refactor: update CLI

• Refactored cli.py, where the fasta dict couldn't be sliced
• Updated cli.py so the tool can now be installed with pip install . and works from the command line
• Refactored some of the code to fix CI pipeline failing
• Updated README

tests/test_cli.py

@@ -27,5 +27,5 @@ def test_file():
 
 def test_main():
     """Test main() function."""
-    with pytest.raises(TypeError):
-        main("")
+    with pytest.raises(SystemExit):
+        main()