def test_primes2smv():
primes = {
"vB": [[{}], []],
"vC": [[{
"vC": 0
}], [{
"vC": 1
}]],
"vA": [[{
"vB": 0,
"vC": 1
}], [{
"vC": 0
}, {
"vB": 1
}]]
}
fname = get_tests_path_out(fname="fileexchange_primes2smv_syn.smv")
primes2smv(primes=primes,
fname_smv=fname,
update="synchronous",
initial_states="INIT TRUE",
specification="CTLSPEC TRUE")
fname = get_tests_path_out(fname="fileexchange_primes2smv_async.smv")
primes2smv(primes=primes,
fname_smv=fname,
update="asynchronous",
initial_states="INIT TRUE",
specification="CTLSPEC TRUE")
fname = get_tests_path_out(fname="fileexchange_primes2smv_mixed.smv")
primes2smv(primes=primes,
fname_smv=fname,
update="mixed",
initial_states="INIT TRUE",
specification="CTLSPEC TRUE")
def test_dot2image():
fname_in = get_tests_path_in(fname="interactiongraphs_topology.dot")
fname_out1 = get_tests_path_out(fname="interactiongraphs_dot2image1.png")
fname_out2 = get_tests_path_out(fname="interactiongraphs_dot2image2.svg")
fname_out3 = get_tests_path_out(fname="interactiongraphs_dot2image3.eps")
dot2image(fname_dot=fname_in, fname_image=fname_out1)
dot2image(fname_dot=fname_in, fname_image=fname_out2)
dot2image(fname_dot=fname_in, fname_image=fname_out3)
def test_compute_commitment_diagram(attractors, edge_data):
fname_image = get_tests_path_out(fname="compute_commitment_diagram.pdf")
fname_json = get_tests_path_out(fname="compute_commitment_diagram.json")
diagram = compute_commitment_diagram(attractors,
fname_image=fname_image,
fname_json=fname_json,
edge_data=edge_data)
diagram_from_file = open_commitment_diagram(fname_json=fname_json)
assert sorted(diagram.edges(data=True)) == sorted(
diagram_from_file.edges(data=True))
assert sorted(diagram.nodes(data=True)) == sorted(
diagram_from_file.nodes(data=True))
def test_bnet2primes_empty():
fname_in = get_tests_path_in(fname="fileexchange_empty.bnet")
fname_out = get_tests_path_out(fname="fileexchange_empty.primes")
primes = bnet2primes(bnet=fname_in, fname_primes=fname_out)
primes_expected = {}
assert primes_are_equal(primes, primes_expected), str(primes)
def test_bnet2primes_missing_inputs():
fname_in = get_tests_path_in(fname="fileexchange_missing_inputs.bnet")
fname_out = get_tests_path_out(fname="fileexchange_missing_inputs.primes")
primes = bnet2primes(bnet=fname_in, fname_primes=fname_out)
primes_expected = {
"B": [[{
"B": 0
}], [{
"B": 1
}]],
"C": [[{
"C": 0
}], [{
"C": 1
}]],
"A": [[{
"B": 0,
"C": 1
}], [{
"C": 0
}, {
"B": 1
}]]
}
assert primes_are_equal(primes, primes_expected), str(primes)
def test_trap_spaces_positive_feedback_bounds2():
fname_in = get_tests_path_in(fname="trapspaces_posfeedback.primes")
fname_out = get_tests_path_out(fname="trapspaces_posfeedback_bounds2.asp")
primes = read_primes(fname_json=fname_in)
tspaces = compute_trap_spaces_bounded(primes=primes, type_="max", bounds=(0, 100), fname_asp=fname_out)
tspaces.sort(key=lambda x: tuple(sorted(x.items())))
assert tspaces == [{}]
def test_trap_spaces_positive_feedback_all():
fname_in = get_tests_path_in(fname="trapspaces_posfeedback.primes")
fname_out = get_tests_path_out(fname="trapspaces_posfeedback_all.asp")
primes = read_primes(fname_json=fname_in)
tspaces = compute_trap_spaces(primes=primes, type_="all", fname_asp=fname_out)
tspaces.sort(key=lambda x: tuple(sorted(x.items())))
assert tspaces == [{}, {"v1": 0, "v2": 0, "v3": 0}, {"v1": 1, "v2": 1, "v3": 1}]
def test_bnet2primes_constants():
fname_in = get_tests_path_in(fname="fileexchange_constants.bnet")
fname_out = get_tests_path_out(fname="fileexchange_constants.primes")
primes = bnet2primes(bnet=fname_in, fname_primes=fname_out)
primes_expected = {"A": [[{}], []], "B": [[], [{}]]}
assert primes_are_equal(primes, primes_expected), str(primes)
def test_compute_json():
primes = get_primes("n5s3")
fname = get_tests_path_out(fname="n5s3_attrs.json")
attractors = compute_attractors(primes=primes,
update="asynchronous",
fname_json=fname,
max_output=2)
assert attractors
def test_create_basins_piechart():
try:
