gff-nostream 1.3.7 → 2.0.0

package/esm/parse.js

@@ -1,57 +1,38 @@
-import * as GFF3 from './util';
+import * as GFF3 from "./util.js";
 const containerAttributes = {
     Parent: 'child_features',
     Derives_from: 'derived_features',
 };
-export class FASTAParser {
-    constructor(seqCallback) {
-        this.seqCallback = seqCallback;
-        this.currentSequence = undefined;
-    }
-    addLine(line) {
-        const defMatch = /^>\s*(\S+)\s*(.*)/.exec(line);
-        if (defMatch) {
-            this._flush();
-            this.currentSequence = { id: defMatch[1], sequence: '' };
-            if (defMatch[2]) {
-                this.currentSequence.description = defMatch[2].trim();
-            }
-        }
-        else if (this.currentSequence && /\S/.test(line)) {
-            this.currentSequence.sequence += line.replaceAll(/\s/g, '');
-        }
-    }
-    _flush() {
-        if (this.currentSequence) {
-            this.seqCallback(this.currentSequence);
-        }
-    }
-    finish() {
-        this._flush();
-    }
-}
+const featureLineRegex = /^\s*[^#\s>]/;
+const commentOrDirectiveRegex = /^\s*(#+)(.*)/;
+const blankLineRegex = /^\s*$/;
+const fastaStartRegex = /^\s*>/;
+const lineEndingRegex = /\r?\n?$/g;
 export default class Parser {
+    featureCallback;
+    endCallback;
+    commentCallback;
+    errorCallback;
+    disableDerivesFromReferences;
+    directiveCallback;
+    bufferSize;
+    eof = false;
+    lineNumber = 0;
+    // features that we have to keep on hand for now because they
+    // might be referenced by something else
+    _underConstructionTopLevel = [];
+    // index of the above by ID
+    _underConstructionById = {};
+    _completedReferences = {};
+    // features that reference something we have not seen yet
+    // structured as:
+    // {  'some_id' : {
+    //     'Parent' : [ orphans that have a Parent attr referencing it ],
+    //     'Derives_from' : [ orphans that have a Derives_from attr referencing it ],
+    //    }
+    // }
+    _underConstructionOrphans = {};
     constructor(args) {
-        this.fastaParser = undefined;
-        // if this is true, the parser ignores the
-        // rest of the lines in the file.  currently
-        // set when the file switches over to FASTA
-        this.eof = false;
-        this.lineNumber = 0;
-        // features that we have to keep on hand for now because they
-        // might be referenced by something else
-        this._underConstructionTopLevel = [];
-        // index of the above by ID
-        this._underConstructionById = {};
-        this._completedReferences = {};
-        // features that reference something we have not seen yet
-        // structured as:
-        // {  'some_id' : {
-        //     'Parent' : [ orphans that have a Parent attr referencing it ],
-        //     'Derives_from' : [ orphans that have a Derives_from attr referencing it ],
-        //    }
-        // }
-        this._underConstructionOrphans = {};
         // eslint-disable-next-line @typescript-eslint/no-empty-function
         const nullFunc = () => { };
         this.featureCallback = args.featureCallback || nullFunc;
@@ -59,29 +40,22 @@ export default class Parser {
         this.commentCallback = args.commentCallback || nullFunc;
         this.errorCallback = args.errorCallback || nullFunc;
         this.directiveCallback = args.directiveCallback || nullFunc;
-        this.sequenceCallback = args.sequenceCallback || nullFunc;
         this.disableDerivesFromReferences =
             args.disableDerivesFromReferences || false;
         // number of lines to buffer
         this.bufferSize = args.bufferSize === undefined ? Infinity : args.bufferSize;
     }
     addLine(line) {
-        // if we have transitioned to a fasta section, just delegate to that parser
-        if (this.fastaParser) {
-            this.fastaParser.addLine(line);
-            return;
-        }
         if (this.eof) {
-            // otherwise, if we are done, ignore this line
             return;
         }
         this.lineNumber += 1;
-        if (/^\s*[^#\s>]/.test(line)) {
+        if (featureLineRegex.test(line)) {
             // feature line, most common case
             this._bufferLine(line);
             return;
         }
-        const match = /^\s*(#+)(.*)/.exec(line);
+        const match = commentOrDirectiveRegex.exec(line);
         if (match) {
             // directive or comment
             const [, hashsigns] = match;
@@ -96,7 +70,6 @@ export default class Parser {
