gff-nostream 1.3.1

package/dist/parse.js.map

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

@@ -0,0 +1,166 @@
+/**
+ * Unescape a string value used in a GFF3 attribute.
+ *
+ * @param stringVal - Escaped GFF3 string value
+ * @returns An unescaped string value
+ */
+export declare function unescape(stringVal: string): string;
+/**
+ * Escape a value for use in a GFF3 attribute value.
+ *
+ * @param rawVal - Raw GFF3 attribute value
+ * @returns An escaped string value
+ */
+export declare function escape(rawVal: string | number): string;
+/**
+ * Escape a value for use in a GFF3 column value.
+ *
+ * @param rawVal - Raw GFF3 column value
+ * @returns An escaped column value
+ */
+export declare function escapeColumn(rawVal: string | number): string;
+/**
+ * Parse the 9th column (attributes) of a GFF3 feature line.
+ *
+ * @param attrString - String of GFF3 9th column
+ * @returns Parsed attributes
+ */
+export declare function parseAttributes(attrString: string): GFF3Attributes;
+/**
+ * Parse a GFF3 feature line
+ *
+ * @param line - GFF3 feature line
+ * @returns The parsed feature
+ */
+export declare function parseFeature(line: string): GFF3FeatureLine;
+/**
+ * Parse a GFF3 directive line.
+ *
+ * @param line - GFF3 directive line
+ * @returns The parsed directive
+ */
+export declare function parseDirective(line: string): GFF3Directive | GFF3SequenceRegionDirective | GFF3GenomeBuildDirective | null;
+/**
+ * Format an attributes object into a string suitable for the 9th column of GFF3.
+ *
+ * @param attrs - Attributes
+ * @returns GFF3 9th column string
+ */
+export declare function formatAttributes(attrs: GFF3Attributes): string;
+/**
+ * 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 declare function formatFeature(featureOrFeatures: GFF3FeatureLine | GFF3FeatureLineWithRefs | (GFF3FeatureLine | GFF3FeatureLineWithRefs)[]): string;
+/**
+ * Format a directive into a line of GFF3.
+ *
+ * @param directive - A directive object
+ * @returns A directive line string
+ */
+export declare function formatDirective(directive: GFF3Directive): string;
+/**
+ * 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 declare function formatComment(comment: GFF3Comment): string;
+/**
+ * Format a sequence object as FASTA
+ *
+ * @param seq - A sequence object
+ * @returns Formatted single FASTA sequence string
+ */
+export declare function formatSequence(seq: GFF3Sequence): string;
+/**
+ * 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 declare function formatItem(itemOrItems: GFF3FeatureLineWithRefs | GFF3Directive | GFF3Comment | GFF3Sequence | (GFF3FeatureLineWithRefs | GFF3Directive | GFF3Comment | GFF3Sequence)[]): string | string[];
+/** A record of GFF3 attribute identifiers and the values of those identifiers */
+export type GFF3Attributes = Record<string, string[] | undefined>;
+/** A representation of a single line of a GFF3 file */
+export interface GFF3FeatureLine {
+    /** The ID of the landmark used to establish the coordinate system for the current feature */
+    seq_id: string | null;
+    /** A free text qualifier intended to describe the algorithm or operating procedure that generated this feature */
+    source: string | null;
+    /** The type of the feature */
+    type: string | null;
+    /** The start coordinates of the feature */
+    start: number | null;
+    /** The end coordinates of the feature */
+    end: number | null;
+    /** The score of the feature */
+    score: number | null;
+    /** The strand of the feature */
+    strand: string | null;
+    /** For features of type "CDS", the phase indicates where the next codon begins relative to the 5' end of the current CDS feature */
+    phase: string | null;
+    /** Feature attributes */
+    attributes: GFF3Attributes | null;
+}
+/**
+ * A GFF3 Feature line that includes references to other features defined in
+ * their "Parent" or "Derives_from" attributes
+ */
+export interface GFF3FeatureLineWithRefs extends GFF3FeatureLine {
+    /** An array of child features */
+    child_features: GFF3Feature[];
+    /** An array of features derived from this feature */
+    derived_features: GFF3Feature[];
+}
+/**
+ * A GFF3 feature, which may include multiple individual feature lines
+ */
+export type GFF3Feature = GFF3FeatureLineWithRefs[];
+/** A GFF3 directive */
+export interface GFF3Directive {
+    /** The name of the directive */
+    directive: string;
+    /** The string value of the directive */
+    value?: string;
+}
+/** A GFF3 sequence-region directive */
+export interface GFF3SequenceRegionDirective extends GFF3Directive {
+    /** The string value of the directive */
+    value: string;
+    /** The sequence ID parsed from the directive */
+    seq_id: string;
+    /** The sequence start parsed from the directive */
+    start: string;
+    /** The sequence end parsed from the directive */
+    end: string;
+}
+/** A GFF3 genome-build directive */
+export interface GFF3GenomeBuildDirective extends GFF3Directive {
+    /** The string value of the directive */
+    value: string;
+    /** The genome build source parsed from the directive */
+    source: string;
+    /** The genome build name parsed from the directive */
+    buildName: string;
+}
+/** A GFF3 comment */
+export interface GFF3Comment {
+    /** The text of the comment */
+    comment: string;
+}
+/** A GFF3 FASTA single sequence */
+export interface GFF3Sequence {
+    /** The ID of the sequence */
+    id: string;
+    /** The description of the sequence */
+    description?: string;
+    /** The sequence */
+    sequence: string;
+}
+export type GFF3Item = GFF3Feature | GFF3Directive | GFF3Comment | GFF3Sequence;

