def test_attack(n0, n1, numCov, err=.001):
n = n0 + n1
x = [rand.randint(0, 2) for i in range(0, n)]
y = [1 for i in range(0, n)]
for i in range(0, n0):
y[i] = 0
covs = [[rand.randint(0, 1) for i in range(0, n)]
for j in range(0, numCov)]
ORs = []
for i in range(0, numCov):
print i
ret = [x]
ret.append(covs[i])
X = np.asarray(ret).T
X = AC(X, False)
lr = LR(y, X)
res_lr = lr.fit(disp=0)
OR = math.exp(float(res_lr.params[0]))
ret.append(attack(y, covs, OR, err))
ORs.append(OR)
print "The number of matches is: "
for r in ret:
str(len(r))
print ORs
for r in ret:
print r
print len(ret)
def runAnalysis(self,y): log_res=[0 for i in range(0,self.m)]; for i in range(0,self.m): I=[i] I.extend([-1]) x=self.X[:,I]; lr=LR(y,x); res_lr=lr.fit(disp=0) if self.params=="Coef": log_res[i]=float(res_lr.params[0]); if self.params=="Odds": coef=float(res_lr.params[0]); log_res[i]=math.exp(coef); """ if self.params=="pval": log_res[i]=; if self.params=="logpval": pval=; if pval>0: log_res[i]=-np.log10(pval); else: log_res[i]=-1.0; """ return np.asarray(log_res);
def Log_Calc(y, x):
x1 = AC(x, False)
lr = LR(y, x1)
try:
res_lr = lr.fit(disp=0)
except:
return -1
return math.exp(res_lr.params[0])
def test_attack_nocovar(n0, n1, err=.001):
n = n0 + n1
x = [rand.randint(0, 2) for i in range(0, n)]
y = [1 for i in range(0, n)]
for i in range(0, n0):
y[i] = 0
x = AC(x, False)
lr = LR(y, x)
res_lr = lr.fit(disp=0)
OR = math.exp(float(res_lr.params[0]))
ret = attack_no_covar(n0, n1, OR, err)
print "The number of matches is: " + str(len(ret))
print OR
for r in ret:
print r
def attack_no_covar(n0, n1, OR, err=.001):
n = n0 + n1
y = [1 for i in range(0, n)]
for i in range(0, n0):
y[i] = 0
num_match = 0
ret = []
##iterate through all possibilities and test
for i0 in range(0, n0 + 1): ##number in controls with 2 minor alleles
for i1 in range(
0, (n0 - i0 + 1)): ##number in controls with 1 minor alleles
for j0 in range(0, n1 + 1): ##number in cases with 2 minor alleles
for j1 in range(
0,
(n1 - j0 + 1)): ##number in cases with 1 minor alleles
i2 = n0 - i0 - i1
j2 = n1 - j0 - j1
x = [0 for i in range(0, n)]
x[:i0] = [2 for i in range(0, i0)]
cur = i0
x[cur:cur + i1] = [1 for i in range(0, i1)]
cur = cur + i1
cur = cur + i2
x[cur:cur + j0] = [2 for i in range(0, j0)]
cur = cur + j0
x[cur:cur + j1] = [1 for i in range(0, j1)]
res_lr = ""
x = AC(x, False)
lr = LR(y, x)
try:
res_lr = lr.fit(disp=0)
except:
#print x;
continue
try:
OR_cur = math.exp(float(res_lr.params[0]))
except:
continue
if round_sig(OR_cur, err) == round_sig(OR, err):
num_match = num_match + 1
ret.append([i0, i1, i2, j0, j1, j2])
#print "match!\n";
return ret
def attack(y, cov, OR, err=.001, bnd=.5, numStep=10):
n = n0 + n1
num_match = 0
ret = []
COV = [y]
COV.extend(cov)
COV = np.asarray(COV).T
iter = IterTable(COV)
cur = 0
iter.next()
[yCur, covCur] = iter.get()
while not iter.isDone():
#print cur;
cur = cur + 1
[yCur, covCur] = iter.get()
lr = LR(yCur, AC(covCur, False))
try:
res_lr = lr.fit(disp=0)
except:
iter.next()
continue
OR_cur = 1.0
try:
OR_cur = math.exp(float(res_lr.params[0]))
except:
iter.next()
continue
if abs(OR_cur - OR) < err:
print "match"
num_match = num_match + 1
ret.append(iter.getTable())
#if abs(OR-OR_cur)/OR_cur>bnd:
#for i in range(0,numStep):
#iter.next();
iter.next()
