From 0ad8004e1fce2795fbe38f76cc61687200646ff9 Mon Sep 17 00:00:00 2001
From: Bart Mesuere <Bart.Mesuere@UGent.be>
Date: Mon, 8 Jul 2024 10:02:22 +0200
Subject: [PATCH] write to file if needed

---
 lib/commands/unipept/unipept_subcommand.ts | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/lib/commands/unipept/unipept_subcommand.ts b/lib/commands/unipept/unipept_subcommand.ts
index fc43d6b6..78777153 100644
--- a/lib/commands/unipept/unipept_subcommand.ts
+++ b/lib/commands/unipept/unipept_subcommand.ts
@@ -1,5 +1,5 @@
 import { Command, Option } from "commander";
-import { createReadStream, readFileSync } from "fs";
+import { createReadStream, createWriteStream, readFileSync } from "fs";
 import { createInterface } from "node:readline";
 import { Interface } from "readline";
 import { Formatter } from "../../formatters/formatter.js";
@@ -14,10 +14,11 @@ export abstract class UnipeptSubcommand {
   user_agent: string;
   host = "https://api.unipept.ugent.be";
   url?: string;
-  selectedFields?: RegExp[];
-  fasta: boolean;
   formatter?: Formatter;
+  outputStream: NodeJS.WritableStream = process.stdout;
   firstBatch = true;
+  selectedFields?: RegExp[];
+  fasta: boolean;
 
   constructor(name: string) {
     this.name = name;
@@ -53,6 +54,9 @@ export abstract class UnipeptSubcommand {
     this.host = this.getHost();
     this.url = `${this.host}/api/v2/${this.name}.json`;
     this.formatter = FormatterFactory.getFormatter(this.options.format);
+    if (this.options.output) {
+      this.outputStream = createWriteStream(this.options.output);
+    }
 
     let slice = [];
 
@@ -81,10 +85,10 @@ export abstract class UnipeptSubcommand {
 
     if (this.firstBatch) {
       this.firstBatch = false;
-      process.stdout.write(this.formatter.header(result, this.fasta));
+      this.outputStream.write(this.formatter.header(result, this.fasta));
     }
 
-    process.stdout.write(this.formatter.format(result, this.fasta));
+    this.outputStream.write(this.formatter.format(result, this.fasta));
   }
 
   private constructRequestBody(slice: string[]): URLSearchParams {