package/dist/util.js

@@ -0,0 +1,274 @@
+"use strict";
+// Fast, low-level functions for parsing and formatting GFF3.
+// JavaScript port of Robert Buels's Bio::GFF3::LowLevel Perl module.
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.unescape = unescape;
+exports.escape = escape;
+exports.escapeColumn = escapeColumn;
+exports.parseAttributes = parseAttributes;
+exports.parseFeature = parseFeature;
+exports.parseDirective = parseDirective;
+exports.formatAttributes = formatAttributes;
+exports.formatFeature = formatFeature;
+exports.formatDirective = formatDirective;
+exports.formatComment = formatComment;
+exports.formatSequence = formatSequence;
+exports.formatItem = formatItem;
+/**
+ * Unescape a string value used in a GFF3 attribute.
+ *
+ * @param stringVal - Escaped GFF3 string value
+ * @returns An unescaped string value
+ */
+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 `%${hex}`;
+    });
+}
+/**
+ * Escape a value for use in a GFF3 attribute value.
+ *
+ * @param rawVal - Raw GFF3 attribute value
+ * @returns An escaped string value
+ */
+function escape(rawVal) {
+    return _escape(/[\n;\r\t=%&,\u0000-\u001f\u007f-\u00ff]/g, rawVal);
+}
+/**
+ * Escape a value for use in a GFF3 column value.
+ *
+ * @param rawVal - Raw GFF3 column value
+ * @returns An escaped column value
+ */
+function escapeColumn(rawVal) {
+    return _escape(/[\n\r\t%\u0000-\u001f\u007f-\u00ff]/g, rawVal);
+}
+/**
+ * Parse the 9th column (attributes) of a GFF3 feature line.
+ *
+ * @param attrString - String of GFF3 9th column
+ * @returns Parsed attributes
+ */
+function parseAttributes(attrString) {
+    if (!attrString.length || attrString === '.') {
+        return {};
+    }
+    const attrs = {};
+    attrString
+        .replace(/\r?\n$/, '')
+        .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
+ */
+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
+ */
+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$/, '');
+        parsed.value = contents;
+    }
+    // do a little additional parsing for sequence-region and genome-build directives
+    if (name === 'sequence-region') {
+        const c = contents.split(/\s+/, 3);
+        return Object.assign(Object.assign({}, parsed), { seq_id: c[0], start: (_a = c[1]) === null || _a === void 0 ? void 0 : _a.replaceAll(/\D/g, ''), end: (_b = c[2]) === null || _b === void 0 ? void 0 : _b.replaceAll(/\D/g, '') });
+    }
+    else if (name === 'genome-build') {
+        const [source, buildName] = contents.split(/\s+/, 2);
+        return Object.assign(Object.assign({}, parsed), { source,
+            buildName });
+    }
+    return parsed;
+}
+/**
+ * Format an attributes object into a string suitable for the 9th column of GFF3.
+ *
+ * @param attrs - Attributes
+ * @returns GFF3 9th column string
+ */
+function formatAttributes(attrs) {
+    const attrOrder = [];
+    Object.entries(attrs).forEach(([tag, val]) => {
+        if (!val) {
+            return;
+        }
+        let valstring;
+        if (val.hasOwnProperty('toString')) {
+            valstring = escape(val.toString());
+            // } else if (Array.isArray(val.values)) {
+            //   valstring = val.values.map(escape).join(',')
+        }
+        else if (Array.isArray(val)) {
+            valstring = val.map(escape).join(',');
+        }
+        else {
+            valstring = escape(val);
+        }
+        attrOrder.push(`${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
+ */
+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
+ */
+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
+ */
+function formatComment(comment) {
+    return `# ${comment.comment}\n`;
+}
+/**
+ * Format a sequence object as FASTA
+ *
+ * @param seq - A sequence object
+ * @returns Formatted single FASTA sequence string
+ */
+function formatSequence(seq) {
+    return `>${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
+ */
+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

