clustal-js 1.0.2 → 1.0.4

package/CHANGELOG.md

@@ -1,3 +1,8 @@
+# v1.0.3
+
+- Add generated typescript declarations to output
+
+
 ## v1.0.2
 
 - Add dist folder to package.json

package/README.md

@@ -8,7 +8,7 @@ This parses clustal output format
 ## Usage
 
 ```js
-import {parse} from '@gmod/clustal'
+import {parse} from 'clustal-js'
 const file = fs.readFileSync('test.aln', 'utf8')
 const ret = parse(file)
 ```

package/package.json

@@ -1,7 +1,8 @@
 {
   "name": "clustal-js",
-  "version": "1.0.2",
+  "version": "1.0.4",
   "main": "dist/index.js",
+  "repository": "cmdcolin/clustal-js",
   "files": [
     "dist"
   ],

package/dist/index.js

@@ -1,29 +0,0 @@
-import { parseBlocks, parseHeader, getFirstNonEmptyLine } from "./util";
-export function parseIter(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 parse(contents) {
-  const iter = contents.split("\n")[Symbol.iterator]();
-  return parseIter(iter);
-}

package/dist/util.js

@@ -1,80 +0,0 @@
-export function parseVersion(line) {
-  const res = line.match(/\(?(\d+(\.\d+)+)\)?/);
-  return res && res.length > 1 ? res[1] : "";
-}
-export 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
-  };
-}
-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] !== " ") 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
-  };
-}
-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;
-}