = feature.strand === 1 ? 'fivePrimeUTR' : 'threePrimeUTR';
|
|
164
|
+
}
|
|
165
|
+
if (start !== undefined && end !== undefined) {
|
|
166
|
+
hasIntersected = true;
|
|
167
|
+
if (start === child.min && end === child.max) {
|
|
168
|
+
parts.push({ min: start, max: end, phase: 0, type: 'CDS' });
|
|
169
|
+
}
|
|
170
|
+
else if (start === child.min) {
|
|
171
|
+
parts.push({ min: start, max: end, phase: 0, type: 'CDS' }, { min: end, max: child.max, type: utrType });
|
|
172
|
+
}
|
|
173
|
+
else if (end === child.max) {
|
|
174
|
+
parts.push({ min: child.min, max: start, type: utrType }, { min: start, max: end, phase: 0, type: 'CDS' });
|
|
175
|
+
}
|
|
176
|
+
else {
|
|
177
|
+
parts.push({ min: child.min, max: start, type: utrType }, { min: start, max: end, phase: 0, type: 'CDS' }, {
|
|
178
|
+
min: end,
|
|
179
|
+
max: child.max,
|
|
180
|
+
type: utrType === 'fivePrimeUTR' ? 'threePrimeUTR' : 'fivePrimeUTR',
|
|
181
|
+
});
|
|
182
|
+
}
|
|
183
|
+
}
|
|
184
|
+
else {
|
|
185
|
+
parts.push({ min: child.min, max: child.max, type: utrType });
|
|
186
|
+
}
|
|
187
|
+
}
|
|
188
|
+
parts.sort(({ min: a }, { min: b }) => a - b);
|
|
189
|
+
if (feature.strand === -1) {
|
|
190
|
+
parts.reverse();
|
|
191
|
+
}
|
|
192
|
+
let nextPhase = 0;
|
|
193
|
+
const phasedParts = parts.map((loc) => {
|
|
194
|
+
if (loc.type !== 'CDS') {
|
|
195
|
+
return loc;
|
|
196
|
+
}
|
|
197
|
+
const phase = nextPhase;
|
|
198
|
+
nextPhase = ((3 - ((loc.max - loc.min - phase + 3) % 3)) % 3);
|
|
199
|
+
return { ...loc, phase };
|
|
200
|
+
});
|
|
201
|
+
transcriptParts.push(phasedParts);
|
|
202
|
+
}
|
|
203
|
+
return transcriptParts;
|
|
204
|
+
}
|
|
205
|
+
function getCdsLocations(feature) {
|
|
206
|
+
const transcriptParts = getTranscriptParts(feature);
|
|
207
|
+
return transcriptParts.map((transcript) => transcript.filter((transcriptPart) => transcriptPart.type === 'CDS'));
|
|
208
|
+
}
|
|
209
|
+
//# sourceMappingURL=annotationFeatureToGFF3.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"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,CACnC,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;QAC5B,MAA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@@ -0,0 +1 @@
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1
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+
export {};
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@@ -0,0 +1,156 @@
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1
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+
"use strict";
