clustal-js 1.0.4 → 2.0.1

package/CHANGELOG.md

@@ -1,8 +1,19 @@
+# v2.0.1
+
+- Fix preversion build script
+
+# v2.0.0
+
+- Parse pairwise format, outputted by e.g. EMBOSS needle, etc
+
+# v1.0.4
+
+- Fix package name in README
+
 # v1.0.3
 
 - Add generated typescript declarations to output
 
-
 ## v1.0.2
 
 - Add dist folder to package.json

package/README.md

@@ -4,11 +4,10 @@
 
 This parses clustal output format
 
-
 ## Usage
 
-```js
-import {parse} from 'clustal-js'
+```typescript
+import { parse } from 'clustal-js'
 const file = fs.readFileSync('test.aln', 'utf8')
 const ret = parse(file)
 ```
@@ -57,6 +56,103 @@ Output
            version: '1.2.4' } }
 ```
 
+### Parse pairwise outputs
+
+```typescript
+import { parsePairwise } from 'clustal-js'
+const file = fs.readFileSync('test.aln', 'utf8')
+const ret = parse(file)
+```
+
+Input test.aln (e.g. from EMBOSS needle)
+
+```
+########################################
+# Program: needle
+# Rundate: Mon  5 Feb 2024 17:52:19
+# Commandline: needle
+#    -auto
+#    -stdout
+#    -asequence emboss_needle-R20240205-175207-0261-70863964-p1m.asequence
+#    -bsequence emboss_needle-R20240205-175207-0261-70863964-p1m.bsequence
+# Align_format: srspair
+# Report_file: stdout
+########################################
+
+#=======================================
+#
+# Aligned_sequences: 2
+# 1: a
+# 2: b
+# Matrix: EBLOSUM62
+# Gap_penalty: 10.0
+# Extend_penalty: 0.5
+#
+# Length: 614
+# Identity:     221/614 (36.0%)
+# Similarity:   221/614 (36.0%)
+# Gaps:         393/614 (64.0%)
+# Score: 1114.0
+#
+#
+#=======================================
+
+a                  1 MGQKGHKDSLYPCGGTPESSLHEALDQCMTALDLFLTNQFSEALSYLKPR     50
+
+b                  0 --------------------------------------------------      0
+
+a                 51 TKESMYHSLTYATILEMQAMMTFDPQDILLAGNMMKEAQMLCQRHRRKSS    100
+
+b                  0 --------------------------------------------------      0
+
+a                101 VTDSFSSLVNRPTLGQFTEEEIHAEVCYAECLLQRAALTFLQGSSHGGAV    150
+
+b                  0 --------------------------------------------------      0
+
+a                151 RPRALHDPSHACSCPPGPGRQHLFLLQDENMVSFIKGGIKVRNSYQTYKE    200
+
+b                  0 --------------------------------------------------      0
+
+a                201 LDSLVQSSQYCKGENHPHFEGGVKLGVGAFNLTLSMLPTRILRLLEFVGF    250
+
+b                  0 --------------------------------------------------      0
+
+a                251 SGNKDYGLLQLEEGASGHSFRSVLCVMLLLCYHTFLTFVLGTGNVNIEEA    300
+
+b                  0 --------------------------------------------------      0
+
+a                301 EKLLKPYLNRYPKGAIFLFFAGRIEVIKGNIDAAIRRFEECCEAQQHWKQ    350
+
+b                  0 --------------------------------------------------      0
+
+a                351 FHHMCYWELMWCFTYKGQWKMSYFYADLLSKENCWSKATYIYMKAAYLSM    400
+                                                               ||||||||
+b                  1 ------------------------------------------MKAAYLSM      8
+
+a                401 FGKEDHKPFGDDEVELFRAVPGLKLKIAGKSLPTEKFAIRKSRRYFSSNP    450
+                     ||||||||||||||||||||||||||||||||||||||||||||||||||
+b                  9 FGKEDHKPFGDDEVELFRAVPGLKLKIAGKSLPTEKFAIRKSRRYFSSNP     58
+
+a                451 ISLPVPALEMMYIWNGYAVIGKQPKLTDGILEIITKAEEMLEKGPENEYS    500
+                     ||||||||||||||||||||||||||||||||||||||||||||||||||
+b                 59 ISLPVPALEMMYIWNGYAVIGKQPKLTDGILEIITKAEEMLEKGPENEYS    108
+
+a                501 VDDECLVKLLKGLCLKYLGRVQEAEENFRSISANEKKIKYDHYLIPNALL    550
+                     ||||||||||||||||||||||||||||||||||||||||||||||||||
+b                109 VDDECLVKLLKGLCLKYLGRVQEAEENFRSISANEKKIKYDHYLIPNALL    158
+
+a                551 ELALLLMEQDRNEEAIKLLESAKQNYKNYSMESRTHFRIQAATLQAKSSL    600
+                     ||||||||||||||||||||||||||||||||||||||||||||||||||
+b                159 ELALLLMEQDRNEEAIKLLESAKQNYKNYSMESRTHFRIQAATLQAKSSL    208
+
+a                601 ENSSRSMVSSVSL-    613
+                     |||||||||||||
+b                209 ENSSRSMVSSVSL*    222
+
+
+#---------------------------------------
+#---------------------------------------
+```
 