                     if (directive.directive === 'FASTA') {
                         this._emitAllUnderConstructionFeatures();
                         this.eof = true;
-                        this.fastaParser = new FASTAParser(this.sequenceCallback);
                     }
                     else {
                         this._emitItem(directive);
@@ -104,31 +77,32 @@ export default class Parser {
                 }
             }
             else {
-                contents = contents.replace(/\s*/, '');
-                this._emitItem({ comment: contents });
+                this._emitItem({ comment: contents.trimStart() });
             }
         }
-        else if (/^\s*$/.test(line)) {
+        else if (blankLineRegex.test(line)) {
             // blank line, do nothing
         }
-        else if (/^\s*>/.test(line)) {
-            // implicit beginning of a FASTA section
+        else if (fastaStartRegex.test(line)) {
+            // implicit beginning of a FASTA section, stop parsing
             this._emitAllUnderConstructionFeatures();
             this.eof = true;
-            this.fastaParser = new FASTAParser(this.sequenceCallback);
-            this.fastaParser.addLine(line);
         }
         else {
             // it's a parse error
-            const errLine = line.replaceAll(/\r?\n?$/g, '');
+            const errLine = line.replaceAll(lineEndingRegex, '');
             throw new Error(`GFF3 parse error.  Cannot parse '${errLine}'.`);
         }
     }
+    addParsedFeatureLine(featureLine) {
+        if (this.eof) {
+            return;
+        }
+        this.lineNumber += 1;
+        this._bufferParsedLine(featureLine);
+    }
     finish() {
         this._emitAllUnderConstructionFeatures();
-        if (this.fastaParser) {
-            this.fastaParser.finish();
-        }
         this.endCallback();
     }
     _emitItem(i) {
@@ -144,19 +118,24 @@ export default class Parser {
     }
     _enforceBufferSizeLimit(additionalItemCount = 0) {
         const _unbufferItem = (item) => {
-            var _a, _b;
-            if (item && Array.isArray(item) && ((_b = (_a = item[0].attributes) === null || _a === void 0 ? void 0 : _a.ID) === null || _b === void 0 ? void 0 : _b[0])) {
+            if (item && Array.isArray(item) && item[0].attributes?.ID?.[0]) {
                 const ids = item[0].attributes.ID;
                 ids.forEach(id => {
                     delete this._underConstructionById[id];
                     delete this._completedReferences[id];
                 });
                 item.forEach(i => {
+                    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
                     if (i.child_features) {
-                        i.child_features.forEach(c => _unbufferItem(c));
+                        i.child_features.forEach(c => {
+                            _unbufferItem(c);
+                        });
                     }
+                    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
                     if (i.derived_features) {
-                        i.derived_features.forEach(d => _unbufferItem(d));
+                        i.derived_features.forEach(d => {
+                            _unbufferItem(d);
+                        });
                     }
                 });
             }
@@ -181,29 +160,24 @@ export default class Parser {
         this._completedReferences = {};
         // if we have any orphans hanging around still, this is a
         // problem. die with a parse error
-        if (Array.from(Object.values(this._underConstructionOrphans)).length) {
-            throw new Error(`some features reference other features that do not exist in the file (or in the same '###' scope). ${Object.keys(this._underConstructionOrphans).join(',')}`);
+        const orphanKeys = Object.keys(this._underConstructionOrphans);
+        if (orphanKeys.length) {
+            throw new Error(`some features reference other features that do not exist in the file (or in the same '###' scope). ${orphanKeys.join(',')}`);
         }
     }
-    // do the right thing with a newly-parsed feature line
     _bufferLine(line) {
-        var _a, _b, _c;
-        const rawFeatureLine = GFF3.parseFeature(line);
-        const featureLine = {
-            ...rawFeatureLine,
-            child_features: [],
-            derived_features: [],
-        };
-        // featureLine._lineNumber = this.lineNumber //< debugging aid
-        // NOTE: a feature is an arrayref of one or more feature lines.
