def initialize_fluxtools(infile, ofile="", dumpparser=False):
DUMP = dumpparser or ("-dump" in sys.argv)
if infile=="":
if("-in" in sys.argv):
i = (sys.argv).index("-in")+1
if i<len(sys.argv):
infile=sys.argv[i]
else:
raise SystemExit("Error: use '-in filename' to specify input file.")
else:
raise SystemExit("Error: use '-in filename' to specify input file.")
if os.path.isfile(infile):
datafile = infile
else:
raise SystemExit("Error: "+os.path.abspath(infile)+" File not found.")
outfile=ofile
if outfile == "":
if ("-out" in sys.argv):
i = (sys.argv).index("-out")+1
if i<len(sys.argv):
outfile=sys.argv[i]
else:
outfile="flux-analysis.out"
else:
outfile="flux-analysis.out"
outfile=os.path.abspath(uniqueFileName(outfile))
lines=readmodel(INFILE=datafile)[0]
results = invokeParser(lines, dump=DUMP)
return (results, outfile)
def runparser(datafile, trace=False):
if ("-in" in sys.argv):
i = (sys.argv).index("-in")+1
if i<len(sys.argv):
infile=sys.argv[i]
else:
raise SystemExit("Error: expecting filename after -in")
elif os.path.isfile(datafile):
infile=datafile
else:
raise SystemExit("Error: interpreter (runparser): No Input File Given; use -in option.")
if not os.path.isfile(infile):
raise SystemExit("Error: "+os.path.abspath(infile)+" File not found.")
rates = {}
if os.path.splitext(infile)[1]==".model":
(lines, ics, rates, frozenvars, functions,assignments, fullfile)=readmodel(INFILE=infile)
else:
f=open(infile)
lines = f.readlines()
f.close()
results=invokeParser(lines,dump=trace)
# print "runparser: rates=", rates
return (results, rates, functions, frozenvars, assignments, ics)
def GetCelleratorNetwork(filename, dump=False):
if not os.path.isfile(filename):
print "Error: readPLY: unable to locate file ", os.path.abspath(
filename)
raise SystemExit("File Not Found")
rates = {}
ics = {}
if os.path.splitext(filename)[1] == ".model":
(linesOfData, ics, rates, frozenvars, functions, assignments,
fullfile) = readmodel(INFILE=filename)
else:
f = open(filename)
linesOfData = f.readlines()
f.close()
lines = []
for line in linesOfData:
line = (line.split("#"))[0].strip()
if len(line) > 0: lines.append(line)
linesOfData = lines
# f = open(filename)
# linesOfData = f.readlines()
# f.close()
n = len(linesOfData)
if not ("-quiet" in sys.argv):
print n, " lines read from ", os.path.abspath(filename)
result = []
reactions = []
for i in range(n):
raw = linesOfData[i]
r = Reaction(raw)
reactions.append(r)
if dump: r.Dump()
next = _Handle_Cellerator_Reaction(raw, r)
# result.append()
# print "next = ", next
result = result + next
species = listspecies(reactions)
# result = functionate(result, species)
# print "species = ", species
# print "result = ", result
return (result, rates, ics)
def parser(inputfile="", trace=False):
if not (inputfile == ""):
infile = str(inputfile)
elif ("-in" in sys.argv):
i = (sys.argv).index("-in") + 1
if i < len(sys.argv):
infile = sys.argv[i]
else:
raise SystemExit("Error: expecting filename after -in")
else:
raise SystemExit("No Input File Given; use -in option.")
if not os.path.isfile(infile):
raise SystemExit("Error: " + os.path.abspath(infile) +
" File not found.")
