def patternSearch(fname="networks/6D_Malaria.txt",smallestparam=0,largestparam=46656,getMorseSet=fmg.all_FC,paramsstored=1,resultsfile='malariaresults.txt'):
if paramsstored == 1:
params = parseParams()
else:
params = getAllParams(fname,smallestparam,largestparam,getMorseSet)
N=len(params)
f=open(resultsfile,'w')
for k,(p,m) in enumerate(params):
print "Parameter {} of {}".format(k+1,N)
if type(m) is tuple:
for n in m:
call(["dsgrn network {} analyze morseset {} {} >dsgrn_output.json".format(fname,n,p)],shell=True)
patterns,matches=pm.callPatternMatch(writetofile=0,returnmatches=1)
for q,c in zip(patterns,matches):
f.write("Parameter: {}, Morseset: {}".format(p,n)+'\n')
f.write("Pattern: {}".format(q)+'\n')
f.write("Results: {}".format(c)+'\n')
else:
call(["dsgrn network {} analyze morseset {} {} >dsgrn_output.json".format(fname,m,p)],shell=True)
patterns,matches=pm.callPatternMatch(writetofile=0,returnmatches=1)
for q,c in zip(patterns,matches):
f.write("Parameter: {}, Morseset: {}".format(p,m)+'\n')
f.write("Pattern: {}".format(q)+'\n')
f.write("Results: {}".format(c)+'\n')
f.close()
def search(forcing=1):
if forcing==1:
onewayforcing()
elif forcing==2:
twowayforcing()
else:
print "Unrecognized input argument to search(). Aborting."
return None
pm.callPatternMatch()
def search(forcing=1):
if forcing == 1:
onewayforcing()
elif forcing == 2:
twowayforcing()
else:
print "Unrecognized input argument to search(). Aborting."
return None
pm.callPatternMatch()
def patternSearch(morseset=0,specfile="networks/5D_Model_B.txt",paramfile="5D_Model_B_FCParams.txt",resultsfile='results_5D_B.txt',printtoscreen=0,printparam=0,findallmatches=1,unique_identifier=0):
subprocess.call(["dsgrn network {} domaingraph > dsgrn_domaincells_{:04d}.json".format(specfile,unique_identifier)],shell=True)
R=open(resultsfile,'w',0)
P=open(paramfile,'r')
paramcount=1
for param in P.readlines():
param=param.split()[0]
if printparam and paramcount%1000==0:
print str(paramcount)+' parameters checked'
paramcount+=1
# shell call to dsgrn to produce dsgrn_output.json, which is the input for the pattern matcher
subprocess.call(["dsgrn network {} domaingraph json {} > dsgrn_domaingraph_{:04d}.json".format(specfile,int(param),unique_identifier)],shell=True)
subprocess.call(["dsgrn network {} analyze morseset {} {} >dsgrn_output_{:04d}.json".format(specfile,morseset,int(param),unique_identifier)],shell=True)
try:
patterns,matches=patternmatch.callPatternMatch(fname_morseset='dsgrn_output_{:04d}.json'.format(unique_identifier),fname_domgraph='dsgrn_domaingraph_{:04d}.json'.format(unique_identifier),fname_domcells='dsgrn_domaincells_{:04d}.json'.format(unique_identifier),fname_patterns='patterns.txt',fname_results=resultsfile,writetofile=0,returnmatches=1,printtoscreen=printtoscreen,findallmatches=findallmatches)
except ValueError:
print 'Problem parameter is {}'.format(param)
raise
for pat,match in zip(patterns,matches):
if findallmatches:
R.write("Parameter: {}, Morseset: {}".format(param,morseset)+'\n')
R.write("Pattern: {}".format(pat)+'\n')
R.write("Results: {}".format(match)+'\n')
else:
R.write("Parameter: {}, Morseset: {}".format(param,morseset)+'\n')
R.write("Pattern: {}".format(pat)+'\n')
R.close()
P.close()
def patternSearch(fname="networks/6D_Malaria.txt",
smallestparam=0,
largestparam=46656,
getMorseSet=fmg.all_FC,
paramsstored=1,
resultsfile='malariaresults.txt'):
if paramsstored == 1:
params = parseParams()
else:
params = getAllParams(fname, smallestparam, largestparam, getMorseSet)
N = len(params)
f = open(resultsfile, 'w')
for k, (p, m) in enumerate(params):
print "Parameter {} of {}".format(k + 1, N)
if type(m) is tuple:
for n in m:
call([
"dsgrn network {} analyze morseset {} {} >dsgrn_output.json"
.format(fname, n, p)
],
shell=True)
patterns, matches = pm.callPatternMatch(writetofile=0,
returnmatches=1)
for q, c in zip(patterns, matches):
f.write("Parameter: {}, Morseset: {}".format(p, n) + '\n')
f.write("Pattern: {}".format(q) + '\n')
f.write("Results: {}".format(c) + '\n')
else:
call([
"dsgrn network {} analyze morseset {} {} >dsgrn_output.json".
