def parse_species_from_pathway(data_dir,
p_idx_l=None,
init_spe=60,
atom_followed="C",
end_t=1.0,
species_path=False):
"""
parse unique species list from pathway list
"""
if p_idx_l is None:
return
suffix = naming.get_suffix(data_dir,
init_spe=init_spe,
atom_followed=atom_followed,
end_t=end_t)
prefix = ""
if species_path is True:
prefix = "species_"
f_n_path_name = os.path.join(
data_dir, "output",
prefix + "pathway_name_candidate" + suffix + ".csv")
p_name = np.genfromtxt(f_n_path_name, dtype=str, delimiter=',')
unique_spe = set()
for p_idx in p_idx_l:
matched_spe = re.findall(r"S(\d+)", p_name[p_idx])
for _, s_idx in enumerate(matched_spe):
unique_spe.add(s_idx)
return unique_spe
def path_prob_terminating_with_spe(data_dir,
init_spe=62,
atom_followed="C",
tau=10.0,
end_t=1.0,
species_path=True,
end_s_idx=None,
exclude_idx=None,
time_axis=0):
"""
get pathway and their pathway probability, path ending with spe
"""
if exclude_idx is None:
exclude_idx = []
prefix = ""
if species_path is True:
prefix = "species_"
suffix = naming.get_suffix(data_dir,
init_spe=init_spe,
atom_followed=atom_followed,
end_t=end_t)
f_n_pn = os.path.join(data_dir, "output",
prefix + "pathway_name_candidate" + suffix + ".csv")
f_n_pp = os.path.join(data_dir, "output",
prefix + "pathway_prob" + suffix + ".csv")
path_names = np.loadtxt(f_n_pn, dtype=str, delimiter=",")
data_pp = np.loadtxt(f_n_pp, dtype=float, delimiter=",")
dim_n = len(np.shape(data_pp))
if dim_n == 1:
data_y = data_pp
elif dim_n == 2:
data_y = data_pp[:, time_axis]
# each pathway as a column
d_f_n = pd.DataFrame(path_names, columns=['name'], dtype=str)
d_f_p = pd.DataFrame(data_y, columns=['frequency'], dtype=float)
d_f = pd.concat([d_f_n, d_f_p], axis=1)
# print(d_f.head())
# filter
if end_s_idx is not None:
if isinstance(end_s_idx, int):
d_f = d_f.loc[
lambda x: x['name'].str.endswith("S" + str(end_s_idx))]
elif isinstance(end_s_idx, list):
# got to be a tuple
mask_str = tuple(["S" + str(e_s) for e_s in end_s_idx])
d_f = d_f.loc[lambda x: x['name'].str.endswith(mask_str)]
d_f.sort_values(by='frequency', inplace=True, ascending=False)
d_f.reset_index(drop=True, inplace=True)
print(d_f)
return d_f
def calculate_Merchant_alpha_value(data_dir,
init_spe=10,
atom_followed="C",
end_t=1.0,
species_path=False,
s_idx=10,
r_idx=736):
"""
calculate Merchat alpha value at time point as in time.csv, not at time zero
"""
suffix = naming.get_suffix(data_dir,
init_spe=init_spe,
atom_followed=atom_followed,
end_t=end_t)
prefix = ""
if species_path is True:
prefix = "species_"
spe_conc_mat = np.loadtxt(os.path.join(data_dir, "output",
"concentration_dlsode_M.csv"),
dtype=float,
delimiter=',')
spe_k_mat = np.loadtxt(os.path.join(data_dir, "output",
"drc_dlsode_M.csv"),
dtype=float,
delimiter=',')
reaction_rate_mat = np.loadtxt(os.path.join(data_dir, "output",
"reaction_rate_dlsode_M.csv"),
dtype=float,
delimiter=',')
n_points = np.shape(spe_conc_mat)[0]
spe_total_sink_rate_vec = np.zeros(n_points)
merchant_alpha_v = np.zeros(n_points)
for i in range(1, n_points):
spe_total_sink_rate_vec[i] = spe_conc_mat[i, s_idx] * spe_k_mat[i,
s_idx]
if spe_total_sink_rate_vec[i] > 0:
merchant_alpha_v[i] = reaction_rate_mat[
i, r_idx] / spe_total_sink_rate_vec[i]
