add taxonomy command

lib/commands/unipept.ts

@@ -9,6 +9,7 @@ import { Pept2taxa } from './unipept/pept2taxa.js';
 import { Peptinfo } from './unipept/peptinfo.js';
 import { Protinfo } from './unipept/protinfo.js';
 import { Taxa2lca } from './unipept/taxa2lca.js';
+import { Taxonomy } from './unipept/taxonomy.js';
 
 export class Unipept extends BaseCommand {
 
@@ -37,7 +38,8 @@ The command will give priority to the first way the input is passed, in the orde
       .addCommand(new Pept2taxa().command)
       .addCommand(new Peptinfo().command)
       .addCommand(new Protinfo().command)
-      .addCommand(new Taxa2lca().command);
+      .addCommand(new Taxa2lca().command)
+      .addCommand(new Taxonomy().command);
   }
 
   async run(args?: string[]) {

lib/commands/unipept/taxa2lca.ts

@@ -19,7 +19,7 @@ The command will give priority to the first way NCBI Taxonomy Identifiers are pa
       .description(this.description)
       .option("-a, --all", "report all information fields of NCBI Taxonomy records available in Unipept. Note that this may have a performance penalty.")
       .addOption(new Option("-s --select <fields...>", "select the information fields to return. Selected fields are passed as a comma separated list of field names. Multiple -s (or --select) options may be used."))
-      .argument("[proteins...]", "optionally, 1 or more UniProt ids")
+      .argument("[taxonids...]", "optionally, 1 or more taxon ids")
       .action((args, options) => this.run(args, options));
   }
 

lib/commands/unipept/taxonomy.ts

@@ -0,0 +1,33 @@
+import { Option } from "commander";
+import { UnipeptSubcommand } from "./unipept_subcommand.js";
+
+export class Taxonomy extends UnipeptSubcommand {
+
+  readonly description = `The unipept taxonomy command yields information from the Unipept Taxonomy records for a given list of NCBI Taxonomy Identifiers. The Unipept Taxonomy is a cleaned up version of the NCBI Taxonomy, and its records are also records of the NCBI Taxonomy. The command expects a list of NCBI Taxonomy Identifiers that are passed
+
+- as separate command line arguments
+- in a text file that is passed as an argument to the -i option
+- to standard input
+
+The command will give priority to the first way taxon id's are passed, in the order as listed above. Text files and standard input should have one taxon id per line.`;
+
+  constructor() {
+    super("taxonomy");
+
+    this.command
+      .summary("Fetch taxonomic information from Unipept Taxonomy.")
+      .description(this.description)
+      .option("-a, --all", "report all information fields of NCBI Taxonomy records available in Unipept. Note that this may have a performance penalty.")
+      .addOption(new Option("-s --select <fields...>", "select the information fields to return. Selected fields are passed as a comma separated list of field names. Multiple -s (or --select) options may be used."))
+      .argument("[peptides...]", "optionally, 1 or more peptides")
+      .action((args, options) => this.run(args, options));
+  }
+
+  requiredFields(): string[] {
+    return ["taxon_id"];
+  }
+
+  defaultBatchSize(): number {
+    return 100;
+  }
+}

tests/commands/unipept/taxonomy.test.ts

@@ -0,0 +1,27 @@
+import { jest } from '@jest/globals';
+import { Taxonomy } from "../../../lib/commands/unipept/taxonomy";
+
+let output: string[];
+jest
+  .spyOn(process.stdout, "write")
+  .mockImplementation((data: unknown) => { output.push(data as string); return true; });
+
+beforeEach(() => {
+  output = [];
+});
+
+test('test with default args', async () => {
+  const command = new Taxonomy();
+  await command.run(["216816"], { header: true, format: "csv" });
+  expect(output[0].startsWith("taxon_id,taxon_name,taxon_rank")).toBeTruthy();
+  expect(output[1].startsWith("216816,Bifidobacterium longum,species")).toBeTruthy();
+  expect(output.length).toBe(2);
+});
+
+test('test with fasta', async () => {
+  const command = new Taxonomy();
+  await command.run([">test", "216816"], { header: true, format: "csv" });
+  expect(output[0].startsWith("fasta_header,taxon_id,taxon_name,taxon_rank")).toBeTruthy();
+  expect(output[1].startsWith(">test,216816,Bifidobacterium longum,species")).toBeTruthy();
+  expect(output.length).toBe(2);
+});