def CalKRBias(seq, topo, flank_win, max_dist):
kr_bias = None
KR_pos_list = [] # [[1,5], [1,3]]
posTM = myfunc.GetTMPosition(topo)
NtermState = lcmp.GetNtermState(topo)
numTM = len(posTM)
length = len(seq)
if numTM >= 1:
sum_KR_odd = 0
sum_KR_even = 0
for i in range(numTM + 1):
if i == 0 or i == numTM:
if i == 0:
b = max(0, posTM[i][0] - max_dist)
e = posTM[i][0] + flank_win
else:
b = posTM[i - 1][1] - flank_win
e = min(length, posTM[i - 1][1] + max_dist)
KRpos = GetKRPos(seq, b, e)
else:
if posTM[i][0] - posTM[i - 1][1] > 2 * max_dist:
b1 = posTM[i - 1][1] - flank_win
e1 = posTM[i - 1][1] + max_dist
b2 = posTM[i][0] - max_dist
e2 = posTM[i][0] + flank_win
KRpos = GetKRPos(seq, b1, e1)
KRpos += GetKRPos(seq, b2, e2)
else:
b = posTM[i - 1][1] - flank_win
e = posTM[i][0] + flank_win
# print (b,e)
# print len(seq)
# print "flank_win=",flank_win
# print "i=",i
# print "numTM=", len(posTM)
KRpos = GetKRPos(seq, b, e)
KR_pos_list.append(KRpos)
if i % 2 == 0:
sum_KR_odd += len(KRpos)
else:
sum_KR_even += len(KRpos)
kr_bias = sum_KR_odd - sum_KR_even
# print KR_pos_list
return (kr_bias, KR_pos_list, numTM)
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)
#border color; used when BORDER_WIDTH is above 0
#BORDER_COLOR\t#0000ff
#=================================================================#
# Actual data follows after the "DATA" keyword #
#=================================================================#
DATA
"""
fpout.write(dataset_settings)
for i in range(numSeq):
gid = idList[i]
if gid != 'Consensus':
n_i = 0
n_o = 0
NtermState = lcmp.GetNtermState(seqList[i])
numTM = myfunc.CountTM(seqList[i])
if NtermState == 'o':
n_i = 0
n_o = numTM
else:
n_i = numTM
n_o = 0
fpout.write("%s\t%d\t%d\n" % (gid, n_i, n_o))
fpout.write("\n")
if fpout != sys.stdout:
fpout.close()