if os.path.splitext(infile)[1] == ".model":
(lines, ics, rates, frozenvars, functions, assignments,
fullfile) = readmodel(INFILE=infile)
else:
f = open(infile)
lines = f.readlines()
f.close()
# f=open(infile)
# lines = f.readlines()
# f.close()
results = []
rs = []
for line in lines:
line = StripComments(line, "#")
if line == "": continue
r = Reaction(line)
if "-dump" in sys.argv: r.Dump()
if not r.Arrow() == "Unknown":
results.append(r.Input().strip())
rs.append(r)
if trace or ("-trace" in sys.argv):
print "input: " + str(r.Input()).strip()
elif trace or ("-trace" in sys.argv):
print "input ignored: " + line.strip()
# print results
return rs
def GetCelleratorNetwork(filename, dump=False):
if not os.path.isfile(filename):
print "Error: readPLY: unable to locate file ", os.path.abspath(filename)
raise SystemExit("File Not Found")
rates={}
ics={}
if os.path.splitext(filename)[1]==".model":
(linesOfData, ics, rates, frozenvars, functions,assignments, fullfile)=readmodel(INFILE=filename)
else:
f=open(filename)
linesOfData = f.readlines()
f.close()
lines=[]
for line in linesOfData:
line=(line.split("#"))[0].strip()
if len(line)>0: lines.append(line)
linesOfData = lines
# f = open(filename)
# linesOfData = f.readlines()
# f.close()
n = len(linesOfData)
if not ("-quiet" in sys.argv):
print n," lines read from ", os.path.abspath(filename)
result=[]
reactions = []
for i in range(n):
raw=linesOfData[i]
r=Reaction(raw)
reactions.append(r)
if dump: r.Dump()
next = _Handle_Cellerator_Reaction(raw,r)
# result.append()
# print "next = ", next
result = result + next
species = listspecies(reactions)
# result = functionate(result, species)
# print "species = ", species
# print "result = ", result
return (result,rates,ics)
def parser(inputfile="", trace=False):
if not (inputfile == ""):
infile = str(inputfile)
elif "-in" in sys.argv:
i = (sys.argv).index("-in") + 1
if i < len(sys.argv):
infile = sys.argv[i]
else:
raise SystemExit("Error: expecting filename after -in")
else:
raise SystemExit("No Input File Given; use -in option.")
if not os.path.isfile(infile):
raise SystemExit("Error: " + os.path.abspath(infile) + " File not found.")
if os.path.splitext(infile)[1] == ".model":
(lines, ics, rates, frozenvars, functions, assignments, fullfile) = readmodel(INFILE=infile)
else:
f = open(infile)
lines = f.readlines()
f.close()
# f=open(infile)
# lines = f.readlines()
# f.close()
results = []
rs = []
for line in lines:
line = StripComments(line, "#")
if line == "":
continue
r = Reaction(line)
if "-dump" in sys.argv:
r.Dump()
if not r.Arrow() == "Unknown":
results.append(r.Input().strip())
rs.append(r)
if trace or ("-trace" in sys.argv):
print "input: " + str(r.Input()).strip()
elif trace or ("-trace" in sys.argv):
print "input ignored: " + line.strip()
# print results
return rs
def initialize_fluxtools(infile, ofile="", dumpparser=False):
DUMP = dumpparser or ("-dump" in sys.argv)
if infile == "":
if ("-in" in sys.argv):
i = (sys.argv).index("-in") + 1
if i < len(sys.argv):
infile = sys.argv[i]
else:
raise SystemExit(
"Error: use '-in filename' to specify input file.")
else:
raise SystemExit(
"Error: use '-in filename' to specify input file.")
if os.path.isfile(infile):
datafile = infile
else:
raise SystemExit("Error: " + os.path.abspath(infile) +
" File not found.")
outfile = ofile
if outfile == "":
if ("-out" in sys.argv):
i = (sys.argv).index("-out") + 1
if i < len(sys.argv):
outfile = sys.argv[i]
else:
outfile = "flux-analysis.out"
else:
outfile = "flux-analysis.out"
outfile = os.path.abspath(uniqueFileName(outfile))
lines = readmodel(INFILE=datafile)[0]
results = invokeParser(lines, dump=DUMP)
return (results, outfile)
def expandReactions(r, dump=False, text=False):
inputfile=r
if ("-in" in sys.argv):
i = (sys.argv).index("-in")+1
if i<len(sys.argv):
inputfile=sys.argv[i]
else:
raise SystemExit("Error: expecting filename after -in")
elif inputfile=="":
raise SystemExit("No Input File Given; use -in option.")