# set the first value at time zero to be the same as value at time one
merchant_alpha_v[0] = merchant_alpha_v[1]
merchant_alpha_fn = os.path.join(
data_dir, "output", prefix + "Merchant_alpha_" + "S" + str(s_idx) +
"_R" + str(r_idx) + suffix + ".csv")
np.savetxt(merchant_alpha_fn, merchant_alpha_v, fmt='%.15e')
return
def parse_pathway_contains_species(data_dir,
s_idx_ds=None,
init_spe=60,
atom_followed="C",
end_t=1.0,
species_path=False):
"""
parse pathway contains only species from list or set
ds --> data structure
"""
if s_idx_ds is None:
return
s_idx_set = set(s_idx_ds)
suffix = naming.get_suffix(data_dir,
init_spe=init_spe,
atom_followed=atom_followed,
end_t=end_t)
prefix = ""
if species_path is True:
prefix = "species_"
f_n_path_name = os.path.join(
data_dir, "output",
prefix + "pathway_name_candidate" + suffix + ".csv")
p_name = np.genfromtxt(f_n_path_name, dtype=str, delimiter=',')
path_list = []
for idx, path in enumerate(p_name):
# Contains Species Only From Species List
c_s_o_f_s_l = True
matched_spe = re.findall(r"S(\d+)", path)
for _, s_idx in enumerate(matched_spe):
if s_idx not in s_idx_set:
c_s_o_f_s_l = False
break
if c_s_o_f_s_l is True:
path_list.append(idx)
print(path_list)
return path_list
def path_length_statistics(data_dir,
init_spe=62,
atom_followed="C",
end_t=1.0,
end_spe=None):
"""
path length statistics
"""
d_f = path_prob_terminating_with_spe(data_dir, init_spe, atom_followed,
end_t, end_spe)
count_map = OrderedDict()
for _, val in enumerate(d_f['pathway'][0:20]):
count = int(parse_pattern.parse_path_length(val))
if count in count_map:
count_map[count] += 1
else:
count_map[count] = 1
mat = []
count_map = OrderedDict(sorted(count_map.items()))
for key, value in count_map.items():
mat.append([int(key), int(value)])
suffix = naming.get_suffix(data_dir,
init_spe=init_spe,
atom_followed=atom_followed,
end_t=end_t)
if end_spe is not None:
suffix += "_S" + str(end_spe)
out_f_n = os.path.join(data_dir, "output", "path_length" + suffix + ".csv")
np.savetxt(out_f_n,
mat,
fmt='%d',
delimiter=',',
newline='\n',
header='',
footer='',
comments='# ')
def pathway_time_2_array_index(data_dir,
init_spe=None,
atom_followed="C",
end_t=1.0,
species_path=False,
time=1.0):
"""
pathway time converted to array index, pathway time read from pathway_time_canditate*
"""
suffix = get_suffix(data_dir,
init_spe=init_spe,
atom_followed=atom_followed,
end_t=end_t)
prefix = ""
if species_path is True:
prefix = "species_"
f_n_path_time = os.path.join(
data_dir, "output",
prefix + "pathway_time_candidate" + suffix + ".csv")
p_time = np.genfromtxt(f_n_path_time, dtype=float, delimiter=',')
# in case of two dimensional pathway time
if len(np.shape(p_time)) == 2:
p_time = p_time[0, :]
y_idx = [float(i) for i in range(len(p_time))]
array_idx = interpolation.interp1d(p_time, y_idx, time)
array_idx = int(array_idx)
if array_idx >= len(p_time):
array_idx = len(p_time) - 1
if array_idx < 0:
array_idx = 0
return array_idx
def parse_spe_production_along_path(data_dir,
top_n=10,
spe_idx=10,
init_spe=62,
atom_followed="C",
end_t=1.0,
species_path=False,
axis=0,
path_branching_factor=False,
s_consumption=False,
s_production=True):
"""
parse species peoduction along path, note species might not explictly shown on path
