def test_distances_by_groups(self):
"""distances_by_groups should return correct result.
"""
exp = [\
['Control','Fast',array([[0.729, 0.8 , 0.721, 0.765],
[0.776, 0.744, 0.749, 0.677],
[0.734, 0.777, 0.733, 0.724],
[0.696, 0.675, 0.654, 0.696],
[0.731, 0.758, 0.738, 0.737]])],\
['Control','Control', array([0.625, 0.623, 0.61 , 0.577, 0.615,
0.642, 0.673, 0.682, 0.737, 0.704])],\
['Fast','Fast', array([0.718, 0.666, 0.727, 0.6, 0.578, 0.623])]
]
obs = distances_by_groups(self.distance_header,self.dmat,\
self.treatment_groups)
self.assertEqual(obs, exp)
def test_distances_by_groups(self):
"""distances_by_groups should return correct result.
"""
exp = [\
['Control','Fast',array([[0.729, 0.8 , 0.721, 0.765],
[0.776, 0.744, 0.749, 0.677],
[0.734, 0.777, 0.733, 0.724],
[0.696, 0.675, 0.654, 0.696],
[0.731, 0.758, 0.738, 0.737]])],\
['Control','Control', array([0.625, 0.623, 0.61 , 0.577, 0.615,
0.642, 0.673, 0.682, 0.737, 0.704])],\
['Fast','Fast', array([0.718, 0.666, 0.727, 0.6, 0.578, 0.623])]
]
obs = distances_by_groups(self.distance_header,self.dmat,\
self.treatment_groups)
self.assertEqual(obs,exp)
def setUp(self):
"""setup data function for DistanceHistogramsTests."""
self.working_dir = '/tmp/distance_histogram_tests/'
try:
mkdir(self.working_dir)
except OSError: #except already exisits
pass
self.histogram_dir = self.working_dir + 'histograms/'
try:
mkdir(self.histogram_dir)
except OSError: #except already exisits remove it and make a new one
pass
#Create distance matrix file
self.dmat_file = self.working_dir + 'dmat.txt'
dmat_out = open(self.dmat_file, 'w')
dmat_out.write(DISTANCE_MATRIX_STRING)
dmat_out.close()
self.distance_header, self.dmat = \
parse_distmat(open(self.dmat_file,'U'))
#Create mapping file
self.map_file = self.working_dir + 'map.txt'
map_out = open(self.map_file, 'w')
map_out.write(MAPPING_STRING)
map_out.close()
mapping, header, comments = parse_mapping_file(open(
self.map_file, 'U'))
header[0] = '#' + header[0]
header = [header]
header.extend(mapping)
self.mapping = header
#Create prefs file
self.prefs_file = self.working_dir + 'prefs.txt'
prefs_out = open(self.prefs_file, 'w')
prefs_out.write(str(PREFS))
prefs_out.close()
#Build single field dict for 'Treatment' field.
self.single_field_treatment = defaultdict(dict)
self.treatment_groups = group_by_field(self.mapping, 'Treatment')
self.single_field_treatment['Treatment'] = \
distances_by_groups(self.distance_header,self.dmat,\
self.treatment_groups)
self.paired_field_treatment = {'Treatment_to_Treatment':[\
[('Control','Control'),('Fast','Fast'),\
array([[0.729, 0.8 , 0.721, 0.765],
[0.776, 0.744, 0.749, 0.677],
[0.734, 0.777, 0.733, 0.724],
[0.696, 0.675, 0.654, 0.696],
[0.731, 0.758, 0.738, 0.737]])],\
[('Control','Control'),('Control','Control'),\
array([0.625, 0.623, 0.61 , 0.577, 0.615,
0.642, 0.673, 0.682, 0.737, 0.704])],\
[('Fast','Fast'),('Fast','Fast'),\
array([0.718, 0.666, 0.727, 0.6, 0.578, 0.623])]
]}
self.distances_file = self.working_dir + 'distances_out.txt'
dist_out = open(self.distances_file, 'w')
dist_out.write(DISTANCES_OUT)
dist_out.close()
def setUp(self):
"""setup data function for DistanceHistogramsTests."""
self.working_dir = '/tmp/distance_histogram_tests/'
try:
mkdir(self.working_dir)
except OSError: #except already exisits
pass
self.histogram_dir = path.join(self.working_dir,'histograms')
try:
mkdir(self.histogram_dir)
except OSError: #except already exisits remove it and make a new one
pass
#Create distance matrix file
self.dmat_file = self.working_dir+'dmat.txt'
dmat_out = open(self.dmat_file,'w')
dmat_out.write(DISTANCE_MATRIX_STRING)
dmat_out.close()
self.distance_header, self.dmat = \
parse_distmat(open(self.dmat_file,'U'))
#Create mapping file
self.map_file = self.working_dir+'map.txt'
map_out = open(self.map_file,'w')
map_out.write(MAPPING_STRING)
map_out.close()
mapping, header, comments = parse_mapping_file(open(self.map_file,'U'))
header[0] = '#'+header[0]
header = [header]
header.extend(mapping)
self.mapping=header
#Create prefs file
self.prefs_file = self.working_dir+'prefs.txt'
prefs_out = open(self.prefs_file,'w')
prefs_out.write(str(PREFS))
prefs_out.close()
#Build single field dict for 'Treatment' field.
self.single_field_treatment = defaultdict(dict)
self.treatment_groups = group_by_field(self.mapping, 'Treatment')
self.single_field_treatment['Treatment'] = \
distances_by_groups(self.distance_header,self.dmat,\
self.treatment_groups)
self.paired_field_treatment = {'Treatment_to_Treatment':[\
[('Control','Control'),('Fast','Fast'),\
array([[0.729, 0.8 , 0.721, 0.765],
[0.776, 0.744, 0.749, 0.677],
[0.734, 0.777, 0.733, 0.724],
[0.696, 0.675, 0.654, 0.696],
[0.731, 0.758, 0.738, 0.737]])],\
[('Control','Control'),('Control','Control'),\
array([0.625, 0.623, 0.61 , 0.577, 0.615,
0.642, 0.673, 0.682, 0.737, 0.704])],\
[('Fast','Fast'),('Fast','Fast'),\
array([0.718, 0.666, 0.727, 0.6, 0.578, 0.623])]
]}
self.distances_file = self.working_dir+'distances_out.txt'
dist_out = open(self.distances_file,'w')
dist_out.write(DISTANCES_OUT)
dist_out.close()