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replace np float and int #17

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replace np float and int #17

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54 changes: 27 additions & 27 deletions SERGIO/sergio.py
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Original file line number Diff line number Diff line change
Expand Up @@ -155,7 +155,7 @@ def build_graph (self, input_file_taregts, input_file_regs, shared_coop_state =
reader = csv.reader(f, delimiter=',')
if (shared_coop_state <= 0):
for row in reader:
nRegs = np.int(row[1])
nRegs = int(float(row[1]))
##################### Raise Error ##########################
if nRegs == 0:
print ("Error: a master regulator (#Regs = 0) appeared in input")
Expand All @@ -165,22 +165,22 @@ def build_graph (self, input_file_taregts, input_file_regs, shared_coop_state =
currInteraction = []
currParents = []
for regId, K, C_state in zip(row[2: 2 + nRegs], row[2+nRegs : 2+2*nRegs], row[2+2*nRegs : 2+3*nRegs]):
currInteraction.append((np.int(regId), np.float(K), np.float(C_state), 0)) # last zero shows half-response, it is modified in another method
allRegs.append(np.int(regId))
currParents.append(np.int(regId))
self.graph_[np.int(regId)]['targets'].append(np.int(row[0]))
currInteraction.append((int(float(regId)), float(K), float(C_state), 0)) # last zero shows half-response, it is modified in another method
allRegs.append(int(float(regId)))
currParents.append(int(float(regId)))
self.graph_[int(float(regId))]['targets'].append(int(float(row[0])))

self.graph_[np.int(row[0])]['params'] = currInteraction
self.graph_[np.int(row[0])]['regs'] = currParents
self.graph_[np.int(row[0])]['level'] = -1 # will be modified later
allTargets.append(np.int(row[0]))
self.graph_[int(float(row[0]))]['params'] = currInteraction
self.graph_[int(float(row[0]))]['regs'] = currParents
self.graph_[int(float(row[0]))]['level'] = -1 # will be modified later
allTargets.append(int(float(row[0])))

#if self.dyn_:
# for b in range(self.nBins_):
# binDict[b].append(gene(np.int(row[0]),'T', b))
# binDict[b].append(gene(int(float(row[0]),'T', b))
else:
for indRow, row in enumerate(reader):
nRegs = np.int(np.float(row[1]))
nRegs = int(float((row[1])))
##################### Raise Error ##########################
if nRegs == 0:
print ("Error: a master regulator (#Regs = 0) appeared in input")
Expand All @@ -190,19 +190,19 @@ def build_graph (self, input_file_taregts, input_file_regs, shared_coop_state =
currInteraction = []
currParents = []
for regId, K, in zip(row[2: 2 + nRegs], row[2+nRegs : 2+2*nRegs]):
currInteraction.append((np.int(np.float(regId)), np.float(K), shared_coop_state, 0)) # last zero shows half-response, it is modified in another method
allRegs.append(np.int(np.float(regId)))
currParents.append(np.int(np.float(regId)))
self.graph_[np.int(np.float(regId))]['targets'].append(np.int(np.float(row[0])))
currInteraction.append((int(float((regId))), float(K), shared_coop_state, 0)) # last zero shows half-response, it is modified in another method
allRegs.append(int(float((regId))))
currParents.append(int(float((regId))))
self.graph_[int(float((regId)))]['targets'].append(int(float((row[0]))))

self.graph_[np.int(np.float(row[0]))]['params'] = currInteraction
self.graph_[np.int(np.float(row[0]))]['regs'] = currParents
self.graph_[np.int(np.float(row[0]))]['level'] = -1 # will be modified later
allTargets.append(np.int(np.float(row[0])))
self.graph_[int(float((row[0])))]['params'] = currInteraction
self.graph_[int(float((row[0])))]['regs'] = currParents
self.graph_[int(float((row[0])))]['level'] = -1 # will be modified later
allTargets.append(int(float((row[0]))))

#if self.dyn_:
# for b in range(self.nBins_):
# binDict[b].append(gene(np.int(row[0]),'T', b))
# binDict[b].append(gene(int(float(row[0]),'T', b))

#self.master_regulators_idx_ = set(np.setdiff1d(allRegs, allTargets))

Expand All @@ -214,14 +214,14 @@ def build_graph (self, input_file_taregts, input_file_regs, shared_coop_state =
print ("Error: Inconsistent number of bins")
sys.exit()

masterRegs.append(int(float(row[0])))
self.graph_[int(float(row[0]))]['rates'] = [np.float(i) for i in row[1:]]
self.graph_[int(float(row[0]))]['regs'] = []
self.graph_[int(float(row[0]))]['level'] = -1
masterRegs.append(int(float(float(row[0]))))
self.graph_[int(float(float(row[0])))]['rates'] = [float(i) for i in row[1:]]
self.graph_[int(float(float(row[0])))]['regs'] = []
self.graph_[int(float(float(row[0])))]['level'] = -1

#if self.dyn_:
# for b in range(self.nBins_):
# binDict[b].append(gene(np.int(row[0]),'MR', b))
# binDict[b].append(gene(int(float(row[0]),'MR', b))

self.master_regulators_idx_ = set(masterRegs)

Expand Down Expand Up @@ -614,15 +614,15 @@ def populate_with_parentCells_(self, binID):

elif np.count_nonzero(parentBins) == 1:
parentBinID = np.nonzero(parentBins)[0][0]
nPopulation = int(round(self.bifurcationMat_[parentBinID, binID] * self.nSC_))
nPopulation = int(float(round(self.bifurcationMat_[parentBinID, binID] * self.nSC_)))
#self.nInitCells_[binID] = nPopulation

#Bifurcation rates of <1/nSC are set to 1/nSC
if nPopulation < 1:
nPopulation = 1
else:
parentBinID = binID
nPopulation = int(max(1, np.random.normal(20,5)))
nPopulation = int(float(max(1, np.random.normal(20,5))))
#self.nInitCells_[binID] = nPopulation

for g in self.binDict[binID]:
Expand Down