def test_read_table_missing_node(self):
"""
Raise FormatError if a node is missing from the header
"""
TRUTH_TABLE = join(self.TABLE_PATH, "missing_node.txt")
with self.assertRaises(FormatError):
LogicNetwork.read_table(TRUTH_TABLE)
def test_read_table_invalid_condition(self):
"""
Raise FormatError if a condition has an invalid state
"""
TRUTH_TABLE = join(self.TABLE_PATH, "invalid_condition.txt")
with self.assertRaises(FormatError):
LogicNetwork.read_table(TRUTH_TABLE)
def test_logic_simple_read_no_header(self):
"""
Test simple network read in (no header)
"""
TRUTH_TABLE = join(self.TABLE_PATH, "no_header.txt")
with self.assertRaises(FormatError):
LogicNetwork.read_table(TRUTH_TABLE)
def test_logic_simple_read_no_node_headers(self):
"""
Test simple network read in (no node headers)
"""
SIMPLE_TRUTH_TABLE = join(self.TABLE_PATH, "no_node_headers.txt")
with self.assertRaises(FormatError):
LogicNetwork.read_table(SIMPLE_TRUTH_TABLE)
def test_read_table_condition_len_mismatch(self):
"""
Raise FormatError if a condition has too many or too few bits in it
"""
TRUTH_TABLE = join(self.TABLE_PATH, "missing_condition.txt")
with self.assertRaises(FormatError):
LogicNetwork.read_table(TRUTH_TABLE)
TRUTH_TABLE = join(self.TABLE_PATH, "extra_condition.txt")
with self.assertRaises(FormatError):
LogicNetwork.read_table(TRUTH_TABLE)
def test_logic_simple_read_no_node_headers(self):
from os.path import dirname, abspath, realpath, join
# Determine the path to the "data" directory of the neet.test module
DATA_PATH = join(dirname(abspath(realpath(__file__))), "data")
# Test simple network read in (no header)
SIMPLE_TRUTH_TABLE = join(
DATA_PATH, "test_simple_no_node_headers-truth_table.txt")
with self.assertRaises(FormatError):
LogicNetwork.read_table(SIMPLE_TRUTH_TABLE)
def test_read_table_skips_empty(self):
"""
Empty lines are skipped when reading truth tables
"""
TRUTH_TABLE = join(self.TABLE_PATH, "empty_lines.txt")
simple = LogicNetwork.read_table(TRUTH_TABLE)
self.assertEqual(simple.names, ['A', 'B', 'C'])
self.assertEqual(simple.table,
[((1, 2), set(['10', '11'])), ((0, ), set(['1'])),
((1, 2, 0), set(['101', '010', '011']))])
def test_logic_simple_read_empty(self):
"""
Test simple network read in (empty table)
"""
TRUTH_TABLE = join(self.TABLE_PATH, "empty_table.txt")
simple = LogicNetwork.read_table(TRUTH_TABLE)
self.assertEqual(simple.names, ['A', 'B', 'C', 'D'])
self.assertEqual(simple.table,
[((0, ), set(['1'])), ((1, ), set(['1'])),
((2, ), set(['1'])), ((3, ), set(['1']))])
def test_logic_simple_read_custom_comment(self):
"""
Test simple network read in with custom comments
"""
TRUTH_TABLE = join(self.TABLE_PATH, "custom_comment.txt")
simple = LogicNetwork.read_table(TRUTH_TABLE)
self.assertEqual(simple.names, ['A', 'B', 'C', 'D'])
self.assertEqual(simple.table,
[((1, 2), set(['11', '10'])), ((0, ), set(['1'])),
((1, 2, 0), set(['010', '011', '101'])),
((3, ), set(['1']))])
def test_logic_simple_read(self):
"""
Read a network from a truth table file
"""
TRUTH_TABLE = join(self.TABLE_PATH, "simple_table.txt")
