optimize performance

lib/commands/base_command.ts

@@ -1,5 +1,5 @@
 import { Command } from "commander";
-import { version } from '../../package.json';
+import { readFileSync } from "fs";
 
 /**
  * This is a base class which provides a common interface for all commands.
@@ -11,8 +11,10 @@ import { version } from '../../package.json';
 export abstract class BaseCommand {
   public program: Command;
   args: string[] | undefined;
+  version: string;
 
   constructor(options?: { exitOverride?: boolean, suppressOutput?: boolean, args?: string[] }) {
+    this.version = JSON.parse(readFileSync(new URL("../../package.json", import.meta.url), "utf8")).version;
     this.program = this.create(options);
     this.args = options?.args;
   }
@@ -37,8 +39,7 @@ export abstract class BaseCommand {
         writeErr: () => { }
       });
     }
-
-    program.version(version);
+    program.version(this.version);
 
     return program;
   }

lib/commands/peptfilter.ts

@@ -1,4 +1,3 @@
-import { Option } from 'commander';
 import { createInterface } from 'node:readline';
 import { BaseCommand } from './base_command.js';
 
@@ -20,23 +19,37 @@ The input should have one peptide per line. FASTA headers are preserved in the o
       .option("-c, --contains <amino acids>", "only retain peptides that contain all of the specified amino acids", (d) => d.split(""));
   }
 
+  /**
+   * Performance note: this implementation takes 4 seconds to run on swissprot. It can be made faster by using line events instead of
+   * async iterators. This alternative implementation runs in 2.5 seconds. However, I decided that the async iterator implementation is
+   * both more readable and more in line with the implementation of the other commands.
+   */
   async run() {
     this.parseArguments();
     const minLen = this.program.opts().minlen;
     const maxlen = this.program.opts().maxlen;
     const lacks = this.program.opts().lacks || [];
     const contains = this.program.opts().contains || [];
 
+    let output = [];
+    let i = 0;
+
     for await (const line of createInterface({ input: process.stdin })) {
+      i++;
       if (line.startsWith(">")) {
-        process.stdout.write(line + "\n");
-        continue;
+        output.push(line);
+      } else if (Peptfilter.checkLength(line, minLen, maxlen) && Peptfilter.checkLacks(line, lacks) && Peptfilter.checkContains(line, contains)) {
+        output.push(line);
       }
-
-      if (Peptfilter.checkLength(line, minLen, maxlen) && Peptfilter.checkLacks(line, lacks) && Peptfilter.checkContains(line, contains)) {
-        process.stdout.write(line + "\n");
+      if (i % 1000 === 0) {
+        output.push("");
+        process.stdout.write(output.join("\n"));
+        output = [];
       }
     }
+
+    output.push("");
+    process.stdout.write(output.join("\n"));
   }
 
   static checkLength(line: string, minLen: number, maxlen: number): boolean {