clustal-js 2.0.0 → 2.0.2

package/CHANGELOG.md

@@ -1,3 +1,7 @@
+# v2.0.1
+
+- Fix preversion build script
+
 # v2.0.0
 
 - Parse pairwise format, outputted by e.g. EMBOSS needle, etc

package/README.md

@@ -1,4 +1,5 @@
-[![Build Status](https://travis-ci.com/cmdcolin/clustal-js.svg?branch=master)](https://travis-ci.com/cmdcolin/clustal-js)
+[![NPM version](https://img.shields.io/npm/v/@gmod/bam.svg?style=flat-square)](https://npmjs.org/package/@gmod/bam)
+[![Build Status](https://img.shields.io/github/actions/workflow/status/cmdcolin/clustal-js/push.yml?branch=master)](https://github.com/cmdcolin/clustal-js/actions?query=branch%3Amaster+workflow%3APush+)
 
 # clustal-js
 

package/dist/index.d.ts

@@ -0,0 +1,35 @@
+export declare function parseClustalIter(arr: Iterator<string>): {
+    consensus: string;
+    alns: {
+        id: string;
+        seq: string;
+    }[];
+    header: {
+        info: string;
+        version: string;
+    };
+};
+interface Row {
+    id: string;
+    seq: string;
+}
+export declare function parsePairwiseIter(arr: string): {
+    consensus: string;
+    alns: [Row, Row];
+};
+export declare function parse(contents: string): {
+    consensus: string;
+    alns: {
+        id: string;
+        seq: string;
+    }[];
+    header: {
+        info: string;
+        version: string;
+    };
+};
+export declare function parsePairwise(contents: string): {
+    consensus: string;
+    alns: [Row, Row];
+};
+export {};

package/dist/index.js

@@ -0,0 +1,54 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.parseClustalIter = parseClustalIter;
+exports.parsePairwiseIter = parsePairwiseIter;
+exports.parse = parse;
+exports.parsePairwise = parsePairwise;
+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 };
+}
+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}`);
+    }
+    if (alns.length !== 2) {
+        throw new Error('More than two sequences in pairwise alignment');
+    }
+    return {
+        consensus,
+        alns: alns,
+    };
+}
+function parse(contents) {
+    const iter = contents.split('\n')[Symbol.iterator]();
+    return parseClustalIter(iter);
+}
+function parsePairwise(contents) {
+    return parsePairwiseIter(contents
+        .split('\n')
+        .filter(f => !f.startsWith('#'))
+        .join('\n'));
+}
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

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

package/dist/pairwise.js

@@ -0,0 +1,57 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getSeqBounds = getSeqBounds;
+exports.parsePairwiseBlock = parsePairwiseBlock;
+exports.parsePairwiseBlocks = parsePairwiseBlocks;
+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];
+}
+// 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.startsWith(' ')) {
+            consensusLine = line;
+        }
+        else {
+            block.push(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 };
+}
+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;
+}
+//# sourceMappingURL=pairwise.js.map

package/dist/pairwise.js.map

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

package/dist/util.js

@@ -0,0 +1,78 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.parseVersion = parseVersion;
+exports.parseHeader = parseHeader;
+exports.getFirstNonEmptyLine = getFirstNonEmptyLine;
+exports.getSeqBounds = getSeqBounds;
+exports.parseBlock = parseBlock;
+exports.parseBlocks = parseBlocks;
+function parseVersion(line) {
+    const res = /\(?(\d+(\.\d+)+)\)?/.exec(line);
+    return res && res.length > 1 ? res[1] : '';
+}
+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 };
+}
+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;
+}
+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];
+}
+// 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].startsWith(' ')) {
+            consensusLine = line;
+        }
+        else {
+            block.push(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 };
+}
+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;
+}
+//# sourceMappingURL=util.js.map

package/dist/util.js.map

@@ -0,0 +1 @@
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package/esm/index.d.ts