if not os.path.isfile(inputfile):
raise SystemExit("Error: "+os.path.abspath(inputfile)+" File not found.")
if os.path.splitext(inputfile)[1]==".model":
(lines, ics, rates, frozenvars, functions,assignments, fullfile)=readmodel(INFILE=inputfile)
else:
f=open(inputfile)
lines = f.readlines()
f.close()
expanded=[]
expandedInput=[]
for line in lines:
line = StripComments(line,"#")
if line=="": continue # ignore blanks
p = Reaction(line)
# print "Expander: input: ", line
p = expand(p)
# print "Expander: expanded: ", p
expanded += p
tp = map(lambda x:x.Input(),p)
expandedInput += tp
# if requested, dump the expanded text reactions to the screen
if ("-dump" in sys.argv): dump=True
if dump:
for line in expandedInput:
print line
# if requested, dump the expanded text reactions to a file
# check to see if file is requested
if ("-out" in sys.argv):
i = (sys.argv).index("-out")+1
if i<len(sys.argv):
outputfile=sys.argv[i]
else:
# print "Error: expecting filename after -out"
outputfile = "expanded-reactions.out"
outputfile = uniqueFileName(outputfile, type ="out")
f=open(outputfile,"w")
for line in expandedInput:
f.write(line+"\n")
f.close()
print "Output written to: "+os.path.abspath(outputfile)
if text == True:
return expandedInput
return expanded
def expandReactions(r, dump=False, text=False):
inputfile = r
if ("-in" in sys.argv):
i = (sys.argv).index("-in") + 1
if i < len(sys.argv):
inputfile = sys.argv[i]
else:
raise SystemExit("Error: expecting filename after -in")
elif inputfile == "":
raise SystemExit("No Input File Given; use -in option.")
if not os.path.isfile(inputfile):
raise SystemExit("Error: " + os.path.abspath(inputfile) +
" File not found.")
if os.path.splitext(inputfile)[1] == ".model":
(lines, ics, rates, frozenvars, functions, assignments,
fullfile) = readmodel(INFILE=inputfile)
else:
f = open(inputfile)
lines = f.readlines()
f.close()
expanded = []
expandedInput = []
for line in lines:
line = StripComments(line, "#")
if line == "": continue # ignore blanks
p = Reaction(line)
# print "Expander: input: ", line
p = expand(p)
# print "Expander: expanded: ", p
expanded += p
tp = map(lambda x: x.Input(), p)
expandedInput += tp
# if requested, dump the expanded text reactions to the screen
if ("-dump" in sys.argv): dump = True
if dump:
for line in expandedInput:
print line
# if requested, dump the expanded text reactions to a file
# check to see if file is requested
if ("-out" in sys.argv):
i = (sys.argv).index("-out") + 1
if i < len(sys.argv):
outputfile = sys.argv[i]
else:
# print "Error: expecting filename after -out"
outputfile = "expanded-reactions.out"
outputfile = uniqueFileName(outputfile, type="out")
f = open(outputfile, "w")
for line in expandedInput:
f.write(line + "\n")
f.close()
print "Output written to: " + os.path.abspath(outputfile)
if text == True:
return expandedInput
return expanded
def generateSimulation(inputfile="", step=1, duration=100, plot=False, format="CSV", \
output="", vars=[], plotcolumns=3, sameplot=True):
formattype = {"CSV": "CSV", "TABLE": "TXT", "TSV": "TSV"}
# input: model file
# return value: none
# output: generates simulation plots from model file
# if invoked from command line, "solver -in filename -run duration step"
holdrates = []
if "-scan" in sys.argv:
i = (sys.argv).index("-scan") + 1
if i + 3 < len(sys.argv):
holdrates.append(sys.argv[i])
scanstart = sys.argv[i + 1]
scanstop = sys.argv[i + 2]
scandelta = sys.argv[i + 3]
else:
sys.exit("Error: expecting 'K min max delta' after keyword -scan")
(r, ic, rates, frozenvars, functions, assignments,
filename) = readmodel(INFILE=inputfile)
(variables, y0, tmpdotpy) = generatePythonFunction(r, rates, ic,
frozenvars, functions,
assignments, holdrates)
f = open(tmpdotpy, "r")
rhs = f.readlines()
f.close()
try:
os.remove(tmpdotpy)
except:
print "Warning: unable to delete " + os.path.abspath(tmpdotpy)
pyfile = ""
if ("-pyfile" in sys.argv):
i = (sys.argv).index("-pyfile") + 1
if i < len(sys.argv):
pyfile = sys.argv[i]
else:
print "Waring: solver: expecting file name after -pyfile option."