but are side products of reaction on pathway
if path_idx is None, use top_n path
if path_idx is not None, instead it is a list, use only selected path, the output file name
thereafter ends with "selected_path"
"""
id_tmp = ""
if spe_idx is None or spe_idx is []:
return
elif isinstance(spe_idx, int):
id_tmp = str(spe_idx)
spe_idx = [spe_idx]
else:
for x_t in spe_idx:
if id_tmp == "":
id_tmp = str(x_t)
else:
id_tmp += "_" + str(x_t)
suffix = naming.get_suffix(data_dir,
init_spe=init_spe,
atom_followed=atom_followed,
end_t=end_t)
prefix = ""
if species_path is True:
prefix = "species_"
f_n_path_name = os.path.join(
data_dir, "output",
prefix + "pathway_name_candidate" + suffix + ".csv")
pathname_data = np.genfromtxt(f_n_path_name, dtype=str, max_rows=top_n + 1)
# in case of two dimensional pathway name
if len(np.shape(pathname_data)) == 2:
pathname_data = pathname_data[:, axis]
net_reactant = psri.parse_reaction_net_reactant(data_dir)
net_product = psri.parse_reaction_net_product(data_dir)
s_p_r_c = psri.parse_species_pair_reaction(data_dir)
if path_branching_factor is True:
atom_scheme = asch.get_atom_scheme(data_dir)
s_idx_name, _ = psri.parse_spe_info(data_dir)
s_p_c = []
for _, p_n in enumerate(pathname_data):
spe_consumption_count = 0
spe_production_count = 0
for s_i in spe_idx:
if s_consumption is True:
spe_consumption_count += parse_pattern.parse_species_along_path_using_reaction(
p_n, net_reactant, s_i, s_p_r_c)
if s_production is True:
spe_production_count += parse_pattern.parse_species_along_path_using_reaction(
p_n, net_product, s_i, s_p_r_c)
path_branching_number = 1
if path_branching_factor is True:
path_branching_number = parse_pattern.calculate_path_branching_number(
pathname=p_n,
net_reactant=net_reactant,
net_product=net_product,
s_idx_name=s_idx_name,
atom_scheme=atom_scheme,
atom_followed=atom_followed)
s_p_c.append((spe_production_count - spe_consumption_count) *
path_branching_number)
if id_tmp != "":
suffix += "_" + id_tmp
f_n_spe_production_count = os.path.join(
data_dir, "output",
prefix + "pathway_species_production_count" + suffix + ".csv")
np.savetxt(f_n_spe_production_count, s_p_c, fmt='%d')
def init_directed_network(data_dir,
path_idx=None,
init_spe=None,
atom_followed="C",
end_t=None,
species_path=False,
time_axis=0):
"""
init directed network
without parallel edges
return networkx.DiGraph
"""
spe_idx_name_dict, _ = psri.parse_spe_info(data_dir)
suffix = get_suffix(data_dir,
init_spe=init_spe,
atom_followed=atom_followed,
end_t=end_t)
prefix = ""
if species_path is True:
prefix = "species_"
f_n_path_name = os.path.join(
data_dir, "output",
prefix + "pathway_name_candidate" + suffix + ".csv")
f_n_path_prob = os.path.join(data_dir, "output",
prefix + "pathway_prob" + suffix + ".csv")
print(f_n_path_name, f_n_path_prob)
p_n = np.genfromtxt(f_n_path_name, dtype=str, delimiter=',')
p_p = np.genfromtxt(f_n_path_prob, dtype=float, delimiter=',')
# in case of two dimensional pathway name
if len(np.shape(p_n)) == 2:
p_n = p_n[:, time_axis]
if len(np.shape(p_p)) == 2:
p_p = p_p[:, time_axis]
# retrieve pathway name and pathway probability before sort
p_n = [p_n[i] for i in path_idx]
p_p = [p_p[i] for i in path_idx]
# set the data type seperately
d_f_n = pd.DataFrame(p_n, columns=['name'], dtype=str)
