def massoc_worker(inputs):
"""
Alternative version of massoc's main pipe.
Uses publisher to send messages instead of sys.stdout.write.
"""
get_input(inputs, publish=True)
run_network(inputs, publish=True)
def test_run_network(self):
"""
Checks whether combine_data returns
a batch object if inputs are supplied.
"""
inputs = {
'biom_file': [(testloc[0] + '/data/test.biom')],
'cluster': None,
'otu_meta': None,
'prefix': None,
'sample_data': None,
'split': None,
'tax_table': None,
'fp': testloc[0],
'otu_table': None,
'tools': ['spiec-easi', 'conet'],
'spiec': None,
'spar': None,
'conet': (os.path.dirname(massoc.__file__)[:-6] + 'tests\\CoNet3'),
'conet_bash': None,
'spar_pval': None,
'spar_boot': None,
'levels': ['family'],
'prev': 20,
'min': None,
'rar': None,
'name': ['test'],
'cores': None
}
write_biom_table(testbiom['test'],
fmt='hdf5',
filepath=(inputs['biom_file'][0]))
get_input(inputs)
inputs['settings'] = inputs['fp'] + '/settings.json'
run_network(inputs)
test = Path(inputs['fp'] + "/conet_family_test.txt")
self.assertTrue(test.is_file())
call(("rm " + inputs['biom_file'][0]))
call(("rm " + inputs['fp'] + "/settings.json"))
call(("rm " + inputs['fp'] + "/test_family.hdf5"))
call(("rm " + inputs['fp'] + "/test_otu.hdf5"))
call(("rm " + inputs['fp'] + "/conet_test_family.txt"))
call(("rm " + inputs['fp'] + "/spiec-easi_test_family.txt"))
def massoc(massoc_args):
"""
Main function for running massoc.
:param massoc_args: Parameters generated through massoc_parser.
:return:
"""
if 'input' in massoc_args:
logger.info('Running input module. ')
get_input(massoc_args)
if 'network' in massoc_args:
logger.info('Running network inference module. ')
run_network(massoc_args)
if 'database' in massoc_args:
logger.info('Working on Neo4j database. ')
run_neo4j(massoc_args)
if 'netstats' in massoc_args:
logger.info('Performing network analysis on Neo4j database. ')
run_netstats(massoc_args)
if 'metastats' in massoc_args:
logger.info('Performing metadata analysis on Neo4j database. ')
run_metastats(massoc_args)
logger.info('Completed tasks! ')
def test_run_netstats(self):
"""
Checks whether combine_data returns
a batch object if inputs are supplied.
"""
inputs = {
'biom_file': [(testloc[0] + '/data/test.biom')],
'cluster': None,
'otu_meta': None,
'prefix': None,
'sample_data': None,
'split': None,
'tax_table': None,
'fp': testloc[0],
'otu_table': None,
'tools': ['spiec-easi', 'conet'],
'spiec': None,
'spar': None,
'conet': (os.path.dirname(massoc.__file__)[:-6] + 'tests\\CoNet3'),
'conet_bash': None,
'spar_pval': None,
'spar_boot': None,
'levels': ['family'],
'prev': 20,
'min': None,
'rar': None,
'name': ['test'],
'cores': None,
'address': 'bolt://localhost:7687',
'username': '******',
'password': '******',
'quit': False,
'clear': False,
'write': False,
'add': False,
'output': 'network',
'logic': ['union', 'difference', 'intersection'],
'neo4j': (os.path.dirname(massoc.__file__)[:-6] + 'tests\\neo4j')
}
write_biom_table(testbiom['test'],
fmt='hdf5',
filepath=(inputs['biom_file'][0]))
get_input(inputs)
inputs['settings'] = inputs['fp'] + '/settings.json'
run_network(inputs)
inputs['job'] = 'start'
run_neo4j(inputs)
inputs['job'] = 'upload'
run_neo4j(inputs)
run_netstats(inputs)
inputs['job'] = 'clear'
run_neo4j(inputs)
inputs['job'] = 'quit'
run_neo4j(inputs)
test = Path(inputs['fp'] + "/difference_network.graphml")
self.assertTrue(test.is_file())
call(("rm " + inputs['biom_file'][0]))
call(("rm " + inputs['fp'] + "/settings.json"))
call(("rm " + inputs['fp'] + "/test_family.hdf5"))
call(("rm " + inputs['fp'] + "/test_otu.hdf5"))
call(("rm " + inputs['fp'] + "/conet_test_family.txt"))
call(("rm " + inputs['fp'] + "/spiec-easi_test_family.txt"))
call(("rm " + inputs['fp'] + "/network.graphml"))
call(("rm " + inputs['fp'] + "/difference_network.graphml"))
call(("rm " + inputs['fp'] + "/union_network.graphml"))
call(("rm " + inputs['fp'] + "/intersection_network.graphml"))