def __read_members(self):
"""reads the membership from a fixed set based on halo_ratios5.tsv
run with the R version"""
with open('testdata/row_memb-49.tsv') as member_mapfile:
member_lines = member_mapfile.readlines()
row_members = {}
for line in member_lines:
row = line.strip().split(' ')
gene = row[0].replace("\"", "")
for col in range(1, len(row)):
if gene not in row_members.keys():
row_members[gene] = []
row_members[gene].append(int(row[col]))
with open('testdata/col_memb-49.tsv') as member_mapfile:
member_lines = member_mapfile.readlines()
column_members = {}
for line in member_lines:
row = line.strip().split(' ')
cond = row[0].replace("\"", "")
for col in range(1, len(row)):
if cond not in column_members.keys():
column_members[cond] = []
column_members[cond].append(int(row[col]))
return memb.OrigMembership(sorted(row_members.keys()),
sorted(column_members.keys()), row_members,
column_members, self.config_params)
def test_free_slots_for_row(self):
"""Happy path for add_cluster_to_row()"""
m = memb.OrigMembership(['R1', 'R2'], ['C1', 'C2'], {
'R1': [1, 5],
'R2': []
}, {
'C1': [3],
'C2': []
}, CONFIG_PARAMS)
self.assertEquals(0, len(m.free_slots_for_row('R1')))
def test_add_cluster_to_column_error_full(self):
# full row memberships can not be added to in the normal case
m = memb.OrigMembership(['R1', 'R2'], ['C1', 'C2'], {
'R1': [1, 5],
'R2': []
}, {
'C1': [3, 4, 5, 6, 7],
'C2': []
}, CONFIG_PARAMS)
self.assertRaises(Exception, m.add_cluster_to_column, 'C1', 2)
def test_replace_row_cluster(self):
m = memb.OrigMembership(['R1', 'R2'], ['C1', 'C2'], {
'R1': [1, 1],
'R2': []
}, {
'C1': [3, 4, 3, 6, 7],
'C2': []
}, CONFIG_PARAMS)
m.replace_row_cluster('R1', 1, 3)
self.assertEquals({1, 3}, m.clusters_for_row('R1'))
self.assertEquals({'R1'}, m.rows_for_cluster(3))
def test_replace_column_cluster(self):
m = memb.OrigMembership(['R1', 'R2'], ['C1', 'C2'], {
'R1': [1, 5],
'R2': []
}, {
'C1': [3, 4, 3, 6, 7],
'C2': []
}, CONFIG_PARAMS)
m.replace_column_cluster('C1', 0, 1)
self.assertEquals({1, 3, 4, 6, 7}, m.clusters_for_column('C1'))
self.assertEquals({'C1'}, m.columns_for_cluster(1))
def test_add_cluster_to_row_error_full_same_cluster(self):
"""add_cluster_to_row() will only work if there are enough 0-slots"""
m = memb.OrigMembership(['R1', 'R2'], ['C1', 'C2'], {
'R1': [1, 5],
'R2': []
}, {
'C1': [3],
'C2': []
}, CONFIG_PARAMS)
m.row_membs[1] = [2, 2] # fill the spaces
self.assertRaises(Exception, m.add_cluster_to_row, 'R2', 2)
def test_add_cluster_to_column_full_force(self):
# full col memberships can be added to if forced
m = memb.OrigMembership(['R1', 'R2'], ['C1', 'C2'], {
'R1': [1, 5],
'R2': []
}, {
'C1': [3, 4, 5, 6, 7],
'C2': []
}, CONFIG_PARAMS)
m.add_cluster_to_column('C1', 2, force=True)
self.assertEquals({2, 3, 4, 5, 6, 7}, m.clusters_for_column('C1'))
self.assertEquals({'C1'}, m.columns_for_cluster(2))
def test_add_cluster_to_row_full_force(self):
# full row memberships can be added to with the force switch
m = memb.OrigMembership(['R1', 'R2'], ['C1', 'C2'], {
'R1': [1, 5],
'R2': []
}, {
'C1': [3],
'C2': []
}, CONFIG_PARAMS)
m.add_cluster_to_row('R1', 3, True)
self.assertEquals({1, 3, 5}, m.clusters_for_row('R1'))
self.assertEquals({'R1'}, m.rows_for_cluster(3))
def test_add_cluster_to_row_twice(self):
"""allow to add duplicate clusters"""
m = memb.OrigMembership(['R1', 'R2'], ['C1', 'C2'], {
'R1': [1, 5],
'R2': []
}, {
'C1': [3],
'C2': []
}, CONFIG_PARAMS)
m.add_cluster_to_row('R2', 1)
m.add_cluster_to_row('R2', 1)
self.assertEquals([1, 1], m.row_membs[1].tolist())
self.assertEquals({1}, m.clusters_for_row('R2'))
self.assertEquals(1, m.num_clusters_for_row('R2'))
def test_add_cluster_to_column_twice(self):
# allow to add duplicate clusters
m = memb.OrigMembership(['R1', 'R2'], ['C1', 'C2'], {
'R1': [1, 5],
'R2': []
}, {
'C1': [3],
