def readEquations(equationSource):
if isinstance(equationSource, basestring):
eq_file = open(equationSource, 'r')
def read():
line = eq_file.readline()
line = line.replace('"', '').replace(',', '')
return line
else:
global l
l = 0
def read():
global l
if l == len(equationSource): raise StopIteration
line = equationSource[l]
line = line.replace('"', '').replace(',', '').strip()
l += 1
return line + '\n'
global newLine
newLine = True
global variables
variables = []
global functions
functions = []
global parameters
parameters = []
def useToken(key, value, Coord1, Coord2, fullLine):
global newLine, variables, obsFunctions, parameters
if key == 1: #1: NAME 2: NUMBER 51: OP 4: NEWLINE 0: ENDMARKER
if newLine == True:
variables.append(giveVar(value))
functions.append(
giveParsed(fullLine[(fullLine.find('=') +
1):len(fullLine)]))
else:
parameters.append(giveVar(value))
newLine = False
elif key == 4:
newLine = True
tokenize(read, useToken)
parameters = sorted(list(set(parameters)), key=spy.default_sort_key)
for entry in variables:
if entry in parameters:
parameters.remove(entry)
return variables, functions, parameters
def readEquations(equationSource):
if isinstance(equationSource, basestring):
eq_file = open(equationSource,'r')
def read():
line = eq_file.readline()
line = line.replace('"','').replace(',','')
return line
else:
global l
l = 0
def read():
global l
if l == len(equationSource): raise StopIteration
line = equationSource[l]
line = line.replace('"','').replace(',','').strip()
l += 1
return line + '\n'
global newLine; newLine = True
global variables; variables = []
global functions; functions = []
global parameters; parameters = []
def useToken(key, value, Coord1, Coord2, fullLine):
global newLine, variables, obsFunctions, parameters
if key == 1: #1: NAME 2: NUMBER 51: OP 4: NEWLINE 0: ENDMARKER
if newLine == True:
variables.append(giveVar(value))
functions.append(giveParsed(fullLine[(fullLine.find('=')+1):len(fullLine)]))
else:
parameters.append(giveVar(value))
newLine = False
elif key == 4:
newLine = True
tokenize(read,useToken)
parameters = sorted(list(set(parameters)), key=spy.default_sort_key)
for entry in variables:
if entry in parameters:
parameters.remove(entry)
return variables, functions, parameters
def readModel(fileName, delimT):
if delimT == 't':
delim = '\t'
else:
delim = delimT
variables = []
parameters = []
flows = []
stoichiometry = []
global l; l = -1
with open(fileName, 'rb') as defFile:
reader = csv.reader(defFile, delimiter=delim, quoting=csv.QUOTE_NONE)
row = reader.next()
for i in range(2,len(row)):
row[i] = row[i].replace('"','')
variables.append(giveVar(row[i]))
lines = 0
stoichiometryList = []
for row in reader:
row[1] = row[1].replace('"','')
row[1] = row[1].replace('^','**')
flows.append(row[1])
lines += 1
for i in range(2,len(row)):
if row[i] == '': num = 0
else:
row[i] = row[i].replace('"','')
if row[i] == '':
row[i] = 0
num = int(row[i])
stoichiometryList.append(num)
stoichiometryT = spy.Matrix(lines,len(variables),stoichiometryList)
stoichiometry = stoichiometryT.transpose()
def read():
global l
l += 1
if l >= len(flows): raise StopIteration
else: return flows[l]
def useToken(key, value, Coord1, Coord2, fullLine):
if key == 1:
parameters.append(giveVar(value))
tokenize(read,useToken)#get parameters from flows
parameters = sorted(list(set(parameters)), key=spy.default_sort_key)
for entry in variables:
if entry in parameters:
parameters.remove(entry)
for f in range(len(flows)):
flows[f] = giveParsed(flows[f])
return variables, parameters, spy.Matrix(len(flows),1,flows), stoichiometry
def readModel(fileName, delimT):
if delimT == 't':
delim = '\t'
else:
delim = delimT
variables = []
parameters = []
flows = []
stoichiometry = []
global l
l = -1
with open(fileName, 'rb') as defFile:
reader = csv.reader(defFile, delimiter=delim, quoting=csv.QUOTE_NONE)
row = reader.next()
for i in range(2, len(row)):
row[i] = row[i].replace('"', '')
variables.append(giveVar(row[i]))
lines = 0
stoichiometryList = []
for row in reader:
row[1] = row[1].replace('"', '')
row[1] = row[1].replace('^', '**')
flows.append(row[1])
lines += 1
for i in range(2, len(row)):
if row[i] == '': num = 0
else:
row[i] = row[i].replace('"', '')
if row[i] == '':
row[i] = 0
num = int(row[i])
stoichiometryList.append(num)
stoichiometryT = spy.Matrix(lines, len(variables), stoichiometryList)
stoichiometry = stoichiometryT.transpose()
def read():
global l
l += 1
if l >= len(flows): raise StopIteration
else: return flows[l]
def useToken(key, value, Coord1, Coord2, fullLine):
if key == 1:
parameters.append(giveVar(value))
tokenize(read, useToken) #get parameters from flows
parameters = sorted(list(set(parameters)), key=spy.default_sort_key)
for entry in variables:
if entry in parameters:
parameters.remove(entry)
for f in range(len(flows)):
flows[f] = giveParsed(flows[f])
return variables, parameters, spy.Matrix(len(flows), 1,
flows), stoichiometry