cleanup

bin/uniprot.ts

@@ -2,13 +2,11 @@
 
 import { Option, program } from 'commander';
 import { createInterface } from 'node:readline';
+import { version } from '../package.json';
 
 const VALID_FORMATS = ["fasta", "gff", "json", "rdf", "sequence", "xml"];
 
-program
-  .version("1.0.0")
-  .summary("Command line interface to UniProt web services.")
-  .description(`Command line interface to UniProt web services.
+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
 
@@ -17,27 +15,45 @@ The uniprot command fetches UniProt entries from the UniProt web services. The c
 
 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.`)
+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) {
+if (accessions.length !== 0) { // input from command line arguments
   accessions.forEach(processUniprotEntry);
-} else {
+} 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")

tsconfig.json

@@ -5,6 +5,7 @@
   "compilerOptions": {
     "outDir": "./dist",
     "module": "NodeNext",
-    "strict": true
+    "strict": true,
+    "resolveJsonModule": true
   }
 }