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package/esm/api.d.ts

@@ -0,0 +1,23 @@
+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;
+}
+export declare function parseStringSync(str: string, inputOptions?: ParseOptions): GFF3Item[];
+export { type GFF3FeatureLine, type GFF3Comment, type GFF3FeatureLineWithRefs, type GFF3Directive, type GFF3Sequence, type GFF3Feature, type GFF3Item, } from './util';

package/esm/api.js

@@ -0,0 +1,42 @@
+import Parser from './parse';
+// shared arg processing for the parse routines
+function _processParseOptions(options) {
+    const out = {
+        encoding: 'utf8',
+        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, inputOptions = {}) {
+    if (!str) {
+        return [];
+    }
+    const options = _processParseOptions(inputOptions);
+    const items = [];
+    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;
+}
+//# sourceMappingURL=api.js.map

package/esm/api.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"api.js","sourceRoot":"","sources":["../src/api.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,SAAS,CAAA;AA0B5B,+CAA+C;AAC/C,SAAS,oBAAoB,CAAC,OAAqB;IACjD,MAAM,GAAG,GAAG;QACV,QAAQ,EAAE,MAAe;QACzB,aAAa,EAAE,IAAI;QACnB,eAAe,EAAE,KAAK;QACtB,cAAc,EAAE,IAAI;QACpB,aAAa,EAAE,KAAK;QACpB,4BAA4B,EAAE,KAAK;QACnC,GAAG,OAAO;KACX,CAAA;IAED,IAAI,OAAO,CAAC,QAAQ,EAAE,CAAC;QACrB,GAAG,CAAC,aAAa,GAAG,IAAI,CAAA;QACxB,GAAG,CAAC,eAAe,GAAG,IAAI,CAAA;QAC1B,GAAG,CAAC,aAAa,GAAG,IAAI,CAAA;QACxB,GAAG,CAAC,cAAc,GAAG,IAAI,CAAA;IAC3B,CAAC;IAED,OAAO,GAAG,CAAA;AACZ,CAAC;AAED,MAAM,UAAU,eAAe,CAC7B,GAAW,EACX,eAA6B,EAAE;IAE/B,IAAI,CAAC,GAAG,EAAE,CAAC;QACT,OAAO,EAAE,CAAA;IACX,CAAC;IAED,MAAM,OAAO,GAAG,oBAAoB,CAAC,YAAY,CAAC,CAAA;IAClD,MAAM,KAAK,GAAe,EAAE,CAAA;IAC5B,MAAM,IAAI,GAAG,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;IAEnC,MAAM,MAAM,GAAG,IAAI,MAAM,CAAC;QACxB,eAAe,EAAE,OAAO,CAAC,aAAa,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,SAAS;QACzD,iBAAiB,EAAE,OAAO,CAAC,eAAe,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,SAAS;QAC7D,eAAe,EAAE,OAAO,CAAC,aAAa,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,SAAS;QACzD,gBAAgB,EAAE,OAAO,CAAC,cAAc,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,SAAS;QAC3D,4BAA4B,EAAE,OAAO,CAAC,4BAA4B,IAAI,KAAK;QAC3E,aAAa,EAAE,GAAG,CAAC,EAAE;YACnB,MAAM,GAAG,CAAA;QACX,CAAC;KACF,CAAC,CAAA;IAEF,GAAG,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAA;IACvD,MAAM,CAAC,MAAM,EAAE,CAAA;IAEf,OAAO,KAAK,CAAA;AACd,CAAC"}

