gff-nostream 1.3.1

package/esm/util.js

@@ -0,0 +1,268 @@
+// Fast, low-level functions for parsing and formatting GFF3.
+// JavaScript port of Robert Buels's Bio::GFF3::LowLevel Perl module.
+/**
+ * Unescape a string value used in a GFF3 attribute.
+ *
+ * @param stringVal - Escaped GFF3 string value
+ * @returns An unescaped string value
+ */
+export function unescape(stringVal) {
+    return stringVal.replaceAll(/%([0-9A-Fa-f]{2})/g, (_match, seq) => String.fromCharCode(parseInt(seq, 16)));
+}
+function _escape(regex, s) {
+    return String(s).replace(regex, ch => {
+        const hex = ch.charCodeAt(0).toString(16).toUpperCase().padStart(2, '0');
+        return `%${hex}`;
+    });
+}
+/**
+ * Escape a value for use in a GFF3 attribute value.
+ *
+ * @param rawVal - Raw GFF3 attribute value
+ * @returns An escaped string value
+ */
+export function escape(rawVal) {
+    return _escape(/[\n;\r\t=%&,\u0000-\u001f\u007f-\u00ff]/g, rawVal);
+}
+/**
+ * Escape a value for use in a GFF3 column value.
+ *
+ * @param rawVal - Raw GFF3 column value
+ * @returns An escaped column value
+ */
+export function escapeColumn(rawVal) {
+    return _escape(/[\n\r\t%\u0000-\u001f\u007f-\u00ff]/g, rawVal);
+}
+/**
+ * Parse the 9th column (attributes) of a GFF3 feature line.
+ *
+ * @param attrString - String of GFF3 9th column
+ * @returns Parsed attributes
+ */
+export function parseAttributes(attrString) {
+    if (!attrString.length || attrString === '.') {
+        return {};
+    }
+    const attrs = {};
+    attrString
+        .replace(/\r?\n$/, '')
+        .split(';')
+        .forEach(a => {
+        var _a;
+        const nv = a.split('=', 2);
+        if (!((_a = nv[1]) === null || _a === void 0 ? void 0 : _a.length)) {
+            return;
+        }
+        nv[0] = nv[0].trim();
+        let arec = attrs[nv[0].trim()];
+        if (!arec) {
+            arec = [];
+            attrs[nv[0]] = arec;
+        }
+        arec.push(...nv[1]
+            .split(',')
+            .map(s => s.trim())
+            .map(unescape));
+    });
+    return attrs;
+}
+/**
+ * Parse a GFF3 feature line
+ *
+ * @param line - GFF3 feature line
+ * @returns The parsed feature
+ */
+export function parseFeature(line) {
+    // split the line into columns and replace '.' with null in each column
+    const f = line.split('\t').map(a => (a === '.' || a === '' ? null : a));
+    // unescape only the ref, source, and type columns
+    const parsed = {
+        seq_id: f[0] && unescape(f[0]),
+        source: f[1] && unescape(f[1]),
+        type: f[2] && unescape(f[2]),
+        start: f[3] === null ? null : parseInt(f[3], 10),
+        end: f[4] === null ? null : parseInt(f[4], 10),
+        score: f[5] === null ? null : parseFloat(f[5]),
+        strand: f[6],
+        phase: f[7],
+        attributes: f[8] === null ? null : parseAttributes(f[8]),
+    };
+    return parsed;
+}
+/**
+ * Parse a GFF3 directive line.
+ *
+ * @param line - GFF3 directive line
+ * @returns The parsed directive
+ */
+export function parseDirective(line) {
+    var _a, _b;
+    const match = /^\s*##\s*(\S+)\s*(.*)/.exec(line);
+    if (!match) {
+        return null;
+    }
+    const [, name] = match;
+    let [, , contents] = match;
+    const parsed = { directive: name };
+    if (contents.length) {
+        contents = contents.replace(/\r?\n$/, '');
+        parsed.value = contents;
+    }
+    // do a little additional parsing for sequence-region and genome-build directives
+    if (name === 'sequence-region') {
+        const c = contents.split(/\s+/, 3);
+        return {
+            ...parsed,
+            seq_id: c[0],
+            start: (_a = c[1]) === null || _a === void 0 ? void 0 : _a.replaceAll(/\D/g, ''),
+            end: (_b = c[2]) === null || _b === void 0 ? void 0 : _b.replaceAll(/\D/g, ''),
+        };
+    }
+    else if (name === 'genome-build') {
+        const [source, buildName] = contents.split(/\s+/, 2);
+        return {
+            ...parsed,
+            source,
+            buildName,
+        };
+    }
+    return parsed;
+}
+/**
+ * Format an attributes object into a string suitable for the 9th column of GFF3.
+ *
+ * @param attrs - Attributes
+ * @returns GFF3 9th column string
+ */
+export function formatAttributes(attrs) {
+    const attrOrder = [];
+    Object.entries(attrs).forEach(([tag, val]) => {