|
|
2
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+
Object.defineProperty(exports, "__esModule", { value: true });
|
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3
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+
/* eslint-disable prefer-destructuring */
|
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4
|
+
/* eslint-disable @typescript-eslint/no-floating-promises */
|
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5
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+
const node_test_1 = require("node:test");
|
|
6
|
+
const chai_1 = require("chai");
|
|
7
|
+
const gff3ToAnnotationFeature_test_1 = require("./gff3ToAnnotationFeature.test");
|
|
8
|
+
const annotationFeatureToGFF3_1 = require("./annotationFeatureToGFF3");
|
|
9
|
+
(0, node_test_1.describe)('annotationFeatureToGFF3', () => {
|
|
10
|
+
(0, node_test_1.it)('Test mandatory columns', () => {
|
|
11
|
+
const annotationFeature = (0, gff3ToAnnotationFeature_test_1.readAnnotationFeatureSnapshot)('test_data/gene.json');
|
|
12
|
+
const [gff3Feature] = (0, annotationFeatureToGFF3_1.annotationFeatureToGFF3)(annotationFeature);
|
|
13
|
+
chai_1.assert.deepEqual(gff3Feature.seq_id, 'chr1');
|
|
14
|
+
chai_1.assert.deepEqual(gff3Feature.type, 'gene');
|
|
15
|
+
chai_1.assert.deepEqual(gff3Feature.start, 1000);
|
|
16
|
+
chai_1.assert.deepEqual(gff3Feature.end, 9000);
|
|
17
|
+
chai_1.assert.deepEqual(gff3Feature.strand, '+');
|
|
18
|
+
chai_1.assert.deepEqual(gff3Feature.score, 123);
|
|
19
|
+
chai_1.assert.deepEqual(gff3Feature.source, 'test_data');
|
|
20
|
+
});
|
|
21
|
+
(0, node_test_1.it)('Feature with no children and no gff_id has no ID attribute', () => {
|
|
22
|
+
const annotationFeature = JSON.parse(`{
|
|
23
|
+
"_id": "66d70e4ccc30b55b65e5f619",
|
|
24
|
+
"refSeq": "chr1",
|
|
25
|
+
"type": "gene",
|
|
26
|
+
"min": 999,
|
|
27
|
+
"max": 9000,
|
|
28
|
+
"strand": 1,
|
|
29
|
+
"attributes": {}
|
|
30
|
+
}`);
|
|
31
|
+
const [gff3Feature] = (0, annotationFeatureToGFF3_1.annotationFeatureToGFF3)(annotationFeature);
|
|
32
|
+
chai_1.assert.isUndefined(gff3Feature.attributes?.ID);
|
|
33
|
+
});
|
|
34
|
+
(0, node_test_1.it)('Feature with children and no gff_id has internal _id as ID', () => {
|
|
35
|
+
const annotationFeature = JSON.parse(`{
|
|
36
|
+
"_id": "66d70e4ccc30b55b65e5f619",
|
|
37
|
+
"refSeq": "chr1",
|
|
38
|
+
"type": "gene",
|
|
39
|
+
"min": 999,
|
|
40
|
+
"max": 9000,
|
|
41
|
+
"strand": 1,
|
|
42
|
+
"attributes": {},
|
|
43
|
+
"children": {
|
|
44
|
+