pyfile = "newsolver.py"
if pyfile == "":
pyfile = utils.timed_file_name(
"solver-for-" + os.path.basename(filename), "py")
#pyfile = utils.uniqueFileName(pyfile, type="py")
f = open(pyfile, "w")
f.write("import numpy as np\n")
f.write("import cellerator.solver\n")
f.write("from scipy.integrate import odeint\n")
f.write("\n")
for line in rhs:
f.write(line)
f.write("\n\n\n")
f.write("def thesolver():\n")
f.write(" filename =\"" + filename + "\"\n")
svars = str(map(utils.deindex, map(str, variables)))
f.write(" variables=" + svars + "\n")
(runtime, stepsize) = getRunParameters(default_duration=duration,
default_step=step)
f.write(" runtime = " + str(runtime) + " \n")
f.write(" stepsize = " + str(stepsize) + " \n")
f.write(" t = np.arange(0,runtime+stepsize,stepsize)\n")
f.write(" y0 = " + str(y0) + "\n")
if "-mxstep" in sys.argv:
i = (sys.argv).index("-mxstep") + 1
if i < len(sys.argv):
mxstep = sys.argv[i]
else:
mxstep = "500000"
if len(holdrates) > 0:
f.write(" global " + holdrates[0] + "\n")
f.write(" results=[]\n")
f.write(" " + holdrates[0] + "=" + str(scanstart) + "\n")
f.write(" while " + holdrates[0] + " <= " + str(scanstop) + ":\n")
f.write(" sol = odeint(ode_function_rhs, y0, t, mxstep=" +
mxstep + ")\n")
f.write(" " + holdrates[0] + "+=" + str(scandelta) + "\n")
f.write(" res=[" + holdrates[0] + "] + list(sol[-1])\n")
f.write(" results.append(res)\n")
f.write(" print res\n")
f.write(" return results\n")
f.write("if __name__==\"__main__\":\n")
f.write(" thesolver()\n\n")
f.close()
return os.path.abspath(pyfile)
f.write(" sol = odeint(ode_function_rhs, y0, t, mxstep=" + mxstep +
")\n")
fmt = format
if "-format" in sys.argv:
i = (sys.argv).index("-format") + 1
if i < len(sys.argv):
fmt = sys.argv[i]
fmt = fmt.upper()
if not fmt in formattype:
print "Error: solver: invalid format = ", fmt, " requested."
fmt = "CSV"
fmt = formattype[fmt]
outfile = output
if ("-out" in sys.argv):
i = (sys.argv).index("-out") + 1
if i < len(sys.argv):
outfile = sys.argv[i]
output = utils.uniqueFileName(outfile, type=fmt)
else:
print "Warning: solver: expecting file name after -out option."
#outfile = "solution."+fmt
if output == "":
basename = os.path.basename(filename)
#basename=basename.split(".")[0]
outfile = utils.timed_file_name("Solution-for-" + basename, fmt)
#f.write(" outfile = \""+utils.uniqueFileName(outfile, type=fmt)+"\"\n")
f.write(" outfile = \"" + outfile + "\"\n")
f.write(" of = open(outfile,\"w\")\n")
f.write(" for i in range(len(t)):\n")
f.write(" time = t[i]\n")
f.write(" data = map(str,sol[i])\n")
demarcater = {"CSV": "\",\"", "TSV": "\"\t\"", "TXT": "\" \""}
f.write(" data = str(time) + " + demarcater[fmt] + "+(" +
demarcater[fmt] + ".join(data))\n")
f.write(" of.write(data+\"\\n\")\n")
f.write(" of.close()\n")
#print "argv is: ", sys.argv
if ("-plot" in sys.argv) or plot == True:
plotvars = vars
f.write(" plotvars = " + svars + "\n")
if ("-plot" in sys.argv):
i = (sys.argv).index("-plot")
if i > 0:
i += 1
while i < len(sys.argv):
nextvar = sys.argv[i]
i += 1
if nextvar[0] == "-": break
nextvar = utils.deindex(str(nextvar))
if nextvar in variables:
plotvars.append(nextvar)
else:
print "Error: requested plot variable: "+nextvar+ " does not "\
+ " exist in the model."
