gff-nostream 3.0.2 → 3.0.5
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/README.md +21 -72
- package/dist/api.js +14 -21
- package/dist/api.js.map +1 -1
- package/dist/util.js +112 -218
- package/dist/util.js.map +1 -1
- package/esm/api.js +14 -21
- package/esm/api.js.map +1 -1
- package/esm/util.js +112 -218
- package/esm/util.js.map +1 -1
- package/package.json +27 -31
- package/src/api.ts +14 -21
- package/src/util.ts +146 -241
package/README.md
CHANGED
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@@ -1,38 +1,29 @@
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# gff-nostream
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[](https://npmjs.org/package/gff-nostream)
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[](https://github.com/GMOD/gff-nostream/actions?query=branch%3Amain+workflow%3APush+)
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Parse GFF3 data.
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[@gmod/gff](https://github.com/GMOD/gff-js) with just basic parsing and no
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node.js stream module usage
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Parse GFF3 data. A simplified version of [@gmod/gff](https://github.com/GMOD/gff-js) with no Node.js stream dependency.
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## Install
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$ npm install
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$ npm install gff-nostream
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## Usage
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```js
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const { parseStringSync } = require('gff-nostream')
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// or in ES6 (recommended)
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import { parseStringSync } from 'gff-nostream'
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import fs from 'fs'
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const fs = require('fs')
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// parse a string of gff3 synchronously
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const stringOfGFF3 = fs.readFileSync('my_annotations.gff3', 'utf8')
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const
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const features = parseStringSync(stringOfGFF3)
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```
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## Object format
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In GFF3, features can have more than one location. We parse features as
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arrayrefs of all the lines that share that feature's ID. Values that are `.` in
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the GFF3 are `null` in the output.
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In GFF3, features can have more than one location. Features are returned as arrays of all lines sharing the same ID. Values that are `.` in GFF3 are `null` in the output.
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A simple feature
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A simple feature located in one place:
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```json
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[
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## API
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#### Table of Contents
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- [ParseOptions](#parseoptions)
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- [disableDerivesFromReferences](#disablederivesfromreferences)
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- [encoding](#encoding)
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- [parseFeatures](#parsefeatures)
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- [parseDirectives](#parsedirectives)
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- [parseComments](#parsecomments)
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- [parseSequences](#parsesequences)
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- [parseAll](#parseall)
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### ParseOptions
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Parser options
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#### disableDerivesFromReferences
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Whether to resolve references to derives from features
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Type:
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[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)
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### `parseStringSync(str: string): GFF3Feature[]`
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Synchronously parse a GFF3 string and return an array of features.
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### `parseStringSyncJBrowse(str: string): JBrowseFeature[]`
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Synchronously parse a GFF3 string and return features in JBrowse format (flat objects with `subfeatures` instead of `child_features`).
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### `parseRecords(records: LineRecord[]): GFF3Feature[]`
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Parse an array of `LineRecord` objects. Useful when managing raw line data directly (e.g. from an indexed file with byte offsets).
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[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)
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### `parseRecordsJBrowse(records: LineRecord[]): JBrowseFeature[]`
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Same as `parseRecords` but returns JBrowse-format features.
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## Publishing
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[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)
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[Trusted publishing](https://docs.npmjs.com/about-trusted-publishing) via GitHub Actions.
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Type:
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[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)
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#### parseSequences
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Whether to parse sequences, default true
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Type:
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[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)
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#### parseAll
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Parse all features, directives, comments, and sequences. Overrides other parsing
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options. Default false.
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Type:
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[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)
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```bash
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npm version patch # or minor/major
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```
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package/dist/api.js
CHANGED
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@@ -27,15 +27,14 @@ function parseStringSyncJBrowse(str) {
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function stringToRecords(str) {
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const lines = str.split(/\r?\n/);
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const records = [];
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for (
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if (line.length === 0 || line[0] === '#') {
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for (const line of lines) {
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if (line.length === 0 || line.startsWith('#')) {
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if (line.startsWith('##FASTA')) {
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break;
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}
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continue;
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}
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if (line
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if (line.startsWith('>')) {
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break;
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}
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records.push({
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const items = [];
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const byId = new Map();
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const orphans = new Map();
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for (
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const record = records[i];
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for (const record of records) {
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const featureLine = (record.hasEscapes
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? (0, util_ts_1.parseFeature)(record.line)
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: (0, util_ts_1.parseFeatureNoUnescape)(record.line));
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featureLine.child_features = [];
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featureLine.derived_features = [];
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if (record.lineHash !== undefined) {
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featureLine.attributes = {};
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}
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featureLine.attributes ??= {};
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featureLine.attributes._lineHash = [String(record.lineHash)];
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}
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const attrs = featureLine.attributes;
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byId.set(id, feature);
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const waiting = orphans.get(id);
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if (waiting) {
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for (
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featureLine.child_features.push(
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for (const w of waiting) {
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featureLine.child_features.push(w);
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orphans.delete(id);
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}
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feature = [featureLine];
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}
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if (parents) {
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for (
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const parentId = parents[j];
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for (const parentId of parents) {
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const parent = byId.get(parentId);
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for (
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for (const p of parent) {
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p.child_features.push(feature);
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const byId = new Map();
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const orphans = new Map();
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for (
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const record = records[i];
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for (const record of records) {
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const feature = record.hasEscapes
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? (0, util_ts_1.parseFeatureJBrowse)(record.line)
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byId.set(id, feature);
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for (
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feature.subfeatures.push(
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for (const w of waiting) {
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feature.subfeatures.push(w);
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orphans.delete(id);
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if (parent) {
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const parents = Array.isArray(parent) ? parent : [parent];
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for (
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const parentId = parents[j];
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for (const parentId of parents) {
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const parentFeature = byId.get(parentId);
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if (parentFeature) {
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parentFeature.subfeatures.push(feature);
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package/dist/api.js.map
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{"version":3,"file":"api.js","sourceRoot":"","sources":["../src/api.ts"],"names":[],"mappings":";;AA4BA,0CAEC;AAQD,wDAEC;
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