clustal-js 1.0.3 → 2.0.0

package/CHANGELOG.md

@@ -1,8 +1,15 @@
+# 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 '@gmod/clustal'
+```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/package.json

@@ -1,6 +1,6 @@
 {
   "name": "clustal-js",
-  "version": "1.0.3",
+  "version": "2.0.0",
   "main": "dist/index.js",
   "repository": "cmdcolin/clustal-js",
   "files": [
@@ -8,28 +8,18 @@
   ],
   "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": {
     "test": "jest",

package/dist/index.d.ts

@@ -1,3 +0,0 @@
-import { Results } from "./types";
-export declare function parseIter(arr: Iterator<string>): Results;
-export declare function parse(contents: string): Results;

package/dist/index.js

@@ -1,25 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.parse = exports.parseIter = void 0;
-const util_1 = require("./util");
-function parseIter(arr) {
-    const line = util_1.getFirstNonEmptyLine(arr);
-    if (!line)
-        throw new Error("Empty file received");
-    const header = util_1.parseHeader(line);
-    const res = 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.parseIter = parseIter;
-function parse(contents) {
-    const iter = contents.split("\n")[Symbol.iterator]();
-    return parseIter(iter);
-}
-exports.parse = parse;

package/dist/types.d.ts

@@ -1,18 +0,0 @@
-export interface Header {
-    version: string;
-    info: string;
-}
-export interface Alignment {
-    id: string;
-    seq: string;
-}
-export interface Block {
-    consensus: string;
-    seqs: string[];
-    ids: string[];
-}
-export interface Results {
-    header: Header;
-    alns: Alignment[];
-    consensus: string;
-}

package/dist/types.js

@@ -1,2 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });

package/dist/util.d.ts

@@ -1,7 +0,0 @@
-import { Header, Block } from "./types";
-export declare function parseVersion(line: string): string;
-export declare function parseHeader(info: string): Header;
-export declare function getFirstNonEmptyLine(arr: Iterator<string>): string;
-export declare function getSeqBounds(line: string): number[];
-export declare function parseBlock(arr: Iterator<string>): Block | undefined;
-export declare function parseBlocks(arr: Iterator<string>): Block | undefined;

package/dist/util.js

@@ -1,75 +0,0 @@
-"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.find((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;