def test_cycle_graph(n: int, edge_sign: int):
primes = cycle_graph(n=n, edge_sign=edge_sign)
ig = primes2igraph(primes)
cycle = networkx.cycle_graph(n=n, create_using=networkx.DiGraph)
assert networkx.is_isomorphic(ig, cycle)
assert_edge_signs_agree(ig, edge_sign, loop_sign=edge_sign)
def test_primes2igraph2():
fname_in = get_tests_path_in(fname="interactiongraphs_irma.primes")
primes = read_primes(fname_json=fname_in)
igraph = primes2igraph(primes=primes)
nodes = sorted(igraph.nodes(data=True))
expected_nodes = [("Ash1", {}), ("Cbf1", {}), ("Gal4", {}), ("Gal80", {}),
("Swi5", {}), ("gal", {})]
assert nodes == expected_nodes
edges = sorted(igraph.edges(data=True))
expected_edges = [("Ash1", "Cbf1", {
"sign": {1}
}), ("Cbf1", "Ash1", {
"sign": {1}
}), ("Gal4", "Swi5", {
"sign": {-1}
}), ("Gal80", "Gal4", {
"sign": {1}
}), ("Swi5", "Gal4", {
"sign": {-1}
}), ("gal", "Ash1", {
"sign": {1}
}), ("gal", "Gal80", {
"sign": {-1}
}), ("gal", "gal", {
"sign": {1}
})]
assert edges == expected_edges
def test_path_graph(n: int, edge_sign: int, loop_sign: int):
primes = path_graph(n=n, edge_sign=edge_sign, loop_sign=loop_sign)
ig = primes2igraph(primes)
path = networkx.path_graph(n=n, create_using=networkx.DiGraph)
path.add_edge(0, 0)
assert networkx.is_isomorphic(ig, path)
assert_edge_signs_agree(ig, edge_sign, loop_sign)
def primes2bns(primes: dict, fname_bns: Optional[str] = None) -> str:
"""
Saves Primes as a *bns* file for the computation of all attractors of the synchronous transition system.
BNS_ is based on :ref:`Dubrova2011 <Dubrova2011>`.
It is available at http://people.kth.se/~dubrova/bns.html.
**arguments**:
* *primes*: prime implicants
* *fname_bns*: name of *bns* file or *None* to return file as string
**example**::
>>> primes2bns(primes, "mapk.bns")
"""
names_sorted = sorted(primes)
lines = ["# " + ", ".join(names_sorted), ""]
lines += [f".v {len(names_sorted)}", ""]
ig = primes2igraph(primes)
for i, name in enumerate(names_sorted):
i += 1
lines += [f"# {name}"]
regulators = sorted(ig.predecessors(name))
number_regs = len(regulators)
ids_regs = " ".join(
[str(names_sorted.index(reg) + 1) for reg in regulators])
lines += [f".n {i} {number_regs} {ids_regs}"]
for v in [0, 1]:
for prime in primes[name][v]:
seq = []
for reg in regulators:
if reg in prime:
if prime[reg] == 1:
seq.append("1")
else:
seq.append("0")
else:
seq.append("-")
if regulators:
seq.append(" ")
seq.append(str(v))
lines += ["".join(seq)]
lines += [""]
text = "\n".join(lines)
if fname_bns:
with open(fname_bns, "w") as f:
f.write(text)
log.info(f"created {fname_bns}")
return text
def test_find_minimal_autonomous_nodes():
primes = get_primes("randomnet_n15k3")
igraph = primes2igraph(primes)
nodes = find_minimal_autonomous_nodes(igraph, core=set())
expected = [{
"Gene8", "Gene9", "Gene1", "Gene2", "Gene3", "Gene4", "Gene5", "Gene6",
"Gene7", "Gene12", "Gene13", "Gene10", "Gene11", "Gene14"
}]
assert expected == nodes
def test_balanced_tree(height: int, branching_factor: int, edge_sign: int,
loop_sign: int):
primes = balanced_tree(height, branching_factor, edge_sign, loop_sign)
ig = primes2igraph(primes)
path = networkx.balanced_tree(r=branching_factor,
h=height,
create_using=networkx.DiGraph)
path.add_edge(0, 0)
assert networkx.is_isomorphic(ig, path)
assert_edge_signs_agree(ig, edge_sign, loop_sign)
def test_primes2igraph1():
fname_in = get_tests_path_in(fname="interactiongraphs_irma.primes")
primes = read_primes(fname_json=fname_in)
igraph = primes2igraph(primes=primes)
nodes = sorted(igraph.nodes())