-        const ids = ((_a = featureLine.attributes) === null || _a === void 0 ? void 0 : _a.ID) || [];
-        const parents = ((_b = featureLine.attributes) === null || _b === void 0 ? void 0 : _b.Parent) || [];
+        this._bufferParsedLine(GFF3.parseFeature(line));
+    }
+    _bufferParsedLine(rawFeatureLine) {
+        const featureLine = rawFeatureLine;
+        featureLine.child_features = [];
+        featureLine.derived_features = [];
+        const ids = featureLine.attributes?.ID || [];
+        const parents = featureLine.attributes?.Parent || [];
         const derives = this.disableDerivesFromReferences
             ? []
-            : ((_c = featureLine.attributes) === null || _c === void 0 ? void 0 : _c.Derives_from) || [];
+            : featureLine.attributes?.Derives_from || [];
         if (!ids.length && !parents.length && !derives.length) {
-            // if it has no IDs and does not refer to anything, we can just
-            // output it
             this._emitItem([featureLine]);
             return;
         }
@@ -211,7 +185,6 @@ export default class Parser {
         ids.forEach(id => {
             const existing = this._underConstructionById[id];
             if (existing) {
-                // another location of the same feature
                 if (existing[existing.length - 1].type !== featureLine.type) {
                     this._parseError(`multi-line feature "${id}" has inconsistent types: "${featureLine.type}", "${existing[existing.length - 1].type}"`);
                 }
@@ -219,37 +192,28 @@ export default class Parser {
                 feature = existing;
             }
             else {
-                // haven't seen it yet, so buffer it so we can attach
-                // child features to it
                 feature = [featureLine];
                 this._enforceBufferSizeLimit(1);
                 if (!parents.length && !derives.length) {
                     this._underConstructionTopLevel.push(feature);
                 }
                 this._underConstructionById[id] = feature;
-                // see if we have anything buffered that refers to it
                 this._resolveReferencesTo(feature, id);
             }
         });
-        // try to resolve all its references
-        this._resolveReferencesFrom(feature || [featureLine], { Parent: parents, Derives_from: derives }, ids);
+        this._resolveReferencesFrom(
+        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+        feature || [featureLine], { Parent: parents, Derives_from: derives }, ids);
     }
     _resolveReferencesTo(feature, id) {
         const references = this._underConstructionOrphans[id];
-        //   references is of the form
-        //   {
-        //     'Parent' : [ orphans that have a Parent attr referencing this feature ],
-        //     'Derives_from' : [ orphans that have a Derives_from attr referencing this feature ],
-        //    }
         if (!references) {
             return;
         }
-        feature.forEach(loc => {
+        for (const loc of feature) {
             loc.child_features.push(...references.Parent);
-        });
-        feature.forEach(loc => {
             loc.derived_features.push(...references.Derives_from);
-        });
+        }
         delete this._underConstructionOrphans[id];
     }
     _parseError(message) {
@@ -257,61 +221,60 @@ export default class Parser {
         this.errorCallback(`${this.lineNumber}: ${message}`);
     }
     _resolveReferencesFrom(feature, references, ids) {
-        // this is all a bit more awkward in javascript than it was in perl
-        function postSet(obj, slot1, slot2) {
-            let subObj = obj[slot1];
-            if (!subObj) {
-                subObj = {};
-                obj[slot1] = subObj;
-            }
-            const returnVal = subObj[slot2] || false;
-            subObj[slot2] = true;
-            return returnVal;
-        }
-        references.Parent.forEach(toId => {
+        for (const toId of references.Parent) {
             const otherFeature = this._underConstructionById[toId];
             if (otherFeature) {
-                const pname = containerAttributes.Parent;
-                if (!ids.filter(id => postSet(this._completedReferences, id, `Parent,${toId}`)).length) {
-                    otherFeature.forEach(location => {
-                        location[pname].push(feature);
-                    });
+                let dominated = false;
+                for (const id of ids) {
+                    const domKey = `Parent,${toId}`;
+                    const rec = this._completedReferences[id] || (this._completedReferences[id] = {});
+                    if (rec[domKey]) {
+                        dominated = true;
+                    }
+                    rec[domKey] = true;
+                }
+                if (!dominated) {
+                    for (const location of otherFeature) {
+                        location.child_features.push(feature);
+                    }
                 }
             }
             else {
                 let ref = this._underConstructionOrphans[toId];
                 if (!ref) {
-                    ref = {
-                        Parent: [],
-                        Derives_from: [],
-                    };
+                    ref = { Parent: [], Derives_from: [] };
                     this._underConstructionOrphans[toId] = ref;
                 }
                 ref.Parent.push(feature);
             }
-        });
-        references.Derives_from.forEach(toId => {
+        }
+        for (const toId of references.Derives_from) {
             const otherFeature = this._underConstructionById[toId];
             if (otherFeature) {
-                const pname = containerAttributes.Derives_from;
-                if (!ids.filter(id => postSet(this._completedReferences, id, `Derives_from,${toId}`)).length) {
-                    otherFeature.forEach(location => {
-                        location[pname].push(feature);
-                    });
+                let dominated = false;
+                for (const id of ids) {
+                    const domKey = `Derives_from,${toId}`;
+                    const rec = this._completedReferences[id] || (this._completedReferences[id] = {});
+                    if (rec[domKey]) {
+                        dominated = true;
+                    }
+                    rec[domKey] = true;
+                }
+                if (!dominated) {
+                    for (const location of otherFeature) {
+                        location.derived_features.push(feature);
+                    }
                 }
             }
             else {
                 let ref = this._underConstructionOrphans[toId];
                 if (!ref) {
-                    ref = {
-                        Parent: [],
-                        Derives_from: [],
-                    };
+                    ref = { Parent: [], Derives_from: [] };
                     this._underConstructionOrphans[toId] = ref;
                 }
                 ref.Derives_from.push(feature);
             }
-        });
+        }
     }
 }
 //# sourceMappingURL=parse.js.map

package/esm/parse.js.map

@@ -1 +1 @@
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package/esm/util.d.ts

@@ -33,6 +33,7 @@ export declare function parseAttributes(attrString: string): GFF3Attributes;
  * @returns The parsed feature
  */
 export declare function parseFeature(line: string): GFF3FeatureLine;
+export declare function parseFieldsArray(f: (string | null | undefined)[]): GFF3FeatureLine;
 /**
  * Parse a GFF3 directive line.
