def test_all(self): logger.setLevel(logging.DEBUG) os.chdir("..") self.setUpForward() self.run_tests() self.setUpReverse() self.run_tests()
v = MetadataUtils(command_line_args = args) # this will read the args and ini file and return a dictionary data_object = v.validate_args() # for attr in dir(data_object): # print("obj.%s = %s" % (attr, getattr(data_object, attr))) # set logging print("\nLog Level set to:", args.loglevel) logger.setLevel(args.loglevel.upper() ) logger.info("Starting pipeline") ############## # # Test cl parameters # ############## # CL RULES: # for ini file: (no plurals) # 1) CL: input_dir ONLY shall be supplied on CL - no input filenames # # 2) All input files should be in the same directory AND of the same format # # 3) Supply a input_file_suffix on the CL if there are varying file types in the # input_dir and you only are using some (default will read all files)
data_object['file_type'] = args.file_type data_object['file_base'] = args.file_base if data_object['site'] == 'vamps': #db_host = 'vampsdb' db_host = 'bpcdb2' #db_name = 'vamps' db_name = 'vamps_user_uploads' db_home = '/xraid2-2/vampsweb/vamps/' else: #db_host = 'vampsdev' db_host = 'bpcdb2' #db_name = 'vamps' db_name = 'vampsdev_user_uploads' db_home = '/xraid2-2/vampsweb/vampsdev/' loggerlevel = logging.DEBUG logger.setLevel(loggerlevel) obj=ConMySQL.New(db_host, db_name, db_home) data_object['db_conn'] = obj.get_conn() runDict = trim_file(data_object) push_to_database(data_object, runDict) data_object['db_conn'].close() logger.info("Finished:trim "+ args.runcode)
if args.platform not in C.known_platforms: sys.exit("unknown platform - Exiting") v = MetadataUtils(command_line_args=args) # this will read the args and ini file and return a dictionary data_object = v.validate_args() # for attr in dir(data_object): # print("obj.%s = %s" % (attr, getattr(data_object, attr))) # set logging print("\nLog Level set to:", args.loglevel) logger.setLevel(args.loglevel.upper()) logger.info("Starting pipeline") ############## # # Test cl parameters # ############## # CL RULES: # for ini file: (no plurals) # 1) CL: input_dir ONLY shall be supplied on CL - no input filenames # # 2) All input files should be in the same directory AND of the same format # # 3) Supply a input_file_suffix on the CL if there are varying file types in the # input_dir and you only are using some (default will read all files)
def test_trim_anchor(self): seq = "GGGCACACATTT" anchors = ["CACACA"] #find it in the exact spot we expect it exact, exactTrimmedOff, trimmed_sequence = trim_anchor_helper("Test Anchor", anchors, 0, 6, 3, seq) self.assertEqual((exact, exactTrimmedOff, trimmed_sequence), ("CACACA", "TTT", "GGGCACACA")) seq = "GGCACACATTT" anchors = ["CACACA"] #find it in an acceptable spot just before it so we give it a freedom of 1 exact, exactTrimmedOff, trimmed_sequence = trim_anchor_helper("Test Anchor", anchors, 1, 6, 3, seq) self.assertEqual((exact, exactTrimmedOff, trimmed_sequence), ("CACACA", "TTT", "GGCACACA")) seq = "GGGGCACACATTT" anchors = ["CACACA"] #find it in an acceptable spot just AFTER it so we give it a freedom of 1 exact, exactTrimmedOff, trimmed_sequence = trim_anchor_helper("Test Anchor", anchors, 1, 6, 3, seq) self.assertEqual((exact, exactTrimmedOff, trimmed_sequence), ("CACACA", "TTT", "GGGGCACACA")) def simple_replace_test(self, placeholder_base, new_x, new_y): result_template_strings = ["xA", "xC", "xG", "xT", "yA", "yC", "yG", "yT"] self.assertEqual(set(expand(placeholder_base + "N")), set(self.replace_template_xy(result_template_strings, new_x, new_y))) print("expanded: " + str(expand(revcomp("GTGAATCATCGAYTCTTTGAAC")))) logger.setLevel(logging.DEBUG) unittest.main()
seq = "GGCACACATTT" anchors = ["CACACA"] #find it in an acceptable spot just before it so we give it a freedom of 1 exact, exactTrimmedOff, trimmed_sequence = trim_anchor_helper( "Test Anchor", anchors, 1, 6, 3, seq) self.assertEqual((exact, exactTrimmedOff, trimmed_sequence), ("CACACA", "TTT", "GGCACACA")) seq = "GGGGCACACATTT" anchors = ["CACACA"] #find it in an acceptable spot just AFTER it so we give it a freedom of 1 exact, exactTrimmedOff, trimmed_sequence = trim_anchor_helper( "Test Anchor", anchors, 1, 6, 3, seq) self.assertEqual((exact, exactTrimmedOff, trimmed_sequence), ("CACACA", "TTT", "GGGGCACACA")) def simple_replace_test(self, placeholder_base, new_x, new_y): result_template_strings = [ "xA", "xC", "xG", "xT", "yA", "yC", "yG", "yT" ] self.assertEqual( set(expand(placeholder_base + "N")), set( self.replace_template_xy(result_template_strings, new_x, new_y))) print "expanded: " + str(expand(revcomp("GTGAATCATCGAYTCTTTGAAC"))) logger.setLevel(logging.DEBUG) unittest.main()