"66d70e4ccc30b55b65e5f618": {
|
|
45
|
+
"_id": "66d70e4ccc30b55b65e5f618",
|
|
46
|
+
"refSeq": "chr1",
|
|
47
|
+
"type": "gene_segment",
|
|
48
|
+
"min": 1049,
|
|
49
|
+
"max": 9000,
|
|
50
|
+
"strand": 1,
|
|
51
|
+
"attributes": {}
|
|
52
|
+
}
|
|
53
|
+
}
|
|
54
|
+
}`);
|
|
55
|
+
const [gff3Feature] = (0, annotationFeatureToGFF3_1.annotationFeatureToGFF3)(annotationFeature);
|
|
56
|
+
chai_1.assert.deepEqual(gff3Feature.attributes?.ID, ['66d70e4ccc30b55b65e5f619']);
|
|
57
|
+
});
|
|
58
|
+
(0, node_test_1.it)('Convert multiple scores', () => {
|
|
59
|
+
const annotationFeature = JSON.parse(`{
|
|
60
|
+
"_id": "66d70e4ccc30b55b65e5f619",
|
|
61
|
+
"refSeq": "chr1",
|
|
62
|
+
"type": "gene",
|
|
63
|
+
"min": 999,
|
|
64
|
+
"max": 9000,
|
|
65
|
+
"strand": 1,
|
|
66
|
+
"attributes": {
|
|
67
|
+
"gff_id": ["gene10001"],
|
|
68
|
+
"gff_score": ["123", "345"]
|
|
69
|
+
}
|
|
70
|
+
}`);
|
|
71
|
+
const [gff3Feature] = (0, annotationFeatureToGFF3_1.annotationFeatureToGFF3)(annotationFeature);
|
|
72
|
+
chai_1.assert.deepEqual(gff3Feature.score, 123);
|
|
73
|
+
});
|
|
74
|
+
(0, node_test_1.it)('Convert invalid score', () => {
|
|
75
|
+
const annotationFeature = JSON.parse(`{
|
|
76
|
+
"_id": "66d70e4ccc30b55b65e5f619",
|
|
77
|
+
"refSeq": "chr1",
|
|
78
|
+
"type": "gene",
|
|
79
|
+
"min": 999,
|
|
80
|
+
"max": 9000,
|
|
81
|
+
"strand": 1,
|
|
82
|
+
"attributes": {
|
|
83
|
+
"gff_id": ["gene10001"],
|
|
84
|
+
"gff_score": ["xyz"]
|
|
85
|
+
}
|
|
86
|
+
}`);
|
|
87
|
+
const [gff3Feature] = (0, annotationFeatureToGFF3_1.annotationFeatureToGFF3)(annotationFeature);
|
|
88
|
+
chai_1.assert.deepEqual(gff3Feature.score, null);
|
|
89
|
+
});
|
|
90
|
+
(0, node_test_1.it)('Convert one gene test attributes', () => {
|
|
91
|
+
const annotationFeature = (0, gff3ToAnnotationFeature_test_1.readAnnotationFeatureSnapshot)('test_data/gene.json');
|
|
92
|
+
const [gff3Feature] = (0, annotationFeatureToGFF3_1.annotationFeatureToGFF3)(annotationFeature);
|
|
93
|
+
chai_1.assert.deepEqual(gff3Feature.attributes?.Name, ['EDEN']);
|
|
94
|
+
chai_1.assert.deepEqual(gff3Feature.attributes?.testid, ['t001', 't003']);
|
|
95
|
+
chai_1.assert.deepEqual(gff3Feature.attributes?.ID, ['gene10001']);
|
|
96
|
+
chai_1.assert.deepEqual(gff3Feature.attributes?.Ontology_term, [
|
|
97
|
+
'GO1234',
|
|
98
|
+
'GO4567',
|
|
99
|
+
'SO1234',
|
|
100
|
+
]);
|
|
101
|
+
chai_1.assert.deepEqual(gff3Feature.attributes?.Alias, ['myalias']);
|
|
102
|
+
chai_1.assert.deepEqual(gff3Feature.attributes?.Target, ['mytarget']);
