def __init__(self,name,dir=None,parent=None):
super(ProjectSnp,self).__init__(name,dir,parent)
self.fsCoding = getFsEncoding(logLevel=False)
self.ui.nbMicrosatLabel.hide()
self.setGenValid(False)
self.ui.genDataLabel.setText("Summary statistics")
self.typesOrdered = ["A","H","X","Y","M"]
self.checkSNPbin = None
#self.ui.frame_11.show()
#self.ui.frame_12.show()
# until now set ascert bias functionality is not activated. (but waiting for further developpment)
# so self.ascert_state_valid is set to True
self.ascert_frame = ControlAscertBias(self)
self.ascert_frame.hide()
self.ascert_state_valid = True
self.setAscertValid(True)
QObject.connect(self.ui.ascertButton,SIGNAL("clicked()"),self.setAscertBias)
class ProjectSnp(ProjectReftable):
""" classe qui représente un projet de simulation
"""
def __init__(self,name,dir=None,parent=None):
super(ProjectSnp,self).__init__(name,dir,parent)
self.fsCoding = getFsEncoding(logLevel=False)
self.ui.nbMicrosatLabel.hide()
self.setGenValid(False)
self.ui.genDataLabel.setText("Summary statistics")
self.typesOrdered = ["A","H","X","Y","M"]
self.checkSNPbin = None
#self.ui.frame_11.show()
#self.ui.frame_12.show()
# until now set ascert bias functionality is not activated. (but waiting for further developpment)
# so self.ascert_state_valid is set to True
self.ascert_frame = ControlAscertBias(self)
self.ascert_frame.hide()
self.ascert_state_valid = True
self.setAscertValid(True)
QObject.connect(self.ui.ascertButton,SIGNAL("clicked()"),self.setAscertBias)
@pyqtSignature("")
def launchReftableGeneration(self):
# SNP Tests remove bin and bin.txt if no reftable was generated + check if MAF was modified
dataFile = str(self.ui.dataFileEdit.text())
if int(self.ui.nbSetsDoneEdit.text() )< 1 or not os.path.exists((u"%s/reftable.bin"%self.dir).encode(self.fsCoding)):
log(3,"No reftable.bin found, try to remove %s and %s"%(dataFile+".bin", dataFile+"bin.txt"))
if os.path.exists((dataFile+".bin").encode(self.fsCoding)) :
os.remove((dataFile+".bin").encode(self.fsCoding))
log(3, "%s removed" % (dataFile+".bin"))
if os.path.exists((dataFile+"bin.txt").encode(self.fsCoding)) :
os.remove((dataFile+"bin.txt").encode(self.fsCoding))
log(3, "%s removed" % (dataFile+"bin.txt"))
else :
f=open(dataFile.encode(self.fsCoding),'r')
words = f.readline().strip().split()
f.close()
commentWordsDict = DataAbstract.getParseCommentWordsDict(words)
f=open((os.path.join(str(self.dir),"maf.txt")).encode(self.fsCoding),'r')
maf = f.readline().strip().lower()
f.close()
if "hudson" in maf :
maf = "hudson"
else :
maf = str(float(maf))
commentWordsDict["maf"] = str(float(commentWordsDict["maf"]))
if str(commentWordsDict["maf"]) != maf :
output.notify(self,"MAF value error","The actual reftable was generated with <MAF=%s> but your data file %s says <MAF=%s> !\nRemove your reftable.bin file or fix your maf data file" % (maf, dataFile ,commentWordsDict["maf"]))
return
if not os.path.exists((dataFile+".bin").encode(self.fsCoding)) :
if self.checkSNPbin == None :
self.checkSNPbin = checkFileExistThread(file=dataFile+".bin", ui=self)
self.checkSNPbin.start()
#checkSNPbin.updateInterfaceForSnpBin()
super(ProjectSnp, self).launchReftableGeneration()
def stopRefTableGen(self):
try :
self.checkSNPbin.terminate()
except Exception :
pass
super(ProjectSnp, self).stopRefTableGen()
def getDataFileFilter(self):
return "SNP datafile (*.snp);;all files (*)"
def dataFileSelectionAndCopy(self,name=None):
""" si tout s'est bien passé, on sauve
"""
if super(ProjectSnp,self).dataFileSelectionAndCopy(name):
self.updateNbStats()
self.save()
def verifyRefTableValid(self):
""" Vérifie si tout est valide pour mettre à jour l'icone de l'onglet reference table, activer ou non le button de lancement du calcul de la reftable, affichage ou non des avertissements sur la taille du reftable.