format(fname, m, p)
],
shell=True)
patterns, matches = pm.callPatternMatch(writetofile=0,
returnmatches=1)
for q, c in zip(patterns, matches):
f.write("Parameter: {}, Morseset: {}".format(p, m) + '\n')
f.write("Pattern: {}".format(q) + '\n')
f.write("Results: {}".format(c) + '\n')
f.close()
def patternSearchSingle(parameter,morseset=0,specfile="networks/5D_Model_B.txt",resultsfile='results.txt',printtoscreen=0):
R=open(resultsfile,'w',0)
# shell call to dsgrn to produce dsgrn_output.json, which is the input for the pattern matcher
subprocess.call(["dsgrn network {} domaingraph > dsgrn_domaincells.json".format(specfile)],shell=True)
subprocess.call(["dsgrn network {} domaingraph json {} > dsgrn_domaingraph.json".format(specfile,int(parameter))],shell=True)
subprocess.call(["dsgrn network {} analyze morseset {} {} >dsgrn_output.json".format(specfile,morseset,parameter)],shell=True)
try:
patterns,matches=patternmatch.callPatternMatch(writetofile=0,returnmatches=1,printtoscreen=printtoscreen)
except ValueError:
print 'Problem parameter is {}'.format(parameter)
raise
for pat,match in zip(patterns,matches):
R.write("Parameter: {}, Morseset: {}".format(parameter,morseset)+'\n')
R.write("Pattern: {}".format(pat)+'\n')
R.write("Results: {}".format(match)+'\n')
R.close()
def patternSearch_paramlist(networkfile,paramlist,resultsfile,patternstr,printtoscreen,findallmatches):
domaincells_jsonstr=getJSONstring(networkfile,['domaingraph'])
results_list=[]
for info in paramlist:
morsegraph,morseset,param = info.replace('|',' ').split()
domaingraph_jsonstr=getJSONstring(networkfile,['domaingraph', 'json',param])
morseset_jsonstr=getJSONstring(networkfile,['analyze', 'morseset', morseset, param])
try:
patterns,matches=patternmatch.callPatternMatch(morseset_jsonstr,domaingraph_jsonstr,domaincells_jsonstr,patternstr,resultsfile,writetofile=0,returnmatches=1,printtoscreen=printtoscreen,findallmatches=findallmatches)
for pat,match in zip(patterns,matches):
if findallmatches:
results_list.append("Parameter: {}, Morse Graph: {}, Morse Set: {}, Pattern: {}, Results: {}".format(param,morsegraph,morseset,pat,match)+'\n')
else:
results_list.append("Parameter: {}, Morse Graph: {}, Morse Set: {}, Pattern: {}".format(param,morsegraph,morseset,pat)+'\n')
except Exception as e:
print 'Problem parameter is {}'.format(param)
print traceback.format_exception_only(type(e),e)
sys.stdout.flush()
with open(resultsfile,'w',0) as R:
for line in results_list:
R.write(line)