expected_nodes = ["Ash1", "Cbf1", "Gal4", "Gal80", "Swi5", "gal"]
assert nodes == expected_nodes
edges = sorted(igraph.edges())
expected_edges = [("Ash1", "Cbf1"), ("Cbf1", "Ash1"), ("Gal4", "Swi5"),
("Gal80", "Gal4"), ("Swi5", "Gal4"), ("gal", "Ash1"),
("gal", "Gal80"), ("gal", "gal")]
assert edges == expected_edges
def test_primes2igraph4():
primes = {
"A": [[{}], []],
"B": [[{
"B": 0
}], [{
"B": 1
}]],
"C": [[{
"C": 1
}], [{
"C": 0
}]],
"D": [[{
"B": 0,
"C": 0
}, {
"B": 1,
"C": 1
}], [{
"B": 1,
"C": 0
}, {
"B": 0,
"C": 1
}]]
}
igraph = primes2igraph(primes=primes)
nodes = sorted(igraph.nodes(data=True))
expected_nodes = [("A", {}), ("B", {}), ("C", {}), ("D", {})]
assert nodes == expected_nodes
edges = sorted(igraph.edges(data=True))
expected_edges = [("B", "B", {
"sign": {1}
}), ("B", "D", {
"sign": {1, -1}
}), ("C", "C", {
"sign": {-1}
}), ("C", "D", {
"sign": {1, -1}
})]
assert edges == expected_edges
def iterative_completeness_algorithm(
primes: dict,
update: str,
compute_counterexample: bool,
max_output: int = 1000) -> Union[Tuple[bool, Optional[dict]], bool]:
"""
The iterative algorithm for deciding whether the minimal trap spaces are complete.
The function is implemented by line-by-line following of the pseudo code algorithm given in
"Approximating attractors of Boolean networks by iterative CTL model checking", Klarner and Siebert 2015.
**arguments**:
* *primes*: prime implicants
* *update*: the update strategy, one of *"asynchronous"*, *"synchronous"*, *"mixed"*
* *compute_counterexample*: whether to compute a counterexample
**returns**:
* *answer*: whether *subspaces* is complete in the STG defined by *primes* and *update*,
* *counterexample*: a state that can not reach one of the minimal trap spaces of *primes* or *None* if no counterexample exists
**example**::
>>> answer, counterexample = completeness_with_counterexample(primes, "asynchronous")
>>> answer
False
>>> state2str(counterexample)
10010111101010100001100001011011111111
"""
primes = percolate(primes=primes, copy=True)
constants_global = find_constants(primes=primes)
remove_all_constants(primes=primes)
min_trap_spaces = compute_trap_spaces(primes=primes,
type_="min",
max_output=max_output)
if min_trap_spaces == [{}]:
if compute_counterexample:
return True, None
else:
return True
current_set = [({}, set([]))]
while current_set:
p, w = current_set.pop()
primes_reduced = copy_primes(primes=primes)
create_constants(primes=primes_reduced, constants=p)
igraph = primes2igraph(primes=primes_reduced)
cgraph = digraph2condensationgraph(digraph=igraph)
cgraph_dash = cgraph.copy()
for U in cgraph.nodes():
if set(U).issubset(set(w)):
cgraph_dash.remove_node(U)
w_dash = w.copy()
refinement = []
top_layer = [
U for U in cgraph_dash.nodes() if cgraph_dash.in_degree(U) == 0
]
for U in top_layer:
u_dash = find_ancestors(igraph, U)
primes_restricted = copy_primes(primes_reduced)
remove_all_variables_except(primes=primes_restricted, names=u_dash)
q = compute_trap_spaces(primes=primes_restricted,
type_="min",
max_output=max_output)
phi = exists_finally_one_of_subspaces(primes=primes_restricted,
subspaces=q)
init = "INIT TRUE"
spec = f"CTLSPEC {phi}"
if compute_counterexample:
answer, counterexample = model_checking(
primes=primes_restricted,
update=update,
initial_states=init,
specification=spec,
enable_counterexample=True)
if not answer:
downstream = [x for x in igraph if x not in U]
arbitrary_state = random_state(downstream)
top_layer_state = counterexample[-1]
counterexample = merge_dicts([
constants_global, p, top_layer_state, arbitrary_state
])
return False, counterexample
