add pept2ec test

eslint.config.js

@@ -10,6 +10,7 @@ export default [
   {
     rules: {
       "@typescript-eslint/no-unused-vars": ["error", { argsIgnorePattern: "^_" }],
+      "@typescript-eslint/ban-ts-comment": "off",
     },
     ignores: ["dist/"]
   }

lib/formatters/csv_formatter.ts

@@ -1,21 +1,38 @@
+import { get } from "http";
 import { Formatter } from "./formatter.js";
 import { stringify } from "csv-stringify/sync";
 
 export class CSVFormatter extends Formatter {
 
   header(sampleData: { [key: string]: string }[], fastaMapper?: boolean | undefined): string {
-    return stringify([this.getKeys(sampleData, fastaMapper)]);
+    return stringify([this.getKeys(this.flatten(sampleData), fastaMapper)]);
   }
 
   footer(): string {
     return "";
   }
 
   convert(data: object[]): string {
-    return stringify(data);
+    return stringify(this.flatten(data as { [key: string]: unknown }[]));
   }
 
-  getKeys(data: { [key: string]: string }[], fastaMapper?: boolean | undefined): string[] {
+  getKeys(data: { [key: string]: unknown }[], fastaMapper?: boolean | undefined): string[] {
     return fastaMapper ? ["fasta_header", ...Object.keys(data[0])] : Object.keys(data[0]);
   }
+
+  flatten(data: { [key: string]: unknown }[]): { [key: string]: unknown }[] {
+    if (this.getKeys(data).includes("ec")) {
+      // @ts-ignore
+      const keys = Object.keys(data[0].ec[0]);
+      data.forEach(row => {
+        keys.forEach(key => {
+          const newKey = key.startsWith("ec") ? key : `ec_${key}`;
+          // @ts-ignore
+          row[newKey] = row.ec.map(e => e[key]).join(" ");
+        });
+        delete row.ec;
+      });
+    }
+    return data;
+  }
 }

tests/commands/unipept/pept2ec.test.ts

@@ -0,0 +1,27 @@
+import { jest } from '@jest/globals';
+import { Pept2ec } from "../../../lib/commands/unipept/pept2ec";
+
+let output: string[];
+const writeSpy = 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 Pept2ec();
+  await command.run(["AALTER"], { header: true, format: "csv" });
+  expect(output[0].startsWith("peptide,total_protein_count,ec_number,ec_protein_count")).toBeTruthy();
+  expect(output[1].startsWith("AALTER,3310,2.3.2.27 3.1.3.3")).toBeTruthy();
+  expect(output.length).toBe(2);
+});
+
+test('test with fasta', async () => {
+  const command = new Pept2ec();
+  await command.run([">test", "AALTER"], { header: true, format: "csv" });
+  expect(output[0].startsWith("fasta_header,peptide,total_protein_count,ec_number,ec_protein_count")).toBeTruthy();
+  expect(output[1].startsWith(">test,AALTER,3310,2.3.2.27 3.1.3.3")).toBeTruthy();
+  expect(output.length).toBe(2);
+});

tests/commands/unipept/pept2lca.test.ts

@@ -0,0 +1,27 @@
+import { jest } from '@jest/globals';
+import { Pept2lca } from "../../../lib/commands/unipept/pept2lca";
+
+let output: string[];
+const writeSpy = 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 Pept2lca();
+  await command.run(["AALTER"], { header: true, format: "csv" });
+  expect(output[0].startsWith("peptide,taxon_id")).toBeTruthy();
+  expect(output[1].startsWith("AALTER,1,root,no rank")).toBeTruthy();
+  expect(output.length).toBe(2);
+});
+
+test('test with fasta', async () => {
+  const command = new Pept2lca();
+  await command.run([">test", "AALTER"], { header: true, format: "csv" });
+  expect(output[0].startsWith("fasta_header,peptide,taxon_id")).toBeTruthy();
+  expect(output[1].startsWith(">test,AALTER,1,root,no rank")).toBeTruthy();
+  expect(output.length).toBe(2);
+});