+        if (!val) {
+            return;
+        }
+        let valstring;
+        if (val.hasOwnProperty('toString')) {
+            valstring = escape(val.toString());
+            // } else if (Array.isArray(val.values)) {
+            //   valstring = val.values.map(escape).join(',')
+        }
+        else if (Array.isArray(val)) {
+            valstring = val.map(escape).join(',');
+        }
+        else {
+            valstring = escape(val);
+        }
+        attrOrder.push(`${escape(tag)}=${valstring}`);
+    });
+    return attrOrder.length ? attrOrder.join(';') : '.';
+}
+function _formatSingleFeature(f, seenFeature) {
+    const attrString = f.attributes === null || f.attributes === undefined
+        ? '.'
+        : formatAttributes(f.attributes);
+    const fields = [
+        f.seq_id === null ? '.' : escapeColumn(f.seq_id),
+        f.source === null ? '.' : escapeColumn(f.source),
+        f.type === null ? '.' : escapeColumn(f.type),
+        f.start === null ? '.' : escapeColumn(f.start),
+        f.end === null ? '.' : escapeColumn(f.end),
+        f.score === null ? '.' : escapeColumn(f.score),
+        f.strand === null ? '.' : escapeColumn(f.strand),
+        f.phase === null ? '.' : escapeColumn(f.phase),
+        attrString,
+    ];
+    const formattedString = `${fields.join('\t')}\n`;
+    // if we have already output this exact feature, skip it
+    if (seenFeature[formattedString]) {
+        return '';
+    }
+    seenFeature[formattedString] = true;
+    return formattedString;
+}
+function _formatFeature(feature, seenFeature) {
+    if (Array.isArray(feature)) {
+        return feature.map(f => _formatFeature(f, seenFeature)).join('');
+    }
+    const strings = [_formatSingleFeature(feature, seenFeature)];
+    if (_isFeatureLineWithRefs(feature)) {
+        strings.push(...feature.child_features.map(f => _formatFeature(f, seenFeature)), ...feature.derived_features.map(f => _formatFeature(f, seenFeature)));
+    }
+    return strings.join('');
+}
+/**
+ * Format a feature object or array of feature objects into one or more lines of
+ * GFF3.
+ *
+ * @param featureOrFeatures - A feature object or array of feature objects
+ * @returns A string of one or more GFF3 lines
+ */
+export function formatFeature(featureOrFeatures) {
+    const seen = {};
+    return _formatFeature(featureOrFeatures, seen);
+}
+/**
+ * Format a directive into a line of GFF3.
+ *
+ * @param directive - A directive object
+ * @returns A directive line string
+ */
+export function formatDirective(directive) {
+    let str = `##${directive.directive}`;
+    if (directive.value) {
+        str += ` ${directive.value}`;
+    }
+    str += '\n';
+    return str;
+}
+/**
+ * Format a comment into a GFF3 comment.
+ * Yes I know this is just adding a # and a newline.
+ *
+ * @param comment - A comment object
+ * @returns A comment line string
+ */
+export function formatComment(comment) {
+    return `# ${comment.comment}\n`;
+}
+/**
+ * Format a sequence object as FASTA
+ *
+ * @param seq - A sequence object
+ * @returns Formatted single FASTA sequence string
+ */
+export function formatSequence(seq) {
+    return `>${seq.id}${seq.description ? ` ${seq.description}` : ''}\n${seq.sequence}\n`;
+}
+/**
+ * Format a directive, comment, sequence, or feature, or array of such items,
+ * into one or more lines of GFF3.
+ *
+ * @param itemOrItems - A comment, sequence, or feature, or array of such items
+ * @returns A formatted string or array of strings
+ */
+export function formatItem(itemOrItems) {
+    function formatSingleItem(item) {
+        if ('attributes' in item) {
+            return formatFeature(item);
+        }
+        if ('directive' in item) {
+            return formatDirective(item);
+        }
+        if ('sequence' in item) {
+            return formatSequence(item);
+        }
+        if ('comment' in item) {
+            return formatComment(item);
+        }
+        return '# (invalid item found during format)\n';
+    }
+    if (Array.isArray(itemOrItems)) {
+        return itemOrItems.map(formatSingleItem);
+    }
+    return formatSingleItem(itemOrItems);
+}
+function _isFeatureLineWithRefs(featureLine) {
+    return (featureLine.child_features !== undefined &&
+        featureLine.derived_features !== undefined);
+}
+//# sourceMappingURL=util.js.map

