class TrimmoaticTest(unittest.TestCase):
def setUp(self):
#chdir('work/')
token = environ.get('KB_AUTH_TOKEN', None)
config_file = environ.get('KB_DEPLOYMENT_CONFIG', None)
config = {}
config_p = ConfigParser()
config_p.read(config_file)
for nameval in config_p.items('Trimmomatic'):
config[nameval[0]] = nameval[1]
#wsURL = config['workspace-url']
#wsClient = workspaceService(wsURL, token=token)
self.token=token
self.cc = Trimmomatic(config)
def tearDown(self):
return
def test_trimmomatic(self):
print "run trim"
ctx={'token':self.token}
input_params={}
input_params['input_ws']='psdehal:1446073144048'
input_params['input_read_library']='rhodo.art.q20.int.PE.reads'
input_params['read_type']='PE'
input_params['quality_encoding']='phred33'
input_params['adapterFa']='TruSeq3-PE.fa'
input_params['seed_mismatches']='2'
input_params['palindrome_clip_threshold']='30'
input_params['simple_clip_threshold']='10'
input_params['crop_length']='200'
input_params['head_crop_length']='1'
input_params['leading_min_quality']='1'
input_params['trailing_min_quality']='1'
input_params['sliding_window_size']='4'
input_params['sliding_window_min_quality']='15'
input_params['min_length']='100'
input_params['output_read_library']='testing'
input_params['output_ws'] = input_params['input_ws']
result=self.cc.runTrimmomatic(ctx, input_params)
print result
assert result[0].find('Completed successfully')>=0
input_params['input_read_library']='rhodo.art.jgi.reads'
result=self.cc.runTrimmomatic(ctx, input_params)
print result
assert result[0].find('Completed successfully')>=0
input_params['input_read_library']='rhodo.art.q50.SE.reads'
input_params['read_type']='SE'
input_params['adapterFa']='TruSeq3-SE.fa'
result=self.cc.runTrimmomatic(ctx, input_params)
print result
assert result[0].find('Completed successfully')>=0
def test_params_trimmomatic(self):
print "run trim parameter tests"
ctx={'token':self.token}
input_params={}
input_params['input_ws']='psdehal:1446073144048'
input_params['input_read_library']='rhodo.art.q20.int.PE.reads'
input_params['read_type'] = None
self.assertRaises(ValueError, lambda: self.cc.parse_trimmomatic_steps(input_params))
input_params['read_type'] = 'XYZ'
self.assertRaises(ValueError, lambda: self.cc.parse_trimmomatic_steps(input_params))
input_params['read_type'] = 'PE'
input_params['quality_encoding'] = None
self.assertRaises(ValueError, lambda: self.cc.parse_trimmomatic_steps(input_params))
input_params['quality_encoding'] = "XYZ"
self.assertRaises(ValueError, lambda: self.cc.parse_trimmomatic_steps(input_params))
input_params['quality_encoding'] = 'phred33'
self.assertRaises(ValueError, lambda: self.cc.parse_trimmomatic_steps(input_params))
input_params['crop_length'] = '1'
input_params['adapterFa'] = None
input_params['seed_mismatches']='2'
self.assertRaises(ValueError, lambda: self.cc.parse_trimmomatic_steps(input_params))
input_params['adapterFa']='TruSeq3-PE.fa'
input_params['palindrome_clip_threshold']='30'
input_params['simple_clip_threshold']='10'
input_params['sliding_window_size']=None
input_params['sliding_window_min_quality']='15'
self.assertRaises(ValueError, lambda: self.cc.parse_trimmomatic_steps(input_params))
def setUp(self):
#chdir('work/')
token = environ.get('KB_AUTH_TOKEN', None)
config_file = environ.get('KB_DEPLOYMENT_CONFIG', None)
config = {}
config_p = ConfigParser()
config_p.read(config_file)
for nameval in config_p.items('Trimmomatic'):
config[nameval[0]] = nameval[1]
#wsURL = config['workspace-url']
#wsClient = workspaceService(wsURL, token=token)
self.token=token
self.cc = Trimmomatic(config)
def get_config():
if not get_config_file():
return None
retconfig = {}
config = ConfigParser()
config.read(get_config_file())
for nameval in config.items(get_service_name() or 'Trimmomatic'):
retconfig[nameval[0]] = nameval[1]
return retconfig
config = get_config()
from Trimmomatic.TrimmomaticImpl import Trimmomatic
impl_Trimmomatic = Trimmomatic(config)
class JSONObjectEncoder(json.JSONEncoder):
def default(self, obj):
if isinstance(obj, set):
return list(obj)
if isinstance(obj, frozenset):
return list(obj)
if hasattr(obj, 'toJSONable'):
return obj.toJSONable()
return json.JSONEncoder.default(self, obj)
sync_methods = {}
async_run_methods = {}