write tests

lib/commands/peptfilter.ts

@@ -22,9 +22,8 @@ The input should have one peptide per line. FASTA headers are preserved in the o
 
   async run() {
     this.parseArguments();
-    console.log(this.program.opts())
-    const minLen = this.program.opts().minLen;
-    const maxlen = this.program.opts().maxLen;
+    const minLen = this.program.opts().minlen;
+    const maxlen = this.program.opts().maxlen;
     const lacks = this.program.opts().lacks || [];
     const contains = this.program.opts().contains || [];
 
@@ -33,6 +32,7 @@ The input should have one peptide per line. FASTA headers are preserved in the o
         process.stdout.write(line + "\n");
         continue;
       }
+
       if (Peptfilter.checkLength(line, minLen, maxlen) && Peptfilter.checkLacks(line, lacks) && Peptfilter.checkContains(line, contains)) {
         process.stdout.write(line + "\n");
       }

tests/commands/peptfilter.test.ts

@@ -0,0 +1,98 @@
+import { Peptfilter } from '../../lib/commands/peptfilter';
+import * as mock from 'mock-stdin';
+
+let output: string[];
+let error: string[];
+const writeSpy = jest
+  .spyOn(process.stdout, "write")
+  .mockImplementation((data: unknown) => { output.push(data as string); return true; });
+const errorSpy = jest
+  .spyOn(process.stderr, "write")
+  .mockImplementation((data: unknown) => { error.push(data as string); return true; });
+
+beforeEach(() => {
+  output = [];
+  error = [];
+});
+
+test('test length filter', async () => {
+  // min length
+  expect(Peptfilter.checkLength('AALER', 4, 10)).toBe(true);
+  expect(Peptfilter.checkLength('AALER', 5, 10)).toBe(true);
+  expect(Peptfilter.checkLength('AALER', 6, 10)).toBe(false);
+
+  // max length
+  expect(Peptfilter.checkLength('AALER', 1, 4)).toBe(false);
+  expect(Peptfilter.checkLength('AALER', 1, 5)).toBe(true);
+  expect(Peptfilter.checkLength('AALER', 1, 6)).toBe(true);
+});
+
+test('test lacks filter', async () => {
+  expect(Peptfilter.checkLacks('AALER', ''.split(""))).toBe(true);
+  expect(Peptfilter.checkLacks('AALER', 'BCD'.split(""))).toBe(true);
+  expect(Peptfilter.checkLacks('AALER', 'A'.split(""))).toBe(false);
+  expect(Peptfilter.checkLacks('AALER', 'AE'.split(""))).toBe(false);
+});
+
+test('test contains filter', async () => {
+  expect(Peptfilter.checkContains('AALER', ''.split(""))).toBe(true);
+  expect(Peptfilter.checkContains('AALER', 'A'.split(""))).toBe(true);
+  expect(Peptfilter.checkContains('AALER', 'AE'.split(""))).toBe(true);
+  expect(Peptfilter.checkContains('AALER', 'BCD'.split(""))).toBe(false);
+  expect(Peptfilter.checkContains('AALER', 'AB'.split(""))).toBe(false);
+});
+
+test('test default filter from stdin', async () => {
+  const stdin = mock.stdin();
+
+  const command = new Peptfilter();
+  const run = command.run();
+
+  stdin.send("AAAA\n");
+  stdin.send("AAAAA\n");
+  stdin.end();
+
+  await run;
+
+  expect(writeSpy).toHaveBeenCalledTimes(1);
+  expect(errorSpy).toHaveBeenCalledTimes(0);
+  expect(output.length).toBe(1);
+});
+
+test('test if it passes fasta from stdin', async () => {
+  const stdin = mock.stdin();
+
+  const command = new Peptfilter();
+  const run = command.run();
+
+  stdin.send(">AA\n");
+  stdin.send("AAA\n");
+  stdin.end();
+
+  await run;
+
+  expect(writeSpy).toHaveBeenCalledTimes(1);
+  expect(errorSpy).toHaveBeenCalledTimes(0);
+  expect(output[0]).toBe(">AA\n");
+});
+
+test('test complex example from stdin', async () => {
+  const stdin = mock.stdin();
+
+  const command = new Peptfilter({ args: ["--minlen", "4", "--maxlen", "10", "--lacks", "B", "--contains", "A"] });
+  const run = command.run();
+
+  stdin.send("A\n");
+  stdin.send("AAAAAAAAAAA\n");
+  stdin.send("AAAAB\n");
+  stdin.send("BBBBB\n");
+  stdin.send("CCCCC\n");
+  stdin.send("CCCCCA\n");
+  stdin.end();
+
+  await run;
+
+  expect(writeSpy).toHaveBeenCalledTimes(1);
+  expect(errorSpy).toHaveBeenCalledTimes(0);
+  expect(output[0]).toBe("CCCCCA\n");
+});