|
|
103
|
+
chai_1.assert.deepEqual(gff3Feature.attributes?.Gap, ['mygap']);
|
|
104
|
+
chai_1.assert.deepEqual(gff3Feature.attributes?.Derives_from, ['myderives']);
|
|
105
|
+
chai_1.assert.deepEqual(gff3Feature.attributes?.Note, ['mynote']);
|
|
106
|
+
chai_1.assert.deepEqual(gff3Feature.attributes?.Dbxref, ['mydbxref']);
|
|
107
|
+
chai_1.assert.deepEqual(gff3Feature.attributes?.Is_circular, ['true']);
|
|
108
|
+
});
|
|
109
|
+
(0, node_test_1.it)('Convert one gene test children', () => {
|
|
110
|
+
const annotationFeature = (0, gff3ToAnnotationFeature_test_1.readAnnotationFeatureSnapshot)('test_data/gene.json');
|
|
111
|
+
const [gff3Feature] = (0, annotationFeatureToGFF3_1.annotationFeatureToGFF3)(annotationFeature);
|
|
112
|
+
const [children] = gff3Feature.child_features;
|
|
113
|
+
const [mrna] = children;
|
|
114
|
+
chai_1.assert.deepEqual(mrna.type, 'mRNA');
|
|
115
|
+
chai_1.assert.deepEqual(mrna.attributes?.Parent, ['gene10001']);
|
|
116
|
+
const [cds] = mrna.child_features[2];
|
|
117
|
+
chai_1.assert.deepEqual(cds.type, 'CDS');
|
|
118
|
+
chai_1.assert.deepEqual(cds.attributes?.ID, ['cds10001']);
|
|
119
|
+
chai_1.assert.deepEqual(cds.attributes?.Parent, ['mRNA10001']);
|
|
120
|
+
});
|
|
121
|
+
(0, node_test_1.it)('Convert CDSs', () => {
|
|
122
|
+
const annotationFeature = (0, gff3ToAnnotationFeature_test_1.readAnnotationFeatureSnapshot)('test_data/gene.json');
|
|
123
|
+
const [gff3Feature] = (0, annotationFeatureToGFF3_1.annotationFeatureToGFF3)(annotationFeature);
|
|
124
|
+
const [children] = gff3Feature.child_features;
|
|
125
|
+
const [mrna] = children;
|
|
126
|
+
const cds10001 = mrna.child_features.filter((child) => {
|
|
127
|
+
const id = child[0].attributes?.ID;
|
|
128
|
+
return id !== undefined && id[0] === 'cds10001';
|
|
129
|
+
});
|
|
130
|
+
chai_1.assert.deepEqual(cds10001.length, 2);
|
|
131
|
+
const cds1_1 = cds10001[0][0];
|
|
132
|
+
chai_1.assert.deepEqual(cds1_1.attributes?.ID, ['cds10001']);
|
|
133
|
+
chai_1.assert.deepEqual(cds1_1.start, 1201);
|
|
134
|
+
chai_1.assert.deepEqual(cds1_1.end, 1500);
|
|
135
|
+
chai_1.assert.deepEqual(cds1_1.phase, '0');
|
|
136
|
+
const cds1_2 = cds10001[1][0];
|
|
137
|
+
chai_1.assert.deepEqual(cds1_2.attributes?.ID, ['cds10001']);
|
|
138
|
+
chai_1.assert.deepEqual(cds1_2.start, 5000);
|
|
139
|
+
chai_1.assert.deepEqual(cds1_2.end, 5100);
|
|
140
|
+
chai_1.assert.deepEqual(cds1_2.phase, '0');
|
|
141
|
+
chai_1.assert.deepEqual(cds1_1.child_features[0][0].attributes?.ID, [
|
|
142
|