return ret
def test_attack_pheno(n, numCov, err=.001):
#n=n0+n1;
x = [rand.randint(0, 2) for i in range(0, n)]
#y=[1 for i in range(0,n)]
#for i in range(0,n0):
# y[i]=0;
covs = [[rand.randint(0, 1) for i in range(0, n)]
for j in range(0, numCov)]
ORs = []
ret = []
for i in range(0, numCov):
print i
y = covs[i]
#ret=[x];
#ret.append(covs[i]);
#X=np.asarray(ret).T
X = AC(x, False)
lr = LR(y, X)
res_lr = lr.fit(disp=0)
OR = math.exp(float(res_lr.params[0]))
n1 = sum(y)
#n=len(y);
n0 = n - n1
ret.append(AL.attack_no_covar(n0, n1, OR, err=.001))
ORs.append(OR)
print "The number of matches is: "
for r in ret:
str(len(r))
print ORs
marg = []
pos = 0
for r in ret:
marg.append([])
for i in r:
marg[pos].append((i[0] + i[3], i[1] + i[4], i[2] + i[5]))
pos = pos + 1
print "\n"
for mar in marg:
print mar
#marg=[list(set(mar)) for mar in marg];
inAll = []
notIn = False
for m in marg[0]:
for mar in marg:
if not m in mar:
notIn = True
if not notIn:
inAll.append(m)
notIn = False
poss = [[ret[j][i] for i in range(0, len(ret[j])) if marg[j][i] in inAll]
for j in range(0, len(ret))]
poss = [[tuple(i) for i in p] for p in poss]
posCov = [(0), (1)]
for i in range(1, m):
dctnew = []
for d in PosCov:
dctnew.append((d + (0)))
dctnew.append((d + (1)))
posCov = dctnew
dctCov = {}
for i in range(0, len(posCov)):
dctCov[posCov[i]] = i
cnt = {}
for c in posCov:
cnt[c] = 0
for i in range(0, len(covs[0])):
cnt[tuple([c[i] for c in covs])] = cnt[tuple([c[i] for c in covs])] + 1
chosen = []
numchose = 0
testAll(chosen, numchose, poss, dctCov, cnt)
def test_attack_pheno(n,numCov,err=.001):
print "Generate Data!"
x=[rand.randint(0,2) for i in range(0,n)]
covs=[[rand.randint(0,1) for i in range(0,n)] for j in range(0,numCov)]
ORs=[];
ret=[];
print "Get ORs!"
for i in range(0,numCov):
print i;
y=covs[i]
#ret=[x];
#ret.append(covs[i]);
#X=np.asarray(ret).T
X=AC(x,False);
lr=LR(y,X);
res_lr=lr.fit(disp=0)
OR=math.exp(float(res_lr.params[0]));
n1=sum(y);
#n=len(y);
n0=n-n1;
ret.append(AL.attack_no_covar(n0,n1,OR,err=.001));
ORs.append(OR)
marg=[]
pos=0;
for r in ret:
marg.append([]);
for i in r:
marg[pos].append((i[0]+i[3],i[1]+i[4],i[2]+i[5]))
pos=pos+1;
print "\n"
for mar in marg:
print mar;
inAll=[];
notIn=False;
for m in marg[0]:
for mar in marg:
if not m in mar:
notIn=True;
if not notIn:
inAll.append(m);
notIn=False;
poss=[[ret[j][i] for i in range(0,len(ret[j])) if marg[j][i] in inAll] for j in range(0,len(ret))];
poss=[[tuple(i) for i in p] for p in poss]
print "Creates list of all possible covariate combinations"
posCov=[(0,),(1,)]
for i in range(1,numCov):
dctnew=[];
for d in posCov:
dctnew.append((d+(0,)))
dctnew.append((d+(1,)))
posCov=dctnew
print "Create map from covariate combinations into possible indices"
dctCov={};
for i in range(0,len(posCov)):
dctCov[posCov[i]]=i;
print "Create map from possible covariate combinations to number of times they occur"
cnt={}
for c in posCov:
cnt[c]=0;
for i in range(0,len(covs[0])):
cnt[tuple([c[i] for c in covs])]=cnt[tuple([c[i] for c in covs])]+1;
print "Iterate over all possible combinations and find possible solutions!"
chosen=[];
numchose=0;
(A,numeq)=makeMat(covs)
ret=testAll(chosen,numchose,poss,dctCov,cnt,A,numeq)
print "Possible solutions:"
print len(ret);
#for r in ret:
#print r;
print ret[0];