package/esm/util.js.map

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package/package.json

@@ -0,0 +1,52 @@
+{
+  "name": "gff-nostream",
+  "version": "1.3.1",
+  "description": "utilities to read GFF3 data",
+  "license": "MIT",
+  "repository": "cmdcolin/gff-nostream",
+  "main": "dist/index.js",
+  "module": "esm/index.js",
+  "author": {
+    "name": "Colin Diesh",
+    "email": "colin.diesh@gmail.com",
+    "url": "https://github.com/cmdcolin"
+  },
+  "files": [
+    "dist",
+    "esm",
+    "src"
+  ],
+  "scripts": {
+    "test": "vitest",
+    "clean": "rimraf dist esm",
+    "lint": "eslint src test",
+    "docs": "documentation readme src/api.ts --section=API  --shallow && npm run format",
+    "format": "prettier --write .",
+    "prebuild": "npm run clean",
+    "build:esm": "tsc --target es2018 --outDir esm",
+    "build:es5": "tsc --target es2015 --module commonjs --outDir dist",
+    "build": "npm run build:es5 && npm run build:esm",
+    "prepublishOnly": "npm run test run && npm run build",
+    "postversion": "git push --follow-tags"
+  },
+  "keywords": [
+    "bionode",
+    "biojs",
+    "gff3",
+    "gff",
+    "genomics"
+  ],
+  "devDependencies": {
+    "@types/node": "^20.14.7",
+    "@typescript-eslint/eslint-plugin": "^8.4.0",
+    "@typescript-eslint/parser": "^8.4.0",
+    "@vitest/coverage-v8": "^2.0.5",
+    "documentation": "^14.0.1",
+    "eslint": "^9.9.1",
+    "prettier": "^3.3.3",
+    "rimraf": "^6.0.1",
+    "typescript": "^5.5.4",
+    "typescript-eslint": "^8.4.0",
+    "vitest": "^2.0.5"
+  }
+}

package/src/api.ts

@@ -0,0 +1,86 @@
+import Parser from './parse'
+import { GFF3Item } from './util'
+
+/** Parser options */
+export interface ParseOptions {
+  /** Whether to resolve references to derives from features */
+  disableDerivesFromReferences?: boolean
+  /** Text encoding of the input GFF3. default 'utf8' */
+  encoding?: BufferEncoding
+  /** Whether to parse features, default true */
+  parseFeatures?: boolean
+  /** Whether to parse directives, default false */
+  parseDirectives?: boolean
+  /** Whether to parse comments, default false */
+  parseComments?: boolean
+  /** Whether to parse sequences, default true */
+  parseSequences?: boolean
+  /**
+   * Parse all features, directives, comments, and sequences. Overrides other
+   * parsing options. Default false.
+   */
+  parseAll?: boolean
+}
+
+type ParseOptionsProcessed = Required<Omit<ParseOptions, 'parseAll'>>
+
+// shared arg processing for the parse routines
+function _processParseOptions(options: ParseOptions): ParseOptionsProcessed {
+  const out = {
+    encoding: 'utf8' as const,
+    parseFeatures: true,
+    parseDirectives: false,
+    parseSequences: true,
+    parseComments: false,
+    disableDerivesFromReferences: false,
+    ...options,
+  }
+
+  if (options.parseAll) {
+    out.parseFeatures = true
+    out.parseDirectives = true
+    out.parseComments = true
+    out.parseSequences = true
+  }
+
+  return out
+}
+
+export function parseStringSync(
+  str: string,
+  inputOptions: ParseOptions = {},
+): GFF3Item[] {
+  if (!str) {
+    return []
+  }
+
+  const options = _processParseOptions(inputOptions)
+  const items: GFF3Item[] = []
+  const push = items.push.bind(items)
+
+  const parser = new Parser({
+    featureCallback: options.parseFeatures ? push : undefined,
+    directiveCallback: options.parseDirectives ? push : undefined,
+    commentCallback: options.parseComments ? push : undefined,
+    sequenceCallback: options.parseSequences ? push : undefined,
+    disableDerivesFromReferences: options.disableDerivesFromReferences || false,
+    errorCallback: err => {
+      throw err
+    },
+  })
+
+  str.split(/\r?\n/).forEach(parser.addLine.bind(parser))
+  parser.finish()
+
+  return items
+}
+
+export {
+  type GFF3FeatureLine,
+  type GFF3Comment,
+  type GFF3FeatureLineWithRefs,
+  type GFF3Directive,
+  type GFF3Sequence,
+  type GFF3Feature,
+  type GFF3Item,
+} from './util'

package/src/index.ts

@@ -0,0 +1,12 @@
+import { parseStringSync } from './api'
+export { parseStringSync }
+
+export type {
+  GFF3Comment,
+  GFF3Feature,
+  GFF3Directive,
+  GFF3FeatureLineWithRefs,
+  GFF3FeatureLine,
+  GFF3Item,
+  GFF3Sequence,
+} from './api'