+
'cds_region10001',
|
|
143
|
+
]);
|
|
144
|
+
chai_1.assert.deepEqual(cds1_1.child_features[0][0].start, 1351);
|
|
145
|
+
chai_1.assert.deepEqual(cds1_1.child_features[0][0].end, 1400);
|
|
146
|
+
chai_1.assert.deepEqual(cds1_1.child_features[0][0].phase, null);
|
|
147
|
+
const cds10004 = mrna.child_features.filter((child) => {
|
|
148
|
+
const id = child[0].attributes?.ID;
|
|
149
|
+
return id !== undefined && id[0] === 'cds10004';
|
|
150
|
+
});
|
|
151
|
+
chai_1.assert.deepEqual(cds10004.length, 2);
|
|
152
|
+
const cds4_1 = cds10004[0][0];
|
|
153
|
+
chai_1.assert.deepEqual(cds4_1.attributes?.ID, ['cds10004']);
|
|
154
|
+
});
|
|
155
|
+
});
|
|
156
|
+
//# sourceMappingURL=annotationFeatureToGFF3.test.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"annotationFeatureToGFF3.test.js","sourceRoot":"","sources":["../../src/GFF3/annotationFeatureToGFF3.test.ts"],"names":[],"mappings":";;AAAA,yCAAyC;AACzC,4DAA4D;AAC5D,yCAAwC;AACxC,+BAA6B;AAC7B,iFAA8E;AAC9E,uEAAmE;AAGnE,IAAA,oBAAQ,EAAC,yBAAyB,EAAE,GAAG,EAAE;IACvC,IAAA,cAAE,EAAC,wBAAwB,EAAE,GAAG,EAAE;QAChC,MAAM,iBAAiB,GAAG,IAAA,4DAA6B,EACrD,qBAAqB,CACtB,CAAA;QACD,MAAM,CAAC,WAAW,CAAC,GAAG,IAAA,iDAAuB,EAAC,iBAAiB,CAAC,CAAA;QAEhE,aAAM,CAAC,SAAS,CAAC,WAAW,CAAC,MAAM,EAAE,MAAM,CAAC,CAAA;QAC5C,aAAM,CAAC,SAAS,CAAC,WAAW,CAAC,IAAI,EAAE,MAAM,CAAC,CAAA;QAC1C,aAAM,CAAC,SAAS,CAAC,WAAW,CAAC,KAAK,EAAE,IAAI,CAAC,CAAA;QACzC,aAAM,CAAC,SAAS,CAAC,WAAW,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;QACvC,aAAM,CAAC,SAAS,CAAC,WAAW,CAAC,MAAM,EAAE,GAAG,CAAC,CAAA;QACzC,aAAM,CAAC,SAAS,CAAC,WAAW,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;QACxC,aAAM,CAAC,SAAS,CAAC,WAAW,CAAC,MAAM,EAAE,WAAW,CAAC,CAAA;IACnD,CAAC,CAAC,CAAA;IACF,IAAA,cAAE,EAAC,4DAA4D,EAAE,GAAG,EAAE;QACpE,MAAM,iBAAiB,GAAG,IAAI,CAAC,KAAK,CAAC;;;;;;;;MAQnC,CAA8B,CAAA;QAChC,MAAM,CAAC,WAAW,CAAC,GAAG,IAAA,iDAAuB,EAAC,iBAAiB,CAAC,CAAA;QAChE,aAAM,CAAC,WAAW,CAAC,WAAW,CAAC,UAAU,EAAE,EAAE,CAAC,CAAA;IAChD,CAAC,CAAC,CAAA;IACF,IAAA,cAAE,EAAC,4DAA4D,EAAE,GAAG,EAAE;QACpE,MAAM,iBAAiB,GAAG,IAAI,CAAC,KAAK,CAAC;;;;;;;;;;;;;;;;;;;MAmBnC,CAA8B,CAAA;QAChC,MAAM,CAAC,WAAW,CAAC,GAAG,IAAA,iDAAuB,EAAC,iBAAiB,CAAC,CAAA;QAChE,aAAM,CAAC,SAAS,CAAC,WAAW,CAAC,UAAU,EAAE,EAAE,EAAE,CAAC,0BAA0B,CAAC,CAAC,CAAA;IAC5E,CAAC,CAAC,CAAA;IACF,IAAA,cAAE,EAAC,yBAAyB,EAAE,GAAG,EAAE;QACjC,MAAM,iBAAiB,GAAG,IAAI,CAAC,KAAK,CAAC;;;;;;;;;;;MAWnC,CAA8B,CAAA;QAChC,MAAM,CAAC,WAAW,CAAC,GAAG,IAAA,iDAAuB,EAAC,iBAAiB,CAAC,CAAA;QAChE,aAAM,CAAC,SAAS,CAAC,WAAW,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;IAC1C,CAAC,CAAC,CAAA;IACF,IAAA,cAAE,EAAC,uBAAuB,EAAE,GAAG,EAAE;QAC/B,MAAM,iBAAiB,GAAG,IAAI,CAAC,KAAK,CAAC;;;;;;;;;;;MAWnC,CAA8B,CAAA;QAChC,MAAM,CAAC,WAAW,CAAC,GAAG,IAAA,iDAAuB,EAAC,iBAAiB,CAAC,CAAA;QAChE,aAAM,CAAC,SAAS,CAAC,WAAW,CAAC,KAAK,EAAE,IAAI,CAAC,CAAA;IAC3C,CAAC,CAAC,CAAA;IACF,IAAA,cAAE,EAAC,kCAAkC,EAAE,GAAG,EAAE;QAC1C,MAAM,iBAAiB,GAAG,IAAA,4DAA6B,EACrD,qBAAqB,CACtB,CAAA;QACD,MAAM,CAAC,WAAW,CAAC,GAAG,IAAA,iDAAuB,EAAC,iBAAiB,CAAC,CAAA;QAEhE,aAAM,CAAC,SAAS,CAAC,WAAW,CAAC,UAAU,EAAE,IAAI,EAAE,CAAC,MAAM,CAAC,CAAC,CAAA;QACxD,aAAM,CAAC,SAAS,CAAC,WAAW,CAAC,UAAU,EAAE,MAAM,EAAE,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC,CAAA;QAClE,aAAM,CAAC,SAAS,CAAC,WAAW,CAAC,UAAU,EAAE,EAAE,EAAE,CAAC,WAAW,CAAC,CAAC,CAAA;QAC3D,aAAM,CAAC,SAAS,CAAC,WAAW,CAAC,UAAU,EAAE,aAAa,EAAE;YACtD,QAAQ;YACR,QAAQ;YACR,QAAQ;SACT,CAAC,CAAA;QACF,aAAM,CAAC,SAAS,CAAC,WAAW,CAAC,UAAU,EAAE,KAAK,EAAE,CAAC,SAAS,CAAC,CAAC,CAAA;QAC5D,aAAM,CAAC,SAAS,CAAC,WAAW,CAAC,UAAU,EAAE,MAAM,EAAE,CAAC,UAAU,CAAC,CAAC,CAAA;QAC9D,aAAM,CAAC,SAAS,CAAC,WAAW,CAAC,UAAU,EAAE,GAAG,EAAE,CAAC,OAAO,CAAC,CAAC,CAAA;QACxD,aAAM,CAAC,SAAS,CAAC,WAAW,CAAC,UAAU,EAAE,YAAY,EAAE,CAAC,WAAW,CAAC,CAAC,CAAA;QACrE,aAAM,CAAC,SAAS,CAAC,WAAW,CAAC,UAAU,EAAE,IAAI,EAAE,CAAC,QAAQ,CAAC,CAAC,CAAA;QAC1D,aAAM,CAAC,SAAS,CAAC,WAAW,CAAC,UAAU,EAAE,MAAM,EAAE,CAAC,UAAU,CAAC,CAAC,CAAA;QAC9D,aAAM,CAAC,SAAS,CAAC,WAAW,CAAC,UAAU,EAAE,WAAW,EAAE,CAAC,MAAM,CAAC,CAAC,CAAA;IACjE,CAAC,CAAC,CAAA;IACF,IAAA,cAAE,EAAC,gCAAgC,EAAE,GAAG,EAAE;QACxC,MAAM,iBAAiB,GAAG,IAAA,4DAA6B,EACrD,qBAAqB,CACtB,CAAA;QACD,MAAM,CAAC,WAAW,CAAC,GAAG,IAAA,iDAAuB,EAAC,iBAAiB,CAAC,CAAA;QAChE,MAAM,CAAC,QAAQ,CAAC,GAAG,WAAW,CAAC,cAAc,CAAA;QAC7C,MAAM,CAAC,IAAI,CAAC,GAAG,QAAQ,CAAA;QACvB,aAAM,CAAC,SAAS,CAAC,IAAI,CAAC,IAAI,EAAE,MAAM,CAAC,CAAA;QACnC,aAAM,CAAC,SAAS,CAAC,IAAI,CAAC,UAAU,EAAE,MAAM,EAAE,CAAC,WAAW,CAAC,CAAC,CAAA;QAExD,MAAM,CAAC,GAAG,CAAC,GAAG,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,CAAA;QACpC,aAAM,CAAC,SAAS,CAAC,GAAG,CAAC,IAAI,EAAE,KAAK,CAAC,CAAA;QACjC,aAAM,CAAC,SAAS,CAAC,GAAG,CAAC,UAAU,EAAE,EAAE,EAAE,CAAC,UAAU,CAAC,CAAC,CAAA;QAClD,aAAM,CAAC,SAAS,CAAC,GAAG,CAAC,UAAU,EAAE,MAAM,EAAE,CAAC,WAAW,CAAC,CAAC,CAAA;IACzD,CAAC,CAAC,CAAA;IACF,IAAA,cAAE,EAAC,cAAc,EAAE,GAAG,EAAE;QACtB,MAAM,iBAAiB,GAAG,IAAA,4DAA6B,EACrD,qBAAqB,CACtB,CAAA;QACD,MAAM,CAAC,WAAW,CAAC,GAAG,IAAA,iDAAuB,EAAC,iBAAiB,CAAC,CAAA;QAChE,MAAM,CAAC,QAAQ,CAAC,GAAG,WAAW,CAAC,cAAc,CAAA;QAC7C,MAAM,CAAC,IAAI,CAAC,GAAG,QAAQ,CAAA;QACvB,MAAM,QAAQ,GAAG,IAAI,CAAC,cAAc,CAAC,MAAM,CAAC,CAAC,KAAK,EAAE,EAAE;YACpD,MAAM,EAAE,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,UAAU,EAAE,EAAE,CAAA;YAClC,OAAO,EAAE,KAAK,SAAS,IAAI,EAAE,CAAC,CAAC,CAAC,KAAK,UAAU,CAAA;QACjD,CAAC,CAAC,CAAA;QACF,aAAM,CAAC,SAAS,CAAC,QAAQ,CAAC,MAAM,EAAE,CAAC,CAAC,CAAA;QAEpC,MAAM,MAAM,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QAC7B,aAAM,CAAC,SAAS,CAAC,MAAM,CAAC,UAAU,EAAE,EAAE,EAAE,CAAC,UAAU,CAAC,CAAC,CAAA;QACrD,aAAM,CAAC,SAAS,CAAC,MAAM,CAAC,KAAK,EAAE,IAAI,CAAC,CAAA;QACpC,aAAM,CAAC,SAAS,CAAC,MAAM,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;QAClC,aAAM,CAAC,SAAS,CAAC,MAAM,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;QAEnC,MAAM,MAAM,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QAC7B,aAAM,CAAC,SAAS,CAAC,MAAM,CAAC,UAAU,EAAE,EAAE,EAAE,CAAC,UAAU,CAAC,CAAC,CAAA;QACrD,aAAM,CAAC,SAAS,CAAC,MAAM,CAAC,KAAK,EAAE,IAAI,CAAC,CAAA;QACpC,aAAM,CAAC,SAAS,CAAC,MAAM,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;QAClC,aAAM,CAAC,SAAS,CAAC,MAAM,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;QAEnC,aAAM,CAAC,SAAS,CAAC,MAAM,CAAC,cAAc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|
|
@@ -1 +1,2 @@
|
|
|
1
|
-
|
|
1
|
+
import { AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
|
|
2
|
+
export declare function readAnnotationFeatureSnapshot(fn: string): AnnotationFeatureSnapshot;
|
|
@@ -1,5 +1,6 @@
|
|
|
1
1
|
"use strict";
|
|
2
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
|
+
exports.readAnnotationFeatureSnapshot = readAnnotationFeatureSnapshot;
|
|
3
4
|
const tslib_1 = require("tslib");
|
|
4
5
|
/* eslint-disable @typescript-eslint/no-floating-promises */
|
|
5
6
|
const node_test_1 = require("node:test");
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"gff3ToAnnotationFeature.test.js","sourceRoot":"","sources":["../../src/GFF3/gff3ToAnnotationFeature.test.ts"],"names":[],"mappings":"
|
|
1
|
+
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|
package/dist/GFF3/index.d.ts
CHANGED
package/dist/GFF3/index.js
CHANGED
|
@@ -1,6 +1,7 @@
|
|
|
1
1
|
"use strict";
|
|
2
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
3
|
const tslib_1 = require("tslib");
|
|
4
|
+
tslib_1.__exportStar(require("./annotationFeatureToGFF3"), exports);
|
|
4
5
|
tslib_1.__exportStar(require("./gffReservedKeys"), exports);
|
|
5
6
|
tslib_1.__exportStar(require("./gff3ToAnnotationFeature"), exports);
|
|
6
7
|
//# sourceMappingURL=index.js.map
|
package/dist/GFF3/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/GFF3/index.ts"],"names":[],"mappings":";;;AAAA,4DAAiC;AACjC,oEAAyC"}
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/GFF3/index.ts"],"names":[],"mappings":";;;AAAA,oEAAyC;AACzC,4DAAiC;AACjC,oEAAyC"}
|