 ### Notes
 

package/dist/index.d.ts

@@ -0,0 +1,36 @@
+export declare function parseClustalIter(arr: Iterator<string>): {
+    consensus: string;
+    alns: {
+        id: any;
+        seq: any;
+    }[];
+    header: {
+        info: string;
+        version: string;
+    };
+};
+export declare function parsePairwiseIter(arr: string): {
+    consensus: string;
+    alns: {
+        id: any;
+        seq: any;
+    }[];
+};
+export declare function parse(contents: string): {
+    consensus: string;
+    alns: {
+        id: any;
+        seq: any;
+    }[];
+    header: {
+        info: string;
+        version: string;
+    };
+};
+export declare function parsePairwise(contents: string): {
+    consensus: string;
+    alns: {
+        id: any;
+        seq: any;
+    }[];
+};

package/dist/index.js

@@ -0,0 +1,49 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.parsePairwise = exports.parse = exports.parsePairwiseIter = exports.parseClustalIter = void 0;
+const pairwise_1 = require("./pairwise");
+const util_1 = require("./util");
+function parseClustalIter(arr) {
+    const line = (0, util_1.getFirstNonEmptyLine)(arr);
+    if (!line) {
+        throw new Error('Empty file received');
+    }
+    const header = (0, util_1.parseHeader)(line);
+    const res = (0, util_1.parseBlocks)(arr);
+    if (res === undefined) {
+        throw new Error('No blocks parsed');
+    }
+    const alns = res.seqs.map((n, index) => ({ id: res.ids[index], seq: n }));
+    const { consensus } = res;
+    if (consensus.length != alns[0].seq.length) {
+        throw new Error(`Consensus length != sequence length. Con ${consensus.length} seq ${alns[0].seq.length}`);
+    }
+    return { consensus, alns, header };
+}
+exports.parseClustalIter = parseClustalIter;
+function parsePairwiseIter(arr) {
+    const res = (0, pairwise_1.parsePairwiseBlocks)(arr.split('\n')[Symbol.iterator]());
+    if (res === undefined) {
+        throw new Error('No blocks parsed');
+    }
+    const alns = res.seqs.map((n, index) => ({ id: res.ids[index], seq: n }));
+    const { consensus } = res;
+    if (consensus.length != alns[0].seq.length) {
+        throw new Error(`Consensus length != sequence length. Con ${consensus.length} seq ${alns[0].seq.length}`);
+    }
+    return { consensus, alns };
+}
+exports.parsePairwiseIter = parsePairwiseIter;
+function parse(contents) {
+    const iter = contents.split('\n')[Symbol.iterator]();
+    return parseClustalIter(iter);
+}
+exports.parse = parse;
+function parsePairwise(contents) {
+    const res = contents
+        .split('\n')
+        .filter(f => !f.startsWith('#'))
+        .join('\n');
+    return parsePairwiseIter(res);
+}
+exports.parsePairwise = parsePairwise;