d_f_p = pd.DataFrame(p_p, columns=['prob'], dtype=float)
d_f = pd.concat([d_f_n, d_f_p], axis=1)
d_f.sort_values(by='prob',
ascending=False,
inplace=True,
na_position='last')
d_f.reset_index(drop=True, inplace=True)
print(d_f.head())
# temporary directed graph
d_g_tmp = nx.DiGraph()
# modify labels
spe_union_find_group = global_settings.get_union_find_group(
DATA_DIR, atom_followed)
# record all nodes
nodes = set()
for _, val in d_f.iterrows():
matched_spe = re.findall(r"S(\d+)", val['name'])
for _, spe in enumerate(matched_spe):
nodes.add(
change_spe_name(spe,
spe_idx_name_dict,
union_find=spe_union_find_group))
for _, val in enumerate(nodes):
d_g_tmp.add_node(val, weight=0.0, label=str(val))
for _, val in d_f.iterrows():
prob = float(val['prob'])
# get rid of R-1000003S90, don't need it here
print(val['name'])
path_name_tmp = re.sub(r"R-\d+S\d+", r'', val['name'])
print(path_name_tmp)
# pathway contains both reaction and species
if species_path is False:
matched_spe = re.findall(r"S(\d+)", path_name_tmp)
matched_reaction = re.findall(r"R(\d+)", path_name_tmp)
for idx, spe in enumerate(matched_spe):
d_g_tmp.node[change_spe_name(
spe, spe_idx_name_dict,
union_find=spe_union_find_group)]['weight'] += 1.0 * prob
if idx > 0:
src = change_spe_name(matched_spe[idx - 1],
spe_idx_name_dict,
union_find=spe_union_find_group)
dest = change_spe_name(spe,
spe_idx_name_dict,
union_find=spe_union_find_group)
rxn = change_rxn_name(matched_reaction[idx - 1])
if d_g_tmp.has_edge(src, dest):
d_g_tmp[src][dest]['weight'] += 1.0 * prob
d_g_tmp[src][dest]['reactions'].add(rxn)
else:
d_g_tmp.add_edge(src,
dest,
reactions=set([rxn]),
weight=1.0 * prob)
else:
matched_spe = re.findall(r"S(\d+)", path_name_tmp)
for idx, spe in enumerate(matched_spe):
d_g_tmp.node[change_spe_name(
spe, spe_idx_name_dict,
union_find=spe_union_find_group)]['weight'] += 1.0 * prob
if idx > 0:
src = change_spe_name(matched_spe[idx - 1],
spe_idx_name_dict,
union_find=spe_union_find_group)
dest = change_spe_name(spe,
spe_idx_name_dict,
union_find=spe_union_find_group)
rxn = '-1'
if d_g_tmp.has_edge(src, dest):
d_g_tmp[src][dest]['weight'] += 1.0 * prob
d_g_tmp[src][dest]['reactions'].add(rxn)
else:
d_g_tmp.add_edge(src,
dest,
reactions=set([rxn]),
weight=1.0 * prob)
# update directed graph, for example,
# 1. reactions is originally a set, combine to get a string of reactions
# 2. smooth and re-normalize node weight
# 3. re-normalize edge weight
node_weight = []
for _, val in enumerate(d_g_tmp.nodes()):
node_weight.append(d_g_tmp.node[val]['weight'])
edge_weight = []
for _, val in enumerate(d_g_tmp.edges()):
edge_weight.append(d_g_tmp[val[0]][val[1]]['weight'])
node_weight = rescale_array(node_weight, 1.0, 5.0)
edge_weight = rescale_array(edge_weight, 3.0, 15.0)
# final directed graph
di_graph = nx.DiGraph()
for idx, val in enumerate(d_g_tmp.nodes()):
di_graph.add_node(val, weight=node_weight[idx])
for idx, val in enumerate(d_g_tmp.edges()):
src = val[0]
dest = val[1]
rxn_set = d_g_tmp[src][dest]['reactions']
rxn_set = sorted(rxn_set, key=lambda x: int(x), reverse=False)
name = ",".join(x for x in rxn_set)
weight = edge_weight[idx]
di_graph.add_edge(src, dest, name=name, weight=weight)
return di_graph