@@ -0,0 +1,35 @@
+export declare function parseClustalIter(arr: Iterator<string>): {
+    consensus: string;
+    alns: {
+        id: string;
+        seq: string;
+    }[];
+    header: {
+        info: string;
+        version: string;
+    };
+};
+interface Row {
+    id: string;
+    seq: string;
+}
+export declare function parsePairwiseIter(arr: string): {
+    consensus: string;
+    alns: [Row, Row];
+};
+export declare function parse(contents: string): {
+    consensus: string;
+    alns: {
+        id: string;
+        seq: string;
+    }[];
+    header: {
+        info: string;
+        version: string;
+    };
+};
+export declare function parsePairwise(contents: string): {
+    consensus: string;
+    alns: [Row, Row];
+};
+export {};

package/esm/index.js

@@ -0,0 +1,48 @@
+import { parsePairwiseBlocks } from './pairwise';
+import { parseBlocks, parseHeader, getFirstNonEmptyLine } from './util';
+export function parseClustalIter(arr) {
+    const line = getFirstNonEmptyLine(arr);
+    if (!line) {
+        throw new Error('Empty file received');
+    }
+    const header = parseHeader(line);
+    const res = 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 };
+}
+export function parsePairwiseIter(arr) {
+    const res = 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}`);
+    }
+    if (alns.length !== 2) {
+        throw new Error('More than two sequences in pairwise alignment');
+    }
+    return {
+        consensus,
+        alns: alns,
+    };
+}
+export function parse(contents) {
+    const iter = contents.split('\n')[Symbol.iterator]();
+    return parseClustalIter(iter);
+}
+export function parsePairwise(contents) {
+    return parsePairwiseIter(contents
+        .split('\n')
+        .filter(f => !f.startsWith('#'))
+        .join('\n'));
+}
+//# sourceMappingURL=index.js.map

package/esm/index.js.map

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package/esm/pairwise.d.ts

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

package/esm/pairwise.js

@@ -0,0 +1,52 @@
+import { getFirstNonEmptyLine } from './util';
+export 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];
+}
+// Use the first block to get the sequence identifiers
+export function parsePairwiseBlock(arr) {
+    let line = getFirstNonEmptyLine(arr);
+    const block = [];
+    let consensusLine = '';
+    if (!line) {
+        return undefined;
+    }
+    while (line) {
+        if (line.startsWith(' ')) {
+            consensusLine = line;
+        }
+        else {
+            block.push(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 };
+}
+export 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;
+}
+//# sourceMappingURL=pairwise.js.map

package/esm/pairwise.js.map

@@ -0,0 +1 @@
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package/esm/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>): string;
+export declare function getSeqBounds(line: string): readonly [number, number];
+export declare function parseBlock(arr: Iterator<string>): {
+    ids: string[];
+    seqs: string[];
+    consensus: string;
+} | undefined;
+export declare function parseBlocks(arr: Iterator<string>): {
+    ids: string[];
+    seqs: string[];
+    consensus: string;
+} | undefined;

package/esm/util.js

@@ -0,0 +1,70 @@
+export function parseVersion(line) {
+    const res = /\(?(\d+(\.\d+)+)\)?/.exec(line);
+    return res && res.length > 1 ? res[1] : '';
+}
+export 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 };
+}
+export 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;
+}
+export 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];
+}
+// Use the first block to get the sequence identifiers
+export function parseBlock(arr) {
+    let line = getFirstNonEmptyLine(arr);
+    const block = [];
+    let consensusLine = '';
+    if (!line) {
+        return undefined;
+    }
+    while (line) {
+        if (line[0].startsWith(' ')) {
+            consensusLine = line;
+        }
+        else {
+            block.push(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 };
+}
+export 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;
+}
+//# sourceMappingURL=util.js.map