package/esm/index.d.ts

@@ -0,0 +1,3 @@
+import { parseStringSync } from './api';
+export { parseStringSync };
+export type { GFF3Comment, GFF3Feature, GFF3Directive, GFF3FeatureLineWithRefs, GFF3FeatureLine, GFF3Item, GFF3Sequence, } from './api';

package/esm/index.js

@@ -0,0 +1,3 @@
+import { parseStringSync } from './api';
+export { parseStringSync };
+//# sourceMappingURL=index.js.map

package/esm/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,eAAe,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,eAAe,EAAE,CAAA"}

package/esm/parse.d.ts

@@ -0,0 +1,55 @@
+import * as GFF3 from './util';
+export declare class FASTAParser {
+    seqCallback: (sequence: GFF3.GFF3Sequence) => void;
+    currentSequence: {
+        id: string;
+        sequence: string;
+        description?: string;
+    } | undefined;
+    constructor(seqCallback: (sequence: GFF3.GFF3Sequence) => void);
+    addLine(line: string): void;
+    private _flush;
+    finish(): void;
+}
+interface ParserArgs {
+    featureCallback?(feature: GFF3.GFF3Feature): void;
+    endCallback?(): void;
+    commentCallback?(comment: GFF3.GFF3Comment): void;
+    errorCallback?(error: string): void;
+    directiveCallback?(directive: GFF3.GFF3Directive): void;
+    sequenceCallback?(sequence: GFF3.GFF3Sequence): void;
+    bufferSize?: number;
+    disableDerivesFromReferences?: boolean;
+}
+export default class Parser {
+    featureCallback: (feature: GFF3.GFF3Feature) => void;
+    endCallback: () => void;
+    commentCallback: (comment: GFF3.GFF3Comment) => void;
+    errorCallback: (error: string) => void;
+    disableDerivesFromReferences: boolean;
+    directiveCallback: (directive: GFF3.GFF3Directive) => void;
+    sequenceCallback: (sequence: GFF3.GFF3Sequence) => void;
+    bufferSize: number;
+    fastaParser: FASTAParser | undefined;
+    eof: boolean;
+    lineNumber: number;
+    private _underConstructionTopLevel;
+    private _underConstructionById;
+    private _completedReferences;
+    private _underConstructionOrphans;
+    constructor(args: ParserArgs);
+    addLine(line: string): void;
+    finish(): void;
+    private _emitItem;
+    private _enforceBufferSizeLimit;
+    /**
+     * return all under-construction features, called when we know
+     * there will be no additional data to attach to them
+     */
+    private _emitAllUnderConstructionFeatures;
+    private _bufferLine;
+    private _resolveReferencesTo;
+    private _parseError;
+    private _resolveReferencesFrom;
+}
+export {};