package/dist/pairwise.d.ts

@@ -0,0 +1,11 @@
+export declare function getSeqBounds(line: string): readonly [number, number];
+export declare function parsePairwiseBlock(arr: Iterator<string>): {
+    ids: any[];
+    seqs: any[];
+    consensus: string;
+} | undefined;
+export declare function parsePairwiseBlocks(arr: Iterator<string>): {
+    ids: any[];
+    seqs: any[];
+    consensus: string;
+} | undefined;

package/dist/pairwise.js

@@ -0,0 +1,57 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.parsePairwiseBlocks = exports.parsePairwiseBlock = exports.getSeqBounds = void 0;
+const util_1 = require("./util");
+function getSeqBounds(line) {
+    const fields = line.split(/\s+/);
+    const k1 = fields[0].length + fields[1].length;
+    const temp = line.slice(k1);
+    const s = k1 + temp.indexOf(fields[2]);
+    const e = s + fields[2].length;
+    return [s, e];
+}
+exports.getSeqBounds = getSeqBounds;
+// Use the first block to get the sequence identifiers
+function parsePairwiseBlock(arr) {
+    let line = (0, util_1.getFirstNonEmptyLine)(arr);
+    const block = [];
+    let consensusLine = '';
+    if (!line) {
+        return undefined;
+    }
+    while (line) {
+        if (line[0] !== ' ') {
+            block.push(line);
+        }
+        else {
+            consensusLine = line;
+        }
+        line = arr.next().value;
+    }
+    const [start, end] = getSeqBounds(block[0]);
+    const fields = block.map(s => s.split(/\s+/));
+    const ids = fields.map(s => s[0]);
+    const seqs = fields.map(s => s[2]);
+    let consensus = consensusLine.slice(start, end);
+    // handle if the consensus trailing whitespace got trimmed
+    const remainder = seqs[0].length - consensus.length;
+    if (remainder) {
+        consensus += ' '.repeat(remainder);
+    }
+    return { ids, seqs, consensus };
+}
+exports.parsePairwiseBlock = parsePairwiseBlock;
+function parsePairwiseBlocks(arr) {
+    let block;
+    const res = parsePairwiseBlock(arr);
+    if (res !== undefined) {
+        while ((block = parsePairwiseBlock(arr))) {
+            for (let i = 0; i < block.seqs.length; i++) {
+                res.seqs[i] += block.seqs[i];
+            }
+            res.consensus += block.consensus;
+        }
+    }
+    return res;
+}
+exports.parsePairwiseBlocks = parsePairwiseBlocks;

package/dist/util.d.ts

@@ -0,0 +1,17 @@
+export declare function parseVersion(line: string): string;
+export declare function parseHeader(info: string): {
+    info: string;
+    version: string;
+};
+export declare function getFirstNonEmptyLine(arr: Iterator<string>): any;
+export declare function getSeqBounds(line: string): readonly [number, number];
+export declare function parseBlock(arr: Iterator<string>): {
+    ids: any[];
+    seqs: any[];
+    consensus: string;
+} | undefined;
+export declare function parseBlocks(arr: Iterator<string>): {
+    ids: any[];
+    seqs: any[];
+    consensus: string;
+} | undefined;