package/esm/util.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -1,30 +1,38 @@
 {
   "name": "clustal-js",
-  "version": "2.0.0",
+  "version": "2.0.2",
   "main": "dist/index.js",
+  "module": "esm/index.js",
   "repository": "cmdcolin/clustal-js",
   "files": [
-    "dist"
+    "dist",
+    "esm",
+    "src"
   ],
   "license": "MIT",
   "devDependencies": {
     "@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",
+    "@types/node": "^22.0.0",
+    "@typescript-eslint/eslint-plugin": "^8.1.0",
+    "@typescript-eslint/parser": "^8.1.0",
+    "eslint": "^9.9.0",
+    "eslint-plugin-unicorn": "^55.0.0",
     "jest": "^29.7.0",
     "prettier": "^3.2.5",
-    "ts-jest": "^29.1.2",
-    "typescript": "^5.3.3"
+    "rimraf": "^6.0.1",
+    "ts-jest": "^29.2.4",
+    "typescript": "^5.3.3",
+    "typescript-eslint": "^8.1.0"
   },
   "scripts": {
+    "clean": "rimraf dist esm",
     "test": "jest",
-    "lint": "eslint --ext .ts src test",
-    "build": "tsc",
+    "lint": "eslint --report-unused-disable-directives --max-warnings 0",
+    "build": "npm run build:esm && npm run build:es5",
+    "build:esm": "tsc --target es2018 --outDir esm",
+    "build:es5": "tsc --target es2015 --module commonjs --outDir dist",
+    "prebuild": "npm run clean",
+    "preversion": "npm run lint && npm test && npm run build",
     "postversion": "git push --follow-tags"
   }
 }

package/src/index.ts

@@ -0,0 +1,65 @@
+import { parsePairwiseBlocks } from './pairwise'
+import { parseBlocks, parseHeader, getFirstNonEmptyLine } from './util'
+
+export function parseClustalIter(arr: Iterator<string>) {
+  const line = getFirstNonEmptyLine(arr)
+  if (!line) {
+    throw new Error('Empty file received')
+  }
+  const header = parseHeader(line)
+
+  const res = 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 }
+}
+
+interface Row {
+  id: string
+  seq: string
+}
+export function parsePairwiseIter(arr: string) {
+  const res = 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}`,
+    )
+  }
+  if (alns.length !== 2) {
+    throw new Error('More than two sequences in pairwise alignment')
+  }
+  return {
+    consensus,
+    alns: alns as [Row, Row],
+  }
+}
+
+export function parse(contents: string) {
+  const iter = contents.split('\n')[Symbol.iterator]()
+  return parseClustalIter(iter)
+}
+
+export function parsePairwise(contents: string) {
+  return parsePairwiseIter(
+    contents
+      .split('\n')
+      .filter(f => !f.startsWith('#'))
+      .join('\n'),
+  )
+}

package/src/pairwise.ts

@@ -0,0 +1,55 @@
+import { getFirstNonEmptyLine } from './util'
+
+export function getSeqBounds(line: string) {
+  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] as const
+}
+
+// Use the first block to get the sequence identifiers
+export function parsePairwiseBlock(arr: Iterator<string>) {
+  let line = getFirstNonEmptyLine(arr)
+  const block = []
+  let consensusLine = ''
+  if (!line) {
+    return undefined
+  }
+
+  while (line) {
+    if (line.startsWith(' ')) {
+      consensusLine = line
+    } else {
+      block.push(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 }
+}
+
+export function parsePairwiseBlocks(arr: Iterator<string>) {
+  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
+}

package/src/util.ts

@@ -0,0 +1,79 @@
+export function parseVersion(line: string) {
+  const res = /\(?(\d+(\.\d+)+)\)?/.exec(line)
+  return res && res.length > 1 ? res[1] : ''
+}
+export function parseHeader(info: string) {
+  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 }
+}
+
+export function getFirstNonEmptyLine(arr: Iterator<string>): string {
+  // 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
+}
+
+export function getSeqBounds(line: string) {
+  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] as const
+}
+
+// Use the first block to get the sequence identifiers
+export function parseBlock(arr: Iterator<string>) {
+  let line = getFirstNonEmptyLine(arr)
+  const block = []
+  let consensusLine = ''
+  if (!line) {
+    return undefined
+  }
+
+  while (line) {
+    if (line[0].startsWith(' ')) {
+      consensusLine = line
+    } else {
+      block.push(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 }
+}
+
+export function parseBlocks(arr: Iterator<string>) {
+  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
+}