'C2': []
}, CONFIG_PARAMS)
m.add_cluster_to_column('C1', 4)
m.add_cluster_to_column('C1', 4)
self.assertEquals([3, 4, 4, 0, 0], m.col_membs[0].tolist())
self.assertEquals({3, 4}, m.clusters_for_column('C1'))
self.assertEquals(2, m.num_clusters_for_column('C1'))
def test_constructor(self):
"""verify initialization"""
m = memb.OrigMembership(['R1', 'R2'], ['C1', 'C2'], {
'R1': [1, 5],
'R2': []
}, {
'C1': [3],
'C2': []
}, CONFIG_PARAMS)
self.assertEquals(43, m.num_clusters())
self.assertEquals(2, m.num_clusters_per_row())
self.assertEquals(5, m.num_clusters_per_column())
self.assertEquals(0.5, m.probability_seeing_row_change())
self.assertEquals(1.0, m.probability_seeing_col_change())
self.assertEquals(1, m.max_changes_per_row())
self.assertEquals(5, m.max_changes_per_col())
self.assertEquals(1, m.min_cluster_rows_allowed())
self.assertEquals(5, m.max_cluster_rows_allowed())
self.assertEquals(0, m.min_cluster_columns_allowed())
self.assertEquals([1, 5], m.row_membs[0].tolist())
self.assertEquals([0, 0], m.row_membs[1].tolist())
self.assertEquals([3, 0, 0, 0, 0], m.col_membs[0].tolist())
self.assertEquals([0, 0, 0, 0, 0], m.col_membs[1].tolist())
self.assertEquals({1, 5}, m.clusters_for_row('R1'))
self.assertEquals({3}, m.clusters_for_column('C1'))
self.assertEquals(2, m.num_clusters_for_row('R1'))
self.assertEquals(1, m.num_clusters_for_column('C1'))
self.assertEquals({'R1'}, m.rows_for_cluster(1))
self.assertEquals({'C1'}, m.columns_for_cluster(3))
self.assertEquals(1, m.num_row_members(1))
self.assertEquals(0, m.num_row_members(7))
self.assertEquals(1, m.num_column_members(3))
self.assertEquals(0, m.num_column_members(7))
self.assertEquals([2, 3], m.clusters_not_in_row('R1', [1, 2, 3, 5]))
self.assertEquals([1, 2, 5],
m.clusters_not_in_column('C1', [1, 2, 3, 5]))
self.assertTrue(m.is_row_in_cluster('R1', 1))
self.assertFalse(m.is_row_in_cluster('R1', 2))
self.assertTrue(m.is_column_in_cluster('C1', 3))
self.assertFalse(m.is_column_in_cluster('C1', 1))
def test_add_cluster_to_column(self):
# happy path for add_cluster_to_column()
m = memb.OrigMembership(['R1', 'R2'], ['C1', 'C2'], {
'R1': [1, 5],
'R2': []
}, {
'C1': [3],
'C2': []
}, CONFIG_PARAMS)
m.add_cluster_to_column('C1', 4)
self.assertEquals({3, 4}, m.clusters_for_column('C1'))
self.assertEquals(2, m.num_clusters_for_column('C1'))
self.assertEquals({'C1'}, m.columns_for_cluster(4))
m.add_cluster_to_column('C2', 3)
self.assertEquals({'C1', 'C2'}, m.columns_for_cluster(3))
self.assertEquals(2, m.num_column_members(3))
def test_add_cluster_to_row(self):
"""Happy path for add_cluster_to_row()"""
m = memb.OrigMembership(['R1', 'R2'], ['C1', 'C2'], {
'R1': [1, 5],
'R2': []
}, {
'C1': [3],
'C2': []
}, CONFIG_PARAMS)
m.add_cluster_to_row('R2', 3)
self.assertEquals({3}, m.clusters_for_row('R2'))
self.assertEquals(1, m.num_clusters_for_row('R2'))
self.assertEquals({'R2'}, m.rows_for_cluster(3))
m.add_cluster_to_row('R2', 1)
self.assertEquals({1, 3}, m.clusters_for_row('R2'))
self.assertEquals(2, m.num_clusters_for_row('R2'))
self.assertEquals({'R1', 'R2'}, m.rows_for_cluster(1))
self.assertEquals(2, m.num_row_members(1))
def __read_members(self):
with open('testdata/row_membership.tsv') as member_mapfile:
member_lines = member_mapfile.readlines()
row_members = {}
for line in member_lines:
row = line.strip().split('\t')
row_members[row[0]] = [int(row[1])]
with open('testdata/column_membership.tsv') as member_mapfile:
member_lines = member_mapfile.readlines()
column_members = {}
for line in member_lines:
row = line.strip().split('\t')
column_members[row[0]] = [int(cluster)
for cluster in row[1].split(':')]
return memb.OrigMembership(sorted(row_members.keys()),
sorted(column_members.keys()),
row_members, column_members,
{'memb.num_clusters': 43,
'memb.clusters_per_row': 2,
'memb.clusters_per_col': 29 })