  *

package/esm/util.js

@@ -1,5 +1,14 @@
 // Fast, low-level functions for parsing and formatting GFF3.
 // JavaScript port of Robert Buels's Bio::GFF3::LowLevel Perl module.
+const escapeRegex = /%([0-9A-Fa-f]{2})/g;
+const directiveRegex = /^\s*##\s*(\S+)\s*(.*)/;
+const lineEndRegex = /\r?\n$/;
+const whitespaceRegex = /\s+/;
+const nonDigitRegex = /\D/g;
+// eslint-disable-next-line no-control-regex
+const attrEscapeRegex = /[\n;\r\t=%&,\u0000-\u001f\u007f-\u00ff]/g;
+// eslint-disable-next-line no-control-regex
+const columnEscapeRegex = /[\n\r\t%\u0000-\u001f\u007f-\u00ff]/g;
 /**
  * Unescape a string value used in a GFF3 attribute.
  *
@@ -7,7 +16,10 @@
  * @returns An unescaped string value
  */
 export function unescape(stringVal) {
-    return stringVal.replaceAll(/%([0-9A-Fa-f]{2})/g, (_match, seq) => String.fromCharCode(parseInt(seq, 16)));
+    if (!stringVal.includes('%')) {
+        return stringVal;
+    }
+    return stringVal.replaceAll(escapeRegex, (_match, seq) => String.fromCharCode(parseInt(seq, 16)));
 }
 function _escape(regex, s) {
     return String(s).replace(regex, ch => {
@@ -22,7 +34,7 @@ function _escape(regex, s) {
  * @returns An escaped string value
  */
 export function escape(rawVal) {
-    return _escape(/[\n;\r\t=%&,\u0000-\u001f\u007f-\u00ff]/g, rawVal);
+    return _escape(attrEscapeRegex, rawVal);
 }
 /**
  * Escape a value for use in a GFF3 column value.
@@ -31,7 +43,7 @@ export function escape(rawVal) {
  * @returns An escaped column value
  */
 export function escapeColumn(rawVal) {
-    return _escape(/[\n\r\t%\u0000-\u001f\u007f-\u00ff]/g, rawVal);
+    return _escape(columnEscapeRegex, rawVal);
 }
 /**
  * Parse the 9th column (attributes) of a GFF3 feature line.