else:
answer = model_checking(primes=primes_restricted,
update=update,
initial_states=init,
specification=spec)
if not answer:
return False
refinement += intersection([p], q)
w_dash.update(u_dash)
for q in intersection(refinement):
q_tilde = find_constants(
primes=percolate(primes=primes, add_constants=q, copy=True))
if q_tilde not in min_trap_spaces:
current_set.append((q_tilde, w_dash))
if compute_counterexample:
return True, None
else:
return True
def test_activities2animation():
fname_in = get_tests_path_in(fname="irma.primes")
fname_out1 = get_tests_path_out(fname="irma*.png")
fname_out2 = get_tests_path_out(fname="irma.gif")
primes = read_primes(fname_json=fname_in)
igraph = primes2igraph(primes)
activities = [
{
"gal": 0,
"Cbf1": 1,
"Gal80": 1,
"Ash1": 0,
"Gal4": 0,
"Swi5": 1
},
{
"gal": 1,
"Cbf1": 1,
"Gal80": 1,
"Ash1": 0,
"Gal4": 0,
"Swi5": 1
},
{
"gal": 1,
"Cbf1": 0,
"Gal80": 1,
"Ash1": 0,
"Gal4": 0,
"Swi5": 1
},
{
"gal": 1,
"Cbf1": 0,
"Gal80": 0,
"Ash1": 0,
"Gal4": 0,
"Swi5": 1
},
{
"gal": 1,
"Cbf1": 0,
"Gal80": 0,
"Ash1": 1,
"Gal4": 0,
"Swi5": 1
},
{
"gal": 1,
"Cbf1": 0,
"Gal80": 0,
"Ash1": 1,
"Gal4": 1,
"Swi5": 1
},
{
"gal": 1,
"Cbf1": 0,
"Gal80": 0,
"Ash1": 1,
"Gal4": 1,
"Swi5": 0
},
]
activities2animation(igraph=igraph,
activities=activities,
fname_tmp=fname_out1,
fname_gif=fname_out2)
def test_styles():
fname_in = get_tests_path_in(fname="interactiongraphs_topology.primes")
fname_out_dot = get_tests_path_out(
fname="interactiongraphs_style_interactionsigns.dot")
fname_out_pdf = get_tests_path_out(
fname="interactiongraphs_style_interactionsigns.pdf")
primes = read_primes(fname_json=fname_in)
igraph = primes2igraph(primes=primes)
add_style_interactionsigns(igraph=igraph)
igraph2dot(igraph=igraph, fname_dot=fname_out_dot)
dot2image(fname_dot=fname_out_dot, fname_image=fname_out_pdf)
igraph2image(igraph=igraph, fname_image=fname_out_pdf)
fname_out_dot = get_tests_path_out(
fname="interactiongraphs_style_activities.dot")
fname_out_pdf = get_tests_path_out(
fname="interactiongraphs_style_activities.pdf")
add_style_interactionsigns(igraph=igraph)
igraph2dot(igraph=igraph, fname_dot=fname_out_dot)
dot2image(fname_dot=fname_out_dot, fname_image=fname_out_pdf)
igraph2image(igraph=igraph, fname_image=fname_out_pdf)
igraph = primes2igraph(primes=primes)
activities = {"v1": 1, "v2": 0, "v3": 1, "v4": 1, "v5": 1, "v6": 0}
add_style_activities(igraph=igraph, activities=activities)
igraph2dot(igraph=igraph, fname_dot=fname_out_dot)
dot2image(fname_dot=fname_out_dot, fname_image=fname_out_pdf)
fname_in = get_tests_path_in(fname="interactiongraphs_topology.primes")
fname_out_dot = get_tests_path_out(
fname="interactiongraphs_style_sccs.dot")
fname_out_pdf = get_tests_path_out(
fname="interactiongraphs_style_sccs.pdf")
primes = read_primes(fname_json=fname_in)
igraph = primes2igraph(primes=primes)
add_style_sccs(igraph=igraph)
igraph2dot(igraph=igraph, fname_dot=fname_out_dot)
dot2image(fname_dot=fname_out_dot, fname_image=fname_out_pdf)
fname_in = get_tests_path_in(fname="interactiongraphs_topology.primes")
fname_out_pdf = get_tests_path_out(fname="interactiongraphs_style_ioc.pdf")
primes = read_primes(fname_json=fname_in)
igraph = primes2igraph(primes=primes)
add_style_inputs(igraph=igraph)
add_style_constants(igraph=igraph)
add_style_outputs(igraph=igraph)
igraph2image(igraph=igraph, fname_image=fname_out_pdf)
fname_in = get_tests_path_in(fname="interactiongraphs_topology.primes")
fname_out_pdf = get_tests_path_out(
fname="interactiongraphs_style_subgrapghs.pdf")
fname_out_dot = get_tests_path_out(
