implement peptfilter

bin/peptfilter.ts

@@ -0,0 +1,6 @@
+#!/usr/bin/env node
+
+import { Peptfilter } from '../lib/commands/peptfilter.js';
+
+const command = new Peptfilter();
+command.run();

lib/commands/peptfilter.ts

@@ -0,0 +1,53 @@
+import { Option } from 'commander';
+import { createInterface } from 'node:readline';
+import { BaseCommand } from './base_command.js';
+
+export class Peptfilter extends BaseCommand {
+
+  readonly description = `The peptfilter command filters a list of peptides according to specific criteria. The command expects a list of peptides that are passed to standard input.
+
+The input should have one peptide per line. FASTA headers are preserved in the output, so that peptides remain bundled.`;
+
+  constructor(options?: { exitOverride?: boolean, suppressOutput?: boolean, args?: string[] }) {
+    super(options);
+
+    this.program
+      .summary("Filter peptides based on specific criteria.")
+      .description(this.description)
+      .option("--minlen <length>", "only retain peptides having at least this many amino acids", (d) => parseInt(d, 10), 5)
+      .option("--maxlen <length>", "only retain peptides having at most this many amino acids", (d) => parseInt(d, 10), 50)
+      .option("-l, --lacks <amino acids>", "only retain peptides that lack all of the specified amino acids", (d) => d.split(""))
+      .option("-c, --contains <amino acids>", "only retain peptides that contain all of the specified amino acids", (d) => d.split(""));
+  }
+
+  async run() {
+    this.parseArguments();
+    console.log(this.program.opts())
+    const minLen = this.program.opts().minLen;
+    const maxlen = this.program.opts().maxLen;
+    const lacks = this.program.opts().lacks || [];
+    const contains = this.program.opts().contains || [];
+
+    for await (const line of createInterface({ input: process.stdin })) {
+      if (line.startsWith(">")) {
+        process.stdout.write(line + "\n");
+        continue;
+      }
+      if (Peptfilter.checkLength(line, minLen, maxlen) && Peptfilter.checkLacks(line, lacks) && Peptfilter.checkContains(line, contains)) {
+        process.stdout.write(line + "\n");
+      }
+    }
+  }
+
+  static checkLength(line: string, minLen: number, maxlen: number): boolean {
+    return line.length >= minLen && line.length <= maxlen;
+  }
+
+  static checkLacks(line: string, lacks: string[]): boolean {
+    return lacks.every((aa: string) => !line.includes(aa));
+  }
+
+  static checkContains(line: string, contains: string[]): boolean {
+    return contains.every((aa: string) => line.includes(aa));
+  }
+}

package.json

@@ -8,13 +8,15 @@
   "private": false,
   "type": "module",
   "bin": {
+    "peptfilter": "./bin/peptfilter.js",
     "uniprot": "./bin/uniprot.js"
   },
   "scripts": {
     "build": "yarn run tsc",
     "lint": "yarn run eslint",
     "test": "yarn run jest",
     "typecheck": "yarn tsc --skipLibCheck --noEmit",
+    "peptfilter": "yarn run tsx bin/peptfilter.ts",
     "uniprot": "yarn run tsx bin/uniprot.ts"
   },
   "dependencies": {