def test_all(self):
logger.setLevel(logging.DEBUG)
os.chdir("..")
self.setUpForward()
self.run_tests()
self.setUpReverse()
self.run_tests()
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()