fname="interactiongraphs_style_subgrapghs.dot")
primes = read_primes(fname_json=fname_in)
igraph = primes2igraph(primes=primes)
subgraphs = [(["v1", "v2"], {}), (["v3", "v4"], {"label": "jo"})]
add_style_subgraphs(igraph=igraph, subgraphs=subgraphs)
igraph2dot(igraph=igraph, fname_dot=fname_out_dot)
dot2image(fname_dot=fname_out_dot, fname_image=fname_out_pdf)
def test_igraph2image():
fname_in = get_tests_path_in(fname="interactiongraphs_irma.primes")
primes = read_primes(fname_json=fname_in)
igraph = primes2igraph(primes=primes)
fname_out = get_tests_path_out(fname="interactiongraphs_igraph2image.png")
igraph2image(igraph=igraph, fname_image=fname_out)
def test_igraph2dot_string():
fname_in = get_tests_path_in(fname="interactiongraphs_irma.primes")
primes = read_primes(fname_json=fname_in)
igraph = primes2igraph(primes=primes)
igraph2dot(igraph=igraph, fname_dot=None)
def test_igraph2dot():
fname_in = get_tests_path_in(fname="interactiongraphs_irma.primes")
fname_out = get_tests_path_out(fname="interactiongraphs_igraph2dot.dot")
primes = read_primes(fname_json=fname_in)
igraph = primes2igraph(primes=primes)
igraph2dot(igraph=igraph, fname_dot=fname_out)
import pyboolnet.state_space
from pyboolnet.interaction_graphs import primes2igraph, igraph2image, local_igraph_of_state, add_style_interactionsigns
from pyboolnet.repository import get_primes
from pyboolnet.state_transition_graphs import create_stg_image
if __name__ == "__main__":
primes = get_primes("remy_tumorigenesis")
create_stg_image(primes, update="asynchronous", fname_image="igraph.pdf")
create_stg_image(primes,
update="asynchronous",
fname_image="igraph2.pdf",
styles=["anonymous", "sccs"])
# advances drawing
igraph = primes2igraph(primes)
for x in igraph.nodes:
if "GF" in x:
igraph.nodes[x]["shape"] = "square"
igraph.nodes[x]["fillcolor"] = "lightblue"
igraph2image(igraph, "igraph3.pdf")
# local interaction graphs
state = pyboolnet.state_space.random_state(primes)
local_igraph = local_igraph_of_state(primes, state)
add_style_interactionsigns(local_igraph)
igraph2image(local_igraph, "local_igraph.pdf")
def compute_commitment_diagram(attractors: dict,
fname_image: Optional[str] = None,
fname_json=None,
edge_data=False) -> networkx.DiGraph:
"""
Computes the commitment diagram for the AttrJson and STG defined in *attractors*, a json object computed by :ref:`AttrJson_compute_json`
The nodes of the diagram represent states that can reach the exact same subset of *attractors*.
Edges indicate the existence of a transition between two nodes in the respective commitment sets.
Edges are labeled by the number of states of the source set that can reach the target set and,
if *EdgeData* is true, additionally by the size of the border.
**arguments**:
* *attractors*: json attractor data, see :ref:`compute_attractors`
* *fname_image*: generate image for diagram
* *fname_json*: save diagram as json
* *edge_data*: toggles computation of additional edge data
**returns**::
* *diagram*: the commitment diagram
**example**::
>>> attractors = compute_attractors(primes, update)
>>> diagram = compute_phenotype_diagram(attractors)
"""
primes = attractors["primes"]
update = attractors["update"]
subspaces = []
for x in attractors["attractors"]:
if x["min_trap_space"]["is_univocal"] and x["min_trap_space"][
"is_faithful"]:
subspaces.append(x["min_trap_space"]["dict"])
else:
subspaces.append(x["state"]["dict"])
log.info("Commitment.compute_diagram(..)")
size_total = size_state_space(primes)
if len(subspaces) == 1:
log.info(" single attractor, trivial case.")