plotvars = list(set(plotvars)) # remove any dupes
f.write(" plotvars = " + str(plotvars) + "\n")
if len(plotvars) == 0:
plotvars = variables
f.write(" plotvars = " + str(plotvars) + "\n")
plotcols = plotcolumns
if ("-plotcolumns" in sys.argv):
i = (sys.argv).index("-plotcolumns") + 1
if i < len(sys.argv):
plotcols = int(sys.argv[i])
plotcols = max(plotcols, 1)
if ("-sameplot" in sys.argv) or sameplot == True:
f.write(
" cellerator.solver.samePlot(sol, t, variables, filename, plotvars)\n"
)
else:
f.write(" cellerator.solver.plotVariables(sol, t, variables, filename,"\
+" plotvars, columns="+str(plotcols)+")\n")
f.write(" return\n\n")
f.write("if __name__==\"__main__\":\n")
f.write(" thesolver()\n\n")
f.close()
return os.path.abspath(pyfile)
def generateSimulation(inputfile="", step=1, duration=100, plot=False, format="CSV", \
output="", vars=[], plotcolumns=3, sameplot=True):
formattype = {"CSV":"CSV","TABLE":"TXT", "TSV":"TSV"}
# input: model file
# return value: none
# output: generates simulation plots from model file
# if invoked from command line, "solver -in filename -run duration step"
holdrates=[]
if "-scan" in sys.argv:
i = (sys.argv).index("-scan")+1
if i+3<len(sys.argv):
holdrates.append(sys.argv[i])
scanstart = sys.argv[i+1]
scanstop = sys.argv[i+2]
scandelta = sys.argv[i+3]
else:
sys.exit("Error: expecting 'K min max delta' after keyword -scan")
(r, ic, rates, frozenvars, functions,assignments, filename)=readmodel(INFILE=inputfile)
(variables, y0, tmpdotpy) = generatePythonFunction(r, rates, ic, frozenvars,
functions, assignments, holdrates)
f=open(tmpdotpy,"r")
rhs=f.readlines()
f.close()
try:
os.remove(tmpdotpy)
except:
print "Warning: unable to delete "+os.path.abspath(tmpdotpy)
pyfile = ""
if ("-pyfile" in sys.argv):
i = (sys.argv).index("-pyfile")+1
if i<len(sys.argv):
pyfile=sys.argv[i]
else:
print "Waring: solver: expecting file name after -pyfile option."