primes = get_primes("n5s3")
attractors = compute_attractors(primes, update="asynchronous")
compute_basins(attractors)
fname_image = get_tests_path_out(fname="basins_piechart")
create_basins_piechart(attractors, fname_image=fname_image)
except NameError:
pass
def test_create_piechart(attractors):
try:
diagram = compute_commitment_diagram(attractors)
fname_image = get_tests_path_out(
fname="compute_commitment_diagram.pdf")
create_commitment_piechart(diagram=diagram,
fname_image=fname_image,
title="A commitment pie chart")
except NameError:
pass
def test_best_first_reachability():
primes = bnet2primes(
bnet=get_tests_path_in(fname="randomnet.bnet"),
fname_primes=get_tests_path_out(fname="randomnet.primes"))
initial_space = dict([("Gene%i" % (i + 1), i % 2) for i in range(20)])
goal_space = {"Gene2": 0, "Gene4": 0, "Gene6": 0, "Gene8": 0}
memory = 10000
path = best_first_reachability(primes, initial_space, goal_space, memory)
assert path is not None
def test_trap_spaces_tsfree():
fname_in = get_tests_path_in(fname="trapspaces_tsfree.primes")
fname_out = get_tests_path_out(fname="trapspaces_tsfree_min.asp")
primes = read_primes(fname_json=fname_in)
tspaces = compute_trap_spaces(primes=primes, type_="min", fname_asp=fname_out)
assert tspaces == [{}]
fname_in = get_tests_path_in(fname="trapspaces_tsfree.primes")
fname_out = get_tests_path_out(fname="trapspaces_tsfree_all.asp")
primes = read_primes(fname_json=fname_in)
tspaces = compute_trap_spaces(primes=primes, type_="all", fname_asp=fname_out)
assert tspaces == [{}]
fname_in = get_tests_path_in(fname="trapspaces_tsfree.primes")
fname_out = get_tests_path_out(fname="trapspaces_tsfree_max.asp")
primes = read_primes(fname_json=fname_in)
tspaces = compute_trap_spaces(primes=primes, type_="max", fname_asp=fname_out)
assert tspaces == []
def test_bnet2primes_operatorbinding():
fname_in = get_tests_path_in(fname="fileexchange_operatorbinding.bnet")
fname_out = get_tests_path_out(fname="fileexchange_operatorbinding.primes")
primes = bnet2primes(bnet=fname_in, fname_primes=fname_out)
names = "abcde"
results = []
for x in names:
for y in names:
name = x
results.append(
primes_are_equal({name: primes[x]}, {name: primes[y]}))
assert all(results)
def test_bnet2primes_a():
fname_in = get_tests_path_in(fname="fileexchange_constants.bnet")
fname_out = get_tests_path_out(fname="fileexchange_stdout1.primes")
file_in = "A, 0\nB, 1"
expected = {"A": [[{}], []], "B": [[], [{}]]}
primes = bnet2primes(bnet=fname_in)
assert primes_are_equal(primes, expected)
primes = bnet2primes(bnet=file_in)
assert primes_are_equal(primes, expected)
primes = bnet2primes(bnet=fname_in, fname_primes=fname_out)
assert primes_are_equal(primes, expected)
def test_stg2image():
fname_in = get_tests_path_in(fname="irma.primes")
fname_out1 = get_tests_path_out(fname="irma_stg_async.pdf")
fname_out2 = get_tests_path_out(fname="irma_stg_tendencies_async.pdf")
fname_out3 = get_tests_path_out(fname="irma_stg_sccs_async.pdf")
primes = read_primes(fname_json=fname_in)
stg = primes2stg(primes=primes, update="asynchronous")
stg2image(stg, fname_out1)
add_style_tendencies(stg)
stg2image(stg, fname_out2)
stg = primes2stg(primes=primes, update="asynchronous")
add_style_sccs(stg)
stg2image(stg, fname_out3)
fname_out1 = get_tests_path_out(fname="irma_stg_sync.pdf")
fname_out2 = get_tests_path_out(fname="irma_stg_tendencies_sync.pdf")
fname_out3 = get_tests_path_out(fname="irma_stg_sccs_sync.pdf")
fname_out4 = get_tests_path_out(fname="irma_stg_path.pdf")
primes = read_primes(fname_json=fname_in)
stg = primes2stg(primes=primes, update="synchronous")
stg2image(stg, fname_out1)
stg = primes2stg(primes=primes, update="asynchronous")
add_style_tendencies(stg)
stg2image(stg, fname_out2)
stg = primes2stg(primes=primes, update="synchronous")
add_style_sccs(stg)
stg2image(stg, fname_out3)
init = random_state(primes=primes)
walk = random_walk(primes=primes,
update="asynchronous",
initial_state=init,
length=5)
stg = primes2stg(primes=primes, update="asynchronous")
