@@ -0,0 +1,1561 @@
+#!/usr/bin/env python%0A%0A'''%0Atest_cis_splice_effects_main.py -- Integration test for %60regtools cis-splice-effects%60%0A%0A    Copyright (c) 2015, The Griffith Lab%0A%0A    Author: Avinash Ramu %3Caramu@genome.wustl.edu%3E%0A%0APermission is hereby granted, free of charge, to any person obtaining a copy%0Aof this software and associated documentation files (the %22Software%22), to deal%0Ain the Software without restriction, including without limitation the rights%0Ato use, copy, modify, merge, publish, distribute, sublicense, and/or sell%0Acopies of the Software, and to permit persons to whom the Software is%0Afurnished to do so, subject to the following conditions:%0A%0AThe above copyright notice and this permission notice shall be included in%0Aall copies or substantial portions of the Software.%0A%0ATHE SOFTWARE IS PROVIDED %22AS IS%22, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR%0AIMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,%0AFITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL%0ATHE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER%0ALIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING%0AFROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER%0ADEALINGS IN THE SOFTWARE.%0A'''%0A%0Afrom integrationtest import IntegrationTest, main%0Aimport unittest%0A%0Aclass TestCisSpliceEffectsHelp(IntegrationTest, unittest.TestCase):%0A    def test_junctions_help(self):%0A        params = %5B%22cis-splice-effects%22, %22-h%22%5D%0A        rv, err = self.execute(params)%0A        self.assertEqual(rv, 0)%0A%0Aif __name__ == %22__main__%22:%0A    main()%0A

Add test for cis-splice-effects main