def detparam(self,s,category):
s1 = s
ss = []
while len(s1)>0 :
plus = s1.find("+")
minus= s1.find("-")
if (plus == -1)and(minus == -1) :
ss.append(s1)
s1 = ""
else :
if plus>=0 : posigne = plus;
else : posigne = minus;
ss.append(s1[:posigne])
s1 = s1[posigne+1:]
for j in range(len(ss)) :
if not isaninteger(ss[j]):
pr = param.HistParameter()
pr.category,pr.prior = category, None
pr.name, pr.value = ss[j], None
if len(self.parameters) >0 :
trouve = False
i = -1
while (not trouve) and (i<len(self.parameters)-1) :
i +=1
trouve = pr.name == self.parameters[i].name
if trouve and (self.parameters[i].category != category):
raise IOScreenError, "%s is used as a %s parameter and %s parameter"%(pr.name,param.HistParameter.categorydict[category],param.HistParameter.categorydict[self.parameters[i].category] )
if not trouve : self.parameters.append(pr)
else :
self.parameters.append(pr)
def checkread(self,textarray,data=None):
if len(self.parameters)>0 :
self.parametersbackup = copy.deepcopy(self.parameters)
self.parameters = []
else : self.parametersbackup = []
ligne0 = textarray[0] #take the first line of the scenario
ligne =ligne0.upper() #put it in uppercase
if ligne.find('SAMPLE')+ligne.find('REFSAMPLE')+ligne.find('MERGE')+ligne.find('VARNE')+ligne.find('SPLIT')+ligne.find('SEXUAL')>-4:
raise IOScreenError, "The first line must provide effective population sizes"
ls = ligne0.split()
self.npop = len(ls)
self.history = History()
Ncur=[]
for l in ls :
NN = Ne0()
NNc = Ne0()
if isaninteger(l): NN.name, NN.val, NNc.name, NNc.val = str(l),int(l),str(l),int(l)
else : NN.name, NN.val, NNc.name, NNc.val = l, None, l, None
self.history.ne0s.append(NN)
Ncur.append(NNc)
if NN.val == None : self.detparam(NN.name,"N")
self.nsamp = 0
self.nrefsamp = 0
nevent = 0
pat = re.compile(r'\s+')
for i,li_n_c in enumerate(textarray[1:]):
li = pat.sub(' ',li_n_c)
if li.upper().find('SAMPLE')+li.upper().find('REFSAMPLE') > -1 :
self.nsamp+=1
if li.upper().find('REFSAMPLE') > -1 :
self.dicoPopRefNindRef[int(li.strip().split(' ')[-3])] = int(li.strip().split(' ')[-1]) + int(li.strip().split(' ')[-2])
self.nrefsamp+=1
if (len(li.strip().split(' ')) < 3)or(len(li.strip().split(' ')) == 4):
raise IOScreenError, "At line %i, the number of words is incorrect"%(i+2)
# verif que le nombre apres "sample" est bien inférieur ou egal au nombre de pop (len(Ncur))
if (li.upper().find(' SAMPLE')>-1) and (int(li.strip().split(' ')[2]) > len(Ncur)):
raise IOScreenError, "At line %i, the population number (%s) is higher than the number of population (%s) defined at line 1"%((i+2),li.split(' ')[-1],len(Ncur))
if (li.upper().find('REFSAMPLE')>-1) and (int(li.strip().split(' ')[2]) > len(Ncur)):
raise IOScreenError, "At line %i, the population number (%s) is higher than the number of population (%s) defined at line 1"%((i+2),li.split(' ')[-1],len(Ncur))
if self.nsamp<1 :
raise IOScreenError, "You must indicate when samples are taken"
if data!=None:
#print self.nsamp,"========", data.nsample
if self.nsamp != data.nsample+self.nrefsamp :
raise IOScreenError, "The number of samples in scenario %s does not match the data file"%(self.number)
if len(textarray)>1 :
for ili0 in range(0,len(textarray)-1) :
for ili1 in range(ili0+1,len(textarray)) :
li0tem = textarray[ili0].split()
li1tem = textarray[ili1].split()
idem = False
if len(li0tem) == len(li1tem) :
idem = True
j = 0
while idem and (j<len(li0tem)) :
idem = (li0tem[j] == li1tem[j])
j +=1
if idem :
raise IOScreenError,"Lines %s and %s of scenario %s are identical"%(ili0+1,ili1+1,self.number)
j,ns = 0, 0
for jli0 in range(1,len(textarray)):
if len(textarray[jli0])>0:
j +=1
li = textarray[jli0]
Li = li.upper()
litem = li.split()
nitems = len(litem)
if Li.find(" SAMPLE")+ Li.find("REFSAMPLE")>-1:
if (nitems<3)or(nitems==4):
raise IOScreenError, "Line %s of scenario %s is incomplete"%(jli0+1,self.number)
self.cevent = Event()
self.cevent.numevent0 = nevent
nevent +=1
if Li.find(" SAMPLE")>-1 :
self.cevent.action = "SAMPLE"
if Li.find("REFSAMPLE")>-1 :
self.cevent.action = "REFSAMPLE"
self.cevent.stime = litem[0]
if isaninteger(litem[0]) : self.cevent.time = int(litem[0])
else : self.detparam(litem[0],"T")
if isaninteger(litem[2]):
self.cevent.pop = int(litem[2])
else :
raise IOScreenError, "Unable to read population number on line %s of scenario %s"%(jli0+1,self.number)
self.cevent.Ne=Ncur[self.cevent.pop-1].val
self.cevent.sNe=Ncur[self.cevent.pop-1].name
ns +=1
self.cevent.sample = ns
self.time_sample.append(self.cevent.time)
if (nitems==5):
if isaninteger(litem[3]):
self.cevent.nindMref = int(litem[3])
else :