@@ -44,26 +56,29 @@ export function parseAttributes(attrString) {
         return {};
     }
     const attrs = {};
-    attrString
-        .replace(/\r?\n$/, '')
-        .split(';')
-        .forEach(a => {
-        var _a;
-        const nv = a.split('=', 2);
-        if (!((_a = nv[1]) === null || _a === void 0 ? void 0 : _a.length)) {
-            return;
+    let str = attrString;
+    if (str.endsWith('\n')) {
+        str = str.slice(0, str.endsWith('\r\n') ? -2 : -1);
+    }
+    for (const a of str.split(';')) {
+        const eqIdx = a.indexOf('=');
+        if (eqIdx === -1) {
+            continue;
+        }
+        const value = a.slice(eqIdx + 1);
+        if (!value.length) {
+            continue;
         }
-        nv[0] = nv[0].trim();
-        let arec = attrs[nv[0].trim()];
+        const tag = a.slice(0, eqIdx).trim();
+        let arec = attrs[tag];
         if (!arec) {
             arec = [];
-            attrs[nv[0]] = arec;
+            attrs[tag] = arec;
         }
-        arec.push(...nv[1]
-            .split(',')
-            .map(s => s.trim())
-            .map(unescape));
-    });
+        for (const s of value.split(',')) {
+            arec.push(unescape(s.trim()));
+        }
+    }
     return attrs;
 }
 /**
@@ -73,21 +88,38 @@ export function parseAttributes(attrString) {
  * @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 parseFieldsArray(line.split('\t'));
+}
+/**
+ * Parse a GFF3 feature from a pre-split fields array
+ *
+ * @param f - Array of 9 GFF3 column values (use null or '.' for empty values)
+ * @returns The parsed feature
+ */
+function norm(a) {
+    return a === '.' || a === '' || a === undefined ? null : a;
+}
+export function parseFieldsArray(f) {
+    const seq_id = norm(f[0]);
+    const source = norm(f[1]);
+    const type = norm(f[2]);
+    const start = norm(f[3]);
+    const end = norm(f[4]);
+    const score = norm(f[5]);
+    const strand = norm(f[6]);
+    const phase = norm(f[7]);
+    const attrString = norm(f[8]);
+    return {
+        seq_id: seq_id ? unescape(seq_id) : null,
+        source: source ? unescape(source) : null,
+        type: type ? unescape(type) : null,
+        start: start === null ? null : parseInt(start, 10),
+        end: end === null ? null : parseInt(end, 10),
+        score: score === null ? null : parseFloat(score),
+        strand,
+        phase,
+        attributes: attrString === null ? null : parseAttributes(attrString),
     };
-    return parsed;
 }
 /**
  * Parse a GFF3 directive line.
@@ -96,8 +128,7 @@ export function parseFeature(line) {
  * @returns The parsed directive
  */
 export function parseDirective(line) {
-    var _a, _b;
-    const match = /^\s*##\s*(\S+)\s*(.*)/.exec(line);
+    const match = directiveRegex.exec(line);
     if (!match) {
         return null;
     }
@@ -105,21 +136,21 @@ export function parseDirective(line) {
     let [, , contents] = match;
     const parsed = { directive: name };
     if (contents.length) {
-        contents = contents.replace(/\r?\n$/, '');
+        contents = contents.replace(lineEndRegex, '');
         parsed.value = contents;
     }
     // do a little additional parsing for sequence-region and genome-build directives
     if (name === 'sequence-region') {
-        const c = contents.split(/\s+/, 3);
+        const c = contents.split(whitespaceRegex, 3);
         return {
             ...parsed,
             seq_id: c[0],
-            start: (_a = c[1]) === null || _a === void 0 ? void 0 : _a.replaceAll(/\D/g, ''),
-            end: (_b = c[2]) === null || _b === void 0 ? void 0 : _b.replaceAll(/\D/g, ''),
+            start: c[1]?.replaceAll(nonDigitRegex, ''),
+            end: c[2]?.replaceAll(nonDigitRegex, ''),
         };
     }
     else if (name === 'genome-build') {
-        const [source, buildName] = contents.split(/\s+/, 2);
+        const [source, buildName] = contents.split(whitespaceRegex, 2);
         return {
             ...parsed,
             source,
@@ -136,28 +167,18 @@ export function parseDirective(line) {
  */
 export function formatAttributes(attrs) {
     const attrOrder = [];
-    Object.entries(attrs).forEach(([tag, val]) => {
+    for (const [tag, val] of Object.entries(attrs)) {
         if (!val) {
-            return;
-        }
-        let valstring;
-        if (val.hasOwnProperty('toString')) {
-            valstring = escape(val.toString());
-            // } else if (Array.isArray(val.values)) {
-            //   valstring = val.values.map(escape).join(',')
+            continue;
         }
-        else if (Array.isArray(val)) {
-            valstring = val.map(escape).join(',');
-        }
-        else {
-            valstring = escape(val);
-        }
-        attrOrder.push(`${escape(tag)}=${valstring}`);
-    });
+        attrOrder.push(`${escape(tag)}=${val.map(escape).join(',')}`);
+    }
     return attrOrder.length ? attrOrder.join(';') : '.';
 }
 function _formatSingleFeature(f, seenFeature) {
-    const attrString = f.attributes === null || f.attributes === undefined
+    const attrString = 
+    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+    f.attributes === null || f.attributes === undefined
         ? '.'
         : formatAttributes(f.attributes);
     const fields = [
@@ -262,7 +283,10 @@ export function formatItem(itemOrItems) {
     return formatSingleItem(itemOrItems);
 }
 function _isFeatureLineWithRefs(featureLine) {
-    return (featureLine.child_features !== undefined &&
+    return (
+    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+    featureLine.child_features !== undefined &&
+        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
         featureLine.derived_features !== undefined);
 }
 //# sourceMappingURL=util.js.map