simple = LogicNetwork.read_table(TRUTH_TABLE)
self.assertEqual(simple.names, ['A', 'B', 'C', 'D'])
self.assertEqual(simple.table,
[((1, 2), set(['11', '10'])), ((0, ), set(['1'])),
((1, 2, 0), set(['010', '011', '101'])),
((3, ), set(['1']))])
def test_logic_simple_read_empty(self):
from os.path import dirname, abspath, realpath, join
# Determine the path to the "data" directory of the neet.test module
DATA_PATH = join(dirname(abspath(realpath(__file__))), "data")
# Test simple network read in (no header)
SIMPLE_TRUTH_TABLE = join(DATA_PATH,
"test_simple_empty-truth_table.txt")
simple = LogicNetwork.read_table(SIMPLE_TRUTH_TABLE)
self.assertEqual(simple.names, ['A', 'B', 'C', 'D'])
self.assertEqual(simple.table,
[((0, ), set(['1'])), ((1, ), set(['1'])),
((2, ), set(['1'])), ((3, ), set(['1']))])
'The p53 GRN with damage present.',
'citation':
'Choi, Minsoo, Jue Shi, Sung Hoon Jung, Xi Chen, and'
' Kwang-Hyun Cho. Attractor Landscape Analysis Reveals'
' Feedback Loops in the p53 Network That Control the'
' Cellular Response to DNA Damage. Science Signaling 5,'
' no. 251 (2012): ra83. doi:10.1126/scisignal.2003363.',
})
MOUSE_CORTICAL_7B_TRUTH_TABLE = join(DATA_PATH,
"mouse_cortical_fig_7B-truth_table.txt")
MOUSE_CORTICAL_7B_EXPRESSIONS = join(
DATA_PATH, "mouse_cortical_fig_7B-logic_expressions.txt")
#: The gene regulatory network for *mouse cortical* (7B edges)
mouse_cortical_7B = LogicNetwork.read_table(MOUSE_CORTICAL_7B_TRUTH_TABLE)
mouse_cortical_7B.metadata.update({
'name':
'mouse_cortical_fig_7B',
'description':
'The gene regulatory network for *mouse cortical*'
' (Taken from figure 7B in citation below).',
'citation':
'Giacomantonio, Clare E., and Geoffrey J. Goodhill. "A'
' Boolean model of the gene regulatory network underlying'
' Mammalian cortical area development." PLoS'
' computational biology 6, no. 9 (2010):'
' e1000936. doi:10.1371/journal.pcbi.1000936',
})
mouse_cortical_7B_from_expr = LogicNetwork.read_logic(
MOUSE_CORTICAL_7B_EXPRESSIONS)
})
MOUSE_CORTICAL_7B_TRUTH_TABLE = join(DATA_PATH,
"mouse_cortical_fig_7B-truth_table.txt")
MOUSE_CORTICAL_7B_EXPRESSIONS = join(
DATA_PATH, "mouse_cortical_fig_7B-logic_expressions.txt")
#: A gene regulatory network model for cortical area development in mice, as
#: described in fig. 7B of [Giacomantonio2010]_.
mouse_cortical_7B = LogicNetwork.read_table(
MOUSE_CORTICAL_7B_TRUTH_TABLE,
metadata={
'name':
'Mouse Cortical Area Development (fig. 7B)',
'description':
'The gene regulatory network for cortical area development '
'in mice. Network taken from fig. 7B.',
'citation':
'C. E. Giacomantonio and G. J. Goodhill, "A Boolean model of '
'the gene regulatory network underlying Mammalian cortical '
'area development," PLoS Comput. Biol., vol. 6, no. 9, Sep. '
'2010. doi:10.1371/journal.pcbi.1000936'
})
mouse_cortical_7B_from_expr = LogicNetwork.read_logic(
MOUSE_CORTICAL_7B_EXPRESSIONS,
metadata={
'name':
'Mouse Cortical Area Development (fig. 7B)',
'description':
'The gene regulatory network for cortical area development '
'in mice. Network taken from fig. 7B.',
'citation':