raise IOScreenError, "Unable to read number of males on line %s of scenario %s"%(jli0+1,self.number)
if isaninteger(litem[4]):
self.cevent.nindFref = int(litem[4])
else :
raise IOScreenError, "Unable to read number of females on line %s of scenario %s"%(jli0+1,self.number)
#print self.cevent.nindMref," ",self.cevent.nindFref
#print " ",data.nind[0]
if Li.find(" SAMPLE") != -1 and (data!=None):
if self.cevent.nindMref+self.cevent.nindFref > data.nind[self.cevent.pop-1] :
raise IOScreenError, "The total number of reference individuals (%s) is larger than that of the data set (%s) on line %s of scenario %s"%(self.cevent.nindMref+self.cevent.nindFref,data.nind[self.cevent.pop-1],jli0+1,self.number)
elif Li.find("VARNE")>-1:
if nitems<4:
raise IOScreenError, "Line %s of scenario %s is incomplete"%(jli0+1,self.number)
self.cevent = Event()
self.cevent.numevent0 = nevent
nevent +=1
self.cevent.action = "VARNE"
self.cevent.stime = litem[0]
if isaninteger(litem[0]) : self.cevent.time = int(litem[0])
else : self.detparam(litem[0],"T")
if isaninteger(litem[2]):
self.cevent.pop = int(litem[2])
else :
raise IOScreenError, "Unable to read population number on line %s of scenario %s"%(jli0+1,self.number)
if isaninteger(litem[3]):
self.cevent.Ne = int(litem[3]);self.cevent.sNe = None
else :
self.cevent.sNe = litem[3];self.cevent.Ne = None
self.detparam(litem[3],"N")
Ncur[self.cevent.pop-1].val=self.cevent.Ne
Ncur[self.cevent.pop-1].name=self.cevent.sNe
elif Li.find("MERGE")>-1:
if nitems<4:
raise IOScreenError, "Line %s of scenario %s is incomplete"%(jli0+1,self.number)
if nitems>4:
raise IOScreenError, "At line %i, the number of words is incorrect"%(i+2)
self.cevent = Event()
self.cevent.numevent0 = nevent
nevent +=1
self.cevent.action = "MERGE"
self.cevent.stime = litem[0]
if isaninteger(litem[0]) : self.cevent.time = int(litem[0])
else : self.detparam(litem[0],"T")
if isaninteger(litem[2]):
self.cevent.pop = int(litem[2])
else :
raise IOScreenError, "Unable to read the first population number on line %s of scenario %s"%(jli0+1,self.number)
if isaninteger(litem[3]):
self.cevent.pop1 = int(litem[3])
else :
raise IOScreenError, "Unable to read the second population number on line %s of scenario %s"%(jli0+1,self.number)
self.cevent.Ne=Ncur[self.cevent.pop-1].val
self.cevent.sNe=Ncur[self.cevent.pop-1].name
elif Li.find("SPLIT")>-1:
if nitems<6:
raise IOScreenError, "Line %s of scenario %s is incomplete"%(jli0+1,self.number)
self.cevent = Event()
self.cevent.numevent0 = nevent
nevent +=1
self.cevent.action = "SPLIT"
self.cevent.stime = litem[0]
if isaninteger(litem[0]) : self.cevent.time = int(litem[0])
else : self.detparam(litem[0],"T")
if isaninteger(litem[2]):
self.cevent.pop = int(litem[2])
else :
raise IOScreenError, "Unable to read the first population number on line %s of scenario %s"%(jli0+1,self.number)
if isaninteger(litem[3]):
self.cevent.pop1 = int(litem[3])
else :
raise IOScreenError, "Unable to read the second population number on line %s of scenario %s"%(jli0+1,self.number)
if isaninteger(litem[4]):
self.cevent.pop2 = int(litem[4])
else :
raise IOScreenError, "Unable to read the third population number on line %s of scenario %s"%(jli0+1,self.number)
if isafloat(litem[5]):
self.cevent.admixrate = float(litem[5])
else :
self.cevent.sadmixrate = litem[5]
self.detparam(litem[5],"A")
self.cevent.Ne=Ncur[self.cevent.pop-1].val
self.cevent.sNe=Ncur[self.cevent.pop-1].name
elif Li.find("SEXUAL")>-1:
if nitems<3:
raise IOScreenError, "Line %s of scenario %s is incomplete"%(jli0+1,self.number)
self.cevent = Event()
self.cevent.numevent0 = nevent
nevent +=1
self.cevent.action = "SEXUAL"
self.cevent.stime = litem[0]
if isaninteger(litem[0]) : self.cevent.time = int(litem[0])
else : self.detparam(litem[0],"T")
if isaninteger(litem[2]):
self.cevent.pop = int(litem[2])
else :
raise IOScreenError, "Unable to read population number on line %s of scenario %s"%(jli0+1,self.number)
self.cevent.Ne=Ncur[self.cevent.pop-1].val
self.cevent.sNe=Ncur[self.cevent.pop-1].name
ns +=1
self.cevent.sample = ns
self.time_sample.append(self.cevent.time)
else :
raise IOScreenError,"Uninterpretable line %s in scenario %s"%(jli0+1,self.number)
self.history.events.append(self.cevent)
if self.cevent.pop>self.popmax : self.popmax=self.cevent.pop
self.setgraphtime()
if len(self.parametersbackup)>0 :
for pb in self.parametersbackup :
trouve = False
i = -1
while (not trouve)and(i<len(self.parameters)-1) :
i +=1
p = self.parameters[i]
trouve = (pb.name == p.name) and (pb.category == p.category)
if trouve : self.parameters[i].value = pb.value