package/dist/util.js

@@ -0,0 +1,78 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.parseBlocks = exports.parseBlock = exports.getSeqBounds = exports.getFirstNonEmptyLine = exports.parseHeader = exports.parseVersion = void 0;
+function parseVersion(line) {
+    const res = line.match(/\(?(\d+(\.\d+)+)\)?/);
+    return res && res.length > 1 ? res[1] : '';
+}
+exports.parseVersion = parseVersion;
+function parseHeader(info) {
+    const knownHeaders = ['CLUSTAL', 'PROBCONS', 'MUSCLE', 'MSAPROBS', 'Kalign'];
+    if (!knownHeaders.some(l => info.startsWith(l))) {
+        console.warn(`${info} is not a known CLUSTAL header: ${knownHeaders.join(',')}, proceeding but could indicate an issue`);
+    }
+    const version = parseVersion(info);
+    return { info, version };
+}
+exports.parseHeader = parseHeader;
+function getFirstNonEmptyLine(arr) {
+    // There should be two blank lines after the header line
+    let line = arr.next();
+    while (!line.done && line.value.trim() === '') {
+        line = arr.next();
+    }
+    return line.value;
+}
+exports.getFirstNonEmptyLine = getFirstNonEmptyLine;
+function getSeqBounds(line) {
+    const fields = line.split(/\s+/);
+    const temp = line.slice(fields[0].length);
+    const s = fields[0].length + temp.indexOf(fields[1]);
+    const e = s + fields[1].length;
+    return [s, e];
+}
+exports.getSeqBounds = getSeqBounds;
+// Use the first block to get the sequence identifiers
+function parseBlock(arr) {
+    let line = getFirstNonEmptyLine(arr);
+    const block = [];
+    let consensusLine = '';
+    if (!line) {
+        return undefined;
+    }
+    while (line) {
+        if (line[0] !== ' ') {
+            block.push(line);
+        }
+        else {
+            consensusLine = line;
+        }
+        line = arr.next().value;
+    }
+    const [start, end] = getSeqBounds(block[0]);
+    const fields = block.map(s => s.split(/\s+/));
+    const ids = fields.map(s => s[0]);
+    const seqs = block.map(s => s.slice(start, end));
+    let consensus = consensusLine.slice(start, end);
+    // handle if the consensus trailing whitespace got trimmed
+    const remainder = seqs[0].length - consensus.length;
+    if (remainder) {
+        consensus += ' '.repeat(remainder);
+    }
+    return { ids, seqs, consensus };
+}
+exports.parseBlock = parseBlock;
+function parseBlocks(arr) {
+    let block;
+    const res = parseBlock(arr);
+    if (res !== undefined) {
+        while ((block = parseBlock(arr))) {
+            for (let i = 0; i < block.seqs.length; i++) {
+                res.seqs[i] += block.seqs[i];
+            }
+            res.consensus += block.consensus;
+        }
+    }
+    return res;
+}
+exports.parseBlocks = parseBlocks;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "clustal-js",
-  "version": "1.0.4",
+  "version": "2.0.1",
   "main": "dist/index.js",
   "repository": "cmdcolin/clustal-js",
   "files": [
@@ -8,33 +8,26 @@
   ],
   "license": "MIT",
   "devDependencies": {
-    "@babel/cli": "^7.12.10",
-    "@babel/core": "^7.12.10",
-    "@babel/plugin-proposal-class-properties": "^7.12.1",
-    "@babel/plugin-transform-runtime": "^7.12.10",
-    "@babel/preset-env": "^7.12.11",
-    "@babel/preset-typescript": "^7.12.7",
-    "@types/jest": "^26.0.20",
-    "@types/node": "^14.14.22",
-    "@typescript-eslint/eslint-plugin": "^4.14.2",
-    "@typescript-eslint/parser": "^4.14.2",
-    "babel-eslint": "^10.0.1",
-    "babel-jest": "^26.6.3",
-    "eslint": "^7.19.0",
-    "eslint-config-airbnb-base": "^14.2.1",
-    "eslint-config-prettier": "^7.2.0",
-    "eslint-plugin-import": "^2.22.1",
-    "eslint-plugin-prettier": "^3.3.1",
-    "jest": "^26.6.3",
-    "jest-cli": "^26.6.3",
-    "prettier": "^2.2.1",
-    "ts-jest": "^26.5.0",
-    "typescript": "^4.1.3"
+    "@types/jest": "^29.5.12",
+    "@types/node": "^20.11.16",
+    "@typescript-eslint/eslint-plugin": "^6.21.0",
+    "@typescript-eslint/parser": "^6.21.0",
+    "eslint": "^8.56.0",
+    "eslint-config-prettier": "^9.1.0",
+    "eslint-plugin-prettier": "^5.1.3",
+    "eslint-plugin-unicorn": "^50.0.1",
+    "jest": "^29.7.0",
+    "prettier": "^3.2.5",
+    "ts-jest": "^29.1.2",
+    "typescript": "^5.3.3"
   },
   "scripts": {
+    "clean": "rimraf dist",
     "test": "jest",
     "lint": "eslint --ext .ts src test",
     "build": "tsc",
+    "prebuild": "npm run clean",
+    "preversion": "npm run lint && npm test && npm run build",
     "postversion": "git push --follow-tags"
   }
 }