def test_prep_sffs_in_dir_no_trim(self): """test_prep_sffs_in_dir should use the no_trim option only if sffinfo exists.""" output_dir = tempfile.mkdtemp() gz_output_dir = tempfile.mkdtemp() try: check_sffinfo() perform_test = True except: perform_test = False if perform_test: prep_sffs_in_dir(self.sff_dir, output_dir, make_flowgram=False, convert_to_flx=False, use_sfftools=True, no_trim=True) fna_fp = os.path.join(output_dir, 'test.fna') self.assertEqual(open(fna_fp).read(), fna_notrim_txt) qual_fp = os.path.join(output_dir, 'test.qual') self.assertEqual(open(qual_fp).read(), qual_notrim_txt) self.assertRaises(TypeError, "gzipped SFF", prep_sffs_in_dir, self.gz_sff_dir, gz_output_dir, make_flowgram=False, convert_to_flx=False, use_sfftools=True, no_trim=True) shutil.rmtree(output_dir) shutil.rmtree(gz_output_dir)
def test_prep_sffs_in_dir_no_trim(self): """test_prep_sffs_in_dir should use the no_trim option only if sffinfo exists.""" output_dir = mkdtemp() gz_output_dir = mkdtemp() try: check_sffinfo() perform_test = True except: perform_test = False if perform_test: prep_sffs_in_dir(self.sff_dir, output_dir, make_flowgram=False, convert_to_flx=False, use_sfftools=True, no_trim=True) fna_fp = os.path.join(output_dir, 'test.fna') self.assertEqual(open(fna_fp).read(), fna_notrim_txt) qual_fp = os.path.join(output_dir, 'test.qual') self.assertEqual(open(qual_fp).read(), qual_notrim_txt) self.assertRaises(TypeError, "gzipped SFF", prep_sffs_in_dir, self.gz_sff_dir, gz_output_dir, make_flowgram=False, convert_to_flx=False, use_sfftools=True, no_trim=True) shutil.rmtree(output_dir) shutil.rmtree(gz_output_dir)