diagram = networkx.DiGraph()
counter_mc = 0
diagram.add_node("0")
diagram.nodes["0"]["attractors"] = subspaces
diagram.nodes["0"]["size"] = size_total
diagram.nodes["0"]["formula"] = "TRUE"
else:
igraph = primes2igraph(primes)
outdag = find_outdag(igraph)
attractor_nodes = [x for A in subspaces for x in A]
critical_nodes = find_ancestors(igraph, attractor_nodes)
outdag = [x for x in outdag if x not in critical_nodes]
igraph.remove_nodes_from(outdag)
log.info(f"excluding the non-critical out-dag nodes {outdag}")
components = networkx.connected_components(igraph.to_undirected())
components = [list(x) for x in components]
log.info(f"working on {len(components)} connected component(s)")
counter_mc = 0
diagrams = []
for component in components:
sub_primes = copy_primes(primes)
remove_all_variables_except(sub_primes, component)
attractors_projected = _project_attractors(subspaces, component)
diagram, count = _compute_diagram_component(
sub_primes, update, attractors_projected, edge_data)
counter_mc += count
diagrams.append(diagram)
factor = 2**len(outdag)
diagram = _cartesian_product_of_diagrams(diagrams, factor, edge_data)
for x in attractors:
diagram.graph[x] = copy_json_data(attractors[x])
nodes_sum = 0
for x in diagram.nodes():
projection = diagram.nodes[x]["attractors"]
diagram.nodes[x]["attractors"] = _lift_attractors(
subspaces, projection)
nodes_sum += diagram.nodes[x]["size"]
if not nodes_sum == size_total:
log.warning(
"commitment diagram does not partition the state space, this may be due to rounding of large numbers."
)
sorted_ids = sorted(diagram, key=lambda x: diagram.nodes[x]["formula"])
mapping = {x: str(sorted_ids.index(x)) for x in diagram}
networkx.relabel_nodes(diagram, mapping, copy=False)
log.info(f"total executions of NuSMV: {counter_mc}")
if fname_image:
commitment_diagram2image(diagram,
fname_image=fname_image,
style_inputs=True,
style_edges=edge_data,
style_ranks=True,
first_index=1)
if fname_json:
save_commitment_diagram(diagram, fname_json)
return diagram
def primes2bnet(primes: dict,
fname_bnet: str = None,
minimize: bool = False,
header: bool = False) -> str:
"""
Saves *primes* as a *bnet* file, including the header *"targets, factors"* for compatibility with :ref:`installation_boolnet`.
Without minimization, the resuting formulas are disjunctions of all prime implicants and may therefore be very long.
If *Minimize=True* then a Python version of the Quine-McCluskey algorithm,
namely :ref:`Prekas2012 <Prekas2012>` which is implemented in :ref:`QuineMcCluskey.primes2mindnf <primes2mindnf>`,
will be used to minimize the number of clauses for each update function.
**arguments**:
* *primes*: prime implicants
* *fname_bnet*: name of *bnet* file or *None* for the string of the file contents
* *minimize*: minimize the Boolean expressions
* *header*: whether to include the "targets, factors" header
**returns**:
* *text_bnet*: str contents of bnet file
**example**::
>>> primes2bnet(primes, "mapk.bnet")
>>> primes2bnet(primes, "mapk.bnet", True)
>>> expr = primes2bnet(primes)
>>> expr = primes2bnet(primes, True)
"""
width = max([len(x) for x in primes]) + 3
igraph = primes2igraph(primes)
constants = sorted(find_constants(primes))
inputs = sorted(find_inputs(primes))
outdag = sorted(find_outdag(igraph))
outdag = [x for x in outdag if x not in constants]
body = sorted(x for x in primes
if all(x not in X for X in [constants, inputs, outdag]))
blocks = [constants, inputs, body, outdag]
blocks = [x for x in blocks if x]
assert len(constants) + len(inputs) + len(body) + len(outdag) == len(
primes)
lines = []
if header:
lines += ["targets, factors"]
if minimize:
expressions = primes2mindnf(primes)
for block in blocks:
for name in block:
lines += [f"{name + ',': <{width}} {expressions[name]}"]
lines += [""]
else:
for block in blocks:
for name in block:
expression = get_dnf(one_implicants=primes[name][1])
lines += [f"{name+',': <{width}} {expression}"]
lines += [""]
text = "\n".join(lines)
if fname_bnet:
with open(fname_bnet, "w") as fp:
fp.writelines(text)
log.info(f"created {fname_bnet}")
return text