Port the uniprot command

.gitignore

@@ -47,3 +47,6 @@ pkg
 
 # For rubinius:
 #*.rbc
+
+node_modules/**
+dist/**

.nvmrc

@@ -0,0 +1 @@
+22

bin/uniprot.ts

@@ -0,0 +1,71 @@
+#!/usr/bin/env node
+
+import { Option, program } from 'commander';
+import { createInterface } from 'node:readline';
+import { version } from '../package.json';
+
+const VALID_FORMATS = ["fasta", "gff", "json", "rdf", "sequence", "xml"];
+
+const description = `Command line interface to UniProt web services.
+
+The uniprot command fetches UniProt entries from the UniProt web services. The command expects a list of UniProt Accession Numbers that are passed
+
+- as separate command line arguments
+- to standard input
+
+The command will give priority to the first way UniProt Accession Numbers are passed, in the order as listed above. The standard input should have one UniProt Accession Number per line.
+
+The uniprot command yields just the protein sequences as a default, but can return several formats.`;
+
+program
+  .version(version)
+  .summary("Command line interface to UniProt web services.")
+  .description(description)
+  .argument("[accessions...]", "UniProt Accession Numbers")
+  .addOption(new Option("-f, --format <format>", `output format`).choices(VALID_FORMATS).default("sequence"));
+
+program.parse(process.argv);
+const format = program.opts().format;
+const accessions = program.args;
+
+if (accessions.length !== 0) { // input from command line arguments
+  accessions.forEach(processUniprotEntry);
+} else { // input from standard input
+  for await (const line of createInterface({ input: process.stdin })) {
+    processUniprotEntry(line.trim());
+  };
+}
+
+/**
+ * Fetches a UniProt entry and writes it to standard output.
+ *
+ * @param accession UniProt Accession Number
+ */
+async function processUniprotEntry(accession: string) {
+  process.stdout.write(await getUniprotEntry(accession, format) + "\n");
+}
+
+/**
+ * Fetches a UniProt entry in the requested format.
+ *
+ * @param accession UniProt Accession Number
+ * @param format output format
+ * @returns UniProt entry in the requested format
+ */
+async function getUniprotEntry(accession: string, format: string): Promise<string> {
+  // The UniProt REST API does not support the "sequence" format, so fetch fasta and remove the header
+  if (format === "sequence") {
+    return (await getUniprotEntry(accession, "fasta"))
+      .split("\n")
+      .slice(1)
+      .join("");
+  } else {
+    const r = await fetch(`https://rest.uniprot.org/uniprotkb/${accession}.${format}`);
+    if (r.ok) {
+      return r.text();
+    } else {
+      process.stderr.write(`Error fetching ${accession}: ${r.status} ${r.statusText}\n`);
+      return "";
+    }
+  }
+}

package.json

@@ -0,0 +1,25 @@
+{
+  "name": "unipept-cli",
+  "version": "4.0.0",
+  "description": "Command line interface to the Unipept web services",
+  "repository": "[email protected]:unipept/unipept-cli.git",
+  "author": "Bart Mesuere <[email protected]>",
+  "license": "MIT",
+  "private": false,
+  "type": "module",
+  "bin": {
+    "uniprot": "./bin/uniprot.js"
+  },
+  "scripts": {
+    "build": "yarn run tsc",
+    "uniprot": "yarn run tsx bin/uniprot.ts"
+  },
+  "dependencies": {
+    "commander": "^12.1.0"
+  },
+  "devDependencies": {
+    "@types/node": "^20.14.2",
+    "tsx": "^4.15.6",
+    "typescript": "^5.4.5"
+  }
+}

tsconfig.json

@@ -0,0 +1,11 @@
+{
+  "include": [
+    "bin/**/*"
+  ],
+  "compilerOptions": {
+    "outDir": "./dist",
+    "module": "NodeNext",
+    "strict": true,
+    "resolveJsonModule": true
+  }
+}

yarn.lock

@@ -0,0 +1,196 @@
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+  dependencies:
+    esbuild "~0.21.4"
+    get-tsconfig "^4.7.5"
+  optionalDependencies:
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+
+typescript@^5.4.5:
+  version "5.4.5"
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