def IsAllIdenticalTopology(topoList): #{{{
numSeq = len(topoList)
if numSeq <= 1:
return True
else:
posTMList = [myfunc.GetTMPosition(topo) for topo in topoList]
NtermStateList = [lcmp.GetNtermState(topo) for topo in topoList]
numTMList = [len(posTM) for posTM in posTMList]
for i in xrange(numSeq - 1):
for j in xrange(i + 1, numSeq):
if not lcmp.IsIdenticalTopology(
NtermStateList[i], NtermStateList[j], numTMList[i],
numTMList[j], posTMList[i], posTMList[j], topoList[i],
topoList[j], min_TM_overlap):
return False
return True
def CountIdenticalTopology(pred_topodict, real_topodict, agreement, TM_type,
fpout_wrong, seqDict, pred_method_item): #{{{
"""
return (cntIDT, cntINV)
"""
numPredTopo = len(pred_topodict)
cntIDT = 0
cntINV = 0
cntDIFF = 0
for seqid in pred_topodict:
predtopo = pred_topodict[seqid]
try:
realtopo = real_topodict[seqid]
except KeyError:
print >> sys.stderr, "%s a nonTM protein predicted as TM protein" % (
seqid)
realtopo = "i" * len(predtopo)
pass
pred_NtermState = lcmp.GetNtermState(predtopo)
real_NtermState = lcmp.GetNtermState(realtopo.replace('.', '-'))
pred_posTM = myfunc.GetTMPosition(predtopo)
real_posTM = myfunc.GetTMPosition(realtopo)
pred_numTM = len(pred_posTM)
real_numTM = len(real_posTM)
# if g_params['isDEBUG'] and seqid == "3cx5I":
# print "pred_NtermState = <%s>"%pred_NtermState
# print "real_NtermState = <%s>"% real_NtermState
# print "pred_posTM = ", pred_posTM
# print "real_posTM = ", real_posTM
if lcmp.IsIdenticalTopology(pred_NtermState, real_NtermState,
pred_numTM, real_numTM, pred_posTM,
real_posTM, predtopo, realtopo,
g_params['min_TM_overlap']):
cntIDT += 1
else:
if fpout_wrong != None:
# output the wrongly predict topology
fpout_wrong.write(">%s Number %d mtd_%s\n" %
(seqid, cntDIFF + 1, pred_method_item))
try:
seq = seqDict[seqid]
fpout_wrong.write("%-10s %s\n" % ("AASeq", seq))
except KeyError:
seq = ""
fpout_wrong.write("%-10s %s\n" % ("RealTop", realtopo))
fpout_wrong.write("%-10s %s\n" % ("PredTop", predtopo))
fpout_wrong.write("\n")
if lcmp.IsInvertedTopology(pred_NtermState, real_NtermState,
pred_numTM, real_numTM, pred_posTM,
real_posTM, predtopo, realtopo,
g_params['min_TM_overlap']):
cntINV += 1
if g_params['isDEBUG']:
print >> sys.stderr, "%-7s(real %3s) nTM=%2d %s" % (
seqid, agreement, real_numTM, realtopo)
print >> sys.stderr, "%-7s(pred %3s) nTM=%2d %s" % (
seqid, agreement, pred_numTM, predtopo)
print >> sys.stderr
cntDIFF += 1
return (cntIDT, cntINV)