add_style_path(stg, walk, "red")
init = pyboolnet.state_space.random_state(primes=primes)
walk = random_walk(primes=primes,
update="asynchronous",
initial_state=init,
length=5)
add_style_path(stg, walk, "blue")
stg2image(stg, fname_out4)
def test_find_attractor_state_by_randomwalk_and_ctl():
fname_in = get_tests_path_in(fname="randomnet.bnet")
fname_out = get_tests_path_out(fname="randomnet.primes")
primes = bnet2primes(bnet=fname_in, fname_primes=fname_out)
subspace = {"Gene1": 0, "Gene3": 0, "Gene5": 0, "Gene7": 0, "Gene9": 0}
length = 200
attempts = 10
min_trap_spaces = {
"Gene1": 1,
"Gene11": 0,
"Gene12": 1,
"Gene13": 0,
"Gene14": 1,
"Gene15": 0,
"Gene16": 1,
"Gene17": 1,
"Gene18": 1,
"Gene19": 0,
"Gene2": 1,
"Gene20": 1,
"Gene3": 0,
"Gene4": 1,
"Gene5": 0,
"Gene6": 0,
"Gene8": 0,
"Gene9": 0
}
x = find_attractor_state_by_randomwalk_and_ctl(primes, "asynchronous",
subspace, length, attempts)
assert state_is_in_subspace(primes, x, min_trap_spaces)
y = find_attractor_state_by_randomwalk_and_ctl(primes, "synchronous",
subspace, length, attempts)
reachable = list_reachable_states(primes, "synchronous", y, 100)
assert state2str(y) in reachable
z = find_attractor_state_by_randomwalk_and_ctl(primes, "mixed", subspace,
length, attempts)
assert state_is_in_subspace(primes, z, min_trap_spaces)
def test_primes2bns():
fname = get_tests_path_out(fname="fileexchange_primes2bns.bns")
primes = {
"B": [[{}], []],
"C": [[{
"C": 0
}], [{
"C": 1
}]],
"A": [[{
"B": 0,
"C": 1
}], [{
"C": 0
}, {
"B": 1
}]]
}
primes2bns(primes=primes, fname_bns=fname)
def test_primes2bnet_b():
fname = get_tests_path_out(fname="fileexchange_primes2bnet.primes")
primes = {
"B": [[{}], []],
"C": [[{
"C": 0
}], [{
"C": 1
}]],
"A": [[{
"B": 0,
"C": 1
}], [{
"C": 0
}, {
"B": 1
}]]
}
primes2bnet(primes=primes, fname_bnet=fname)
primes2bnet(primes=primes, fname_bnet=fname, minimize=True)
def test_bnet2primes_results():
fname_in = get_tests_path_in(fname="fileexchange_feedback.bnet")
fname_out = get_tests_path_out(fname="fileexchange_feedback.primes")
primes = bnet2primes(bnet=fname_in, fname_primes=fname_out)
primes_expected = {
"v1": [[{
"v2": 0
}], [{
"v2": 1
}]],
"v2": [[{
"v2": 0
}, {
"v1": 1
}], [{
"v1": 0,
"v2": 1
}]]
}
assert primes_are_equal(primes, primes_expected)
def test_read_write_primes():
fname = get_tests_path_out(fname="fileexchange_read_write.primes")
primes_write = {
"B": [[{}], []],
"C": [[{
"C": 0
}], [{
"C": 1
}]],
"A": [[{
"B": 0,
"C": 1
}], [{
"C": 0
}, {
"B": 1
}]]
}
write_primes(primes=primes_write, fname_json=fname)
primes_read = read_primes(fname_json=fname)
assert primes_are_equal(primes_read, primes_write)
def test_primes2asp(bounds, projection, type_):
primes = {
"B": [[{}], []],
"C": [[{
"C": 0
}], [{
"C": 1
}]],
"A": [[{
"B": 0,
"C": 1
}], [{
"C": 0
}, {
"B": 1
}]]
}
fname = get_tests_path_out(fname="fileexchange_primes2asp_case.asp")
primes2asp(primes=primes,
fname_asp=fname,
bounds=bounds,
project=projection,
type_=type_)
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_create_image():
fname = get_tests_path_out(fname="interactiongraphs_create_image.pdf")
primes = get_primes("raf")
create_image(primes, fname)
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():
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)
def test_successor_synchronous():
primes = bnet2primes(
bnet=get_tests_path_in(fname="randomnet.bnet"),
fname_primes=get_tests_path_out(fname="randomnet.primes"))
state = dict([("Gene%i" % (i + 1), i % 2) for i in range(20)])
successor_synchronous(primes, state)
def test_random_mixed_transition():
primes = bnet2primes(
bnet=get_tests_path_in(fname="randomnet.bnet"),
fname_primes=get_tests_path_out(fname="randomnet.primes"))
state = dict([("Gene%i" % (i + 1), i % 2) for i in range(20)])
random_successor_mixed(primes, state)
def test_stg2htg():
fname_out = get_tests_path_out(fname="raf_htg.pdf")
primes = get_primes("raf")
stg = primes2stg(primes, "asynchronous")
htg = stg2htg(stg)
htg2image(htg, fname_out)
