def printDict(somedict): return "\n".join(sorted([str(x)+":"+str(y) for x,y in sorted(somedict.items())])) def defaultDict(somelist,defaultval): return dict([x,defaultval] for x in somelist) def assignVal(somedict,somelistofkeys,val): tempdict = somedict for item in somelistofkeys: if somedict[item]==0 or somedict[item]>val: tempdict[item] = val return tempdict if __name__ == "__main__": atomizedrules = bpgModel.getAtomizedRules(sys.argv[-1]) patterns,transformations = bpgModel.getElements(atomizedrules) tprules = [['+','!'],['~Y','~pY'],['0()','*']] transformationpairs, irreversibles = getTransformationPairs(transformations,tprules) names = getNameDictionary(atomizedrules,patterns,transformations,transformationpairs) all_maps = getMaps(names) # use d3js to make graphs
def processActions(strings):
'''implements actions regarding bipartite maps from strings read from actions file'''
allcommands = cleanstrings(strings)
#Commands are processed linearly
successfullyissued = []
tprules = []
while len(allcommands)>0:
current_line = deque(allcommands.popleft())
command = current_line.popleft()
if command == 'read_xml':
# Usage read_xml xyz.xml
assert len(current_line)==1, "Provide exactly one argument for read_xml command"
filename = current_line.popleft()
assert os.path.isfile(filename),"File "+filename+"not found for read_xml command"
atomizedrules = bpgModel.getAtomizedRules(filename)
patterns,transformations = bpgModel.getElements(atomizedrules)
elif command == 'tprule':
# Usage tprule x > y (or) x < y
assert 'make_pairs' not in successfullyissued, "Use tprule before make_pairs"
temp = []
assert len(current_line)==3, "Provide arguments of the form: x > y (or) x < y for tprule"
temp.append(current_line.popleft())
op = current_line.popleft()
assert op in ['>','<'], "Provide arguments of the form: x > y (or) x < y for tprule"
temp.append(current_line.popleft())
if op=='>':
tprules.append(temp)
else:
tprules.append([temp[1],temp[0]])
elif command == 'make_pairs':
# Usage make_pairs
assert 'read_xml' in successfullyissued, "Use read_xml before make_pairs"
assert len(current_line)==0, "make_pairs command takes no arguments"
transformationpairs, irreversibles = bpgMaps.getTransformationPairs(transformations,tprules)
elif command == 'write_elements':
assert len(current_line)>0, "write_elements requires a filename to output to"
if 'make_names' not in successfullyissued:
names = bpgMaps.getNameDictionary(atomizedrules,patterns,transformations,transformationpairs,irreversibles)
successfullyissued.append('make_names')
filename = current_line.popleft()
if len(current_line)==0:
current_line='p-t-tp-r'
printopts = current_line[0].split('-')
for item in printopts:
assert item in ['p','t','tp','ir','r',''],"Option "+item+" not found. Provided options should be a subset of p-t-tp-ir-r with dashes between them"
tempstring = ''
alreadyadded = []
optdict = {'p':'patterns','t':'transformations','tp':'transformationpairs','ir':'irreversibles','r':'reactionrules'}
for item in printopts:
if item not in alreadyadded:
if item=='':
continue
elif item=='p':
templist = sorted([str(x) for x in patterns])
elif item=='t':
templist = sorted([str(x) for x in transformations])
elif item=='tp':
templist = sorted([str(x) for x in transformationpairs])
elif item=='ir':
templist = sorted([str(x) for x in irreversibles])
elif item=='r':
templist = [str(x) for x in atomizedrules]
tempstring = tempstring + "\n["+optdict[item]+"]\n"
tempstring = tempstring + "# " + str(len(templist)) + " " + optdict[item] + "\n"
tempstring = tempstring + "\n".join(templist) + "\n"
alreadyadded.append(item)
with open(filename,'w') as f:
f.write(tempstring)
elif command == 'read_annot':
# Usage: read_annot <list of filenames>
assert len(current_line)>0, "read_annot requires atleast one filename to read from"
if 'make_names' not in successfullyissued:
names = bpgMaps.getNameDictionary(atomizedrules,patterns,transformations,transformationpairs,irreversibles)
successfullyissued.append('make_names')
tempstring = ''
for item in current_line:
assert(os.path.isfile(item)),"File "+item+" not found!"
with open(item) as f:
tempstring = tempstring + f.read()
if 'read_annot' not in successfullyissued:
annot = bpgAnnotate.Annotation()
annot.initialize(names)
annot.processAnnotations(tempstring,names)
elif command == 'make_maps':
if 'make_names' not in successfullyissued:
names = bpgMaps.getNameDictionary(atomizedrules,patterns,transformations,transformationpairs,irreversibles)
successfullyissued.append('make_names')
all_maps = bpgMaps.getMaps(names,0)
elif command == 'make_flow':
assert len(current_line)>1, "provide a seed of the form: start <list of atomic patterns> [end <list of atomic patterns>]"
assert current_line.popleft()=='start',"provide a seed of the form: start <list of atomic patterns> [end <list of atomic patterns>]"
start = []
end = []
startend = 0 # a switch used to create either the start vector or the end vector of patterns
while(len(current_line)>0):
patt = current_line.popleft()
if patt != 'end' and startend == 0:
start.append(patt)
if startend ==1:
end.append(patt)
if patt == 'end':
startend =1
flowlevels = bpgMaps.makeFlow(names,all_maps,start,end)
elif command == 'make_viz':
assert len(current_line) > 0, "provide a filename for writing vizdata"
filename = current_line.popleft()
with open("data.js","w") as f:
f.write("var data = "+bpgMaps.writeJSON(names,all_maps,annot))
f.close()
else:
print "Command not found: "+command
successfullyissued.append(command)
sorted([str(x) + ":" + str(y) for x, y in sorted(somedict.items())]))
def defaultDict(somelist, defaultval):
return dict([x, defaultval] for x in somelist)
def assignVal(somedict, somelistofkeys, val):
tempdict = somedict
for item in somelistofkeys:
if somedict[item] == 0 or somedict[item] > val:
tempdict[item] = val
return tempdict
if __name__ == "__main__":
atomizedrules = bpgModel.getAtomizedRules(sys.argv[-1])
patterns, transformations = bpgModel.getElements(atomizedrules)
tprules = [['+', '!'], ['~Y', '~pY'], ['0()', '*']]
transformationpairs, irreversibles = getTransformationPairs(
transformations, tprules)
names = getNameDictionary(atomizedrules, patterns, transformations,
transformationpairs)
all_maps = getMaps(names)
# use d3js to make graphs