pyfile = "newsolver.py"
if pyfile=="":
pyfile=utils.timed_file_name("solver-for-"+os.path.basename(filename),"py")
#pyfile = utils.uniqueFileName(pyfile, type="py")
f=open(pyfile,"w")
f.write("import numpy as np\n")
f.write("import cellerator.solver\n")
f.write("from scipy.integrate import odeint\n")
f.write("\n")
for line in rhs: f.write(line)
f.write("\n\n\n")
f.write("def thesolver():\n")
f.write(" filename =\""+filename+"\"\n")
svars = str(map(utils.deindex, map(str, variables)))
f.write(" variables="+svars+"\n")
(runtime, stepsize)=getRunParameters(default_duration=duration,default_step=step)
f.write(" runtime = "+str(runtime)+" \n")
f.write(" stepsize = "+str(stepsize)+" \n")
f.write(" t = np.arange(0,runtime+stepsize,stepsize)\n")
f.write(" y0 = "+str(y0)+"\n")
if "-mxstep" in sys.argv:
i=(sys.argv).index("-mxstep")+1
if i<len(sys.argv):
mxstep=sys.argv[i]
else:
mxstep = "500000"
if len(holdrates)>0:
f.write(" global " + holdrates[0] + "\n")
f.write(" results=[]\n")
f.write(" "+holdrates[0]+"="+str(scanstart)+"\n")
f.write(" while "+ holdrates[0]+" <= " + str(scanstop) + ":\n")
f.write(" sol = odeint(ode_function_rhs, y0, t, mxstep="+mxstep+")\n")
f.write(" "+holdrates[0]+"+="+str(scandelta)+"\n")
f.write(" res=["+ holdrates[0] + "] + list(sol[-1])\n")
f.write(" results.append(res)\n")
f.write(" print res\n")
f.write(" return results\n")
f.write("if __name__==\"__main__\":\n")
f.write(" thesolver()\n\n")
f.close()
return os.path.abspath(pyfile)
f.write(" sol = odeint(ode_function_rhs, y0, t, mxstep="+mxstep+")\n")
fmt = format
if "-format" in sys.argv:
i = (sys.argv).index("-format")+1
if i<len(sys.argv):
fmt = sys.argv[i]
fmt = fmt.upper()
if not fmt in formattype:
print "Error: solver: invalid format = ", fmt, " requested."
fmt = "CSV"
fmt = formattype[fmt]
outfile=output
if ("-out" in sys.argv):
i = (sys.argv).index("-out")+1
if i<len(sys.argv):
outfile=sys.argv[i]
output=utils.uniqueFileName(outfile, type=fmt)
else:
print "Warning: solver: expecting file name after -out option."
#outfile = "solution."+fmt
if output=="":
basename = os.path.basename(filename)
#basename=basename.split(".")[0]
outfile = utils.timed_file_name("Solution-for-"+basename,fmt)
#f.write(" outfile = \""+utils.uniqueFileName(outfile, type=fmt)+"\"\n")
f.write(" outfile = \""+outfile+"\"\n")
f.write(" of = open(outfile,\"w\")\n")
f.write(" for i in range(len(t)):\n")
f.write(" time = t[i]\n")
f.write(" data = map(str,sol[i])\n")
demarcater={"CSV":"\",\"","TSV":"\"\t\"","TXT":"\" \""}
f.write(" data = str(time) + " + demarcater[fmt] + "+(" + demarcater[fmt]+".join(data))\n")
f.write(" of.write(data+\"\\n\")\n")
f.write(" of.close()\n")
#print "argv is: ", sys.argv
if ("-plot" in sys.argv) or plot==True:
plotvars = vars
f.write(" plotvars = "+svars+"\n")
if ("-plot" in sys.argv):
i = (sys.argv).index("-plot")
if i>0:
i += 1
while i<len(sys.argv):
nextvar = sys.argv[i]
i += 1
if nextvar[0]=="-": break
nextvar = utils.deindex(str(nextvar))
if nextvar in variables:
plotvars.append(nextvar)
else:
print "Error: requested plot variable: "+nextvar+ " does not "\
+ " exist in the model."
plotvars = list (set (plotvars) ) # remove any dupes
f.write(" plotvars = "+str(plotvars)+"\n")
if len(plotvars)==0:
plotvars = variables
f.write(" plotvars = "+str(plotvars)+"\n")
plotcols = plotcolumns
if ("-plotcolumns" in sys.argv):
i = (sys.argv).index("-plotcolumns") + 1
if i < len(sys.argv):
plotcols=int(sys.argv[i])
plotcols = max(plotcols, 1)
if ("-sameplot" in sys.argv) or sameplot==True:
f.write(" cellerator.solver.samePlot(sol, t, variables, filename, plotvars)\n")
else:
f.write(" cellerator.solver.plotVariables(sol, t, variables, filename,"\
+" plotvars, columns="+str(plotcols)+")\n")
f.write(" return\n\n")
f.write("if __name__==\"__main__\":\n")
f.write(" thesolver()\n\n")
f.close()
return os.path.abspath(pyfile)