"""
if self.gen_state_valid and self.hist_state_valid and self.ascert_state_valid:
self.setTabIcon(0,QIcon(variables.ICONPATH+"/ok.png"))
self.ui.runReftableButton.setDisabled(False)
self.ui.stopReftableButton.setDisabled(False)
self.ui.warningNumTextBrowser.show()
return True
else:
self.setTabIcon(0,QIcon(variables.ICONPATH+"/redcross.png"))
self.ui.runReftableButton.setDisabled(True)
self.ui.stopReftableButton.setDisabled(True)
self.ui.warningNumTextBrowser.hide()
return False
def setAscertBias(self):
log(1,"Entering in ControlAscertBias")
self.setAscertValid(False)
self.ui.refTableStack.addWidget(self.ascert_frame)
self.ui.refTableStack.setCurrentWidget(self.ascert_frame)
def setAscertValid(self,yn):
self.ascert_state_valid = yn
self.verifyRefTableValid()
if yn:
self.ui.ascertButton.setIcon(QIcon(variables.ICONPATH+"/ok.png"))
else:
self.ui.ascertButton.setIcon(QIcon(variables.ICONPATH+"/redcross.png"))
def isSnp(self):
return True
def setGenetic(self):
""" initie la définition des summary statistics
"""
log(1,"Entering in Summary statistics")
#ty = str(self.typeCombo.currentText())
self.ui.refTableStack.addWidget(self.sum_stat_wins)
self.ui.refTableStack.setCurrentWidget(self.sum_stat_wins)
self.setGenValid(False)
self.sum_stat_wins.lockLociSelection()
def getNbSumStats(self):
(nstat,stat_txt) = self.sum_stat_wins.getSumConf()
nb = int(nstat)
if self.ascert_frame.ascYesRadio.isChecked():
nb += 1
return nb
def getNbTotalTaken(self):
nb = 0
for ty in self.data.ntypeloc.keys() :
exec("nb += int(self.sum_stat_wins.ui.taken%sEdit.text())"%ty)
return nb
def getLociTaken(self):
Aval=0
Hval=0
Xval=0
Yval=0
Mval=0
From=1
txt = ""
for ty in self.typesOrdered :
if ty in self.data.ntypeloc.keys() :
exec("%sval= int(self.sum_stat_wins.ui.taken%sEdit.text())"%(ty,ty))
exec("txt += ' %s:%s,'"%(ty, eval('%sval'%ty)))
txt = txt[:-1] + " from locus %s"%self.sum_stat_wins.ui.fromEdit.text()
return txt
def updateNbStats(self):
""" met à jour les informations graphiques sur les
summary stats : le nombre total de stats et le nombre
total de locus concernés par des stats
"""
nb = self.getNbSumStats()
nbTaken = self.getNbTotalTaken()
lociTaken = self.getLociTaken()
if nb > 0:
self.setGenValid(True)
if nb > 1:
plur='s'
else:
plur=''
self.ui.nbSumStatsLabel.setText("Total : %s summary statistic%s"%(nb,plur))
self.ui.nbSequencesLabel.setText("Total : %s taken locus (%s) "%(nbTaken,lociTaken))
def getLocusGroups(self):
""" renvoie une liste des groupes de locus
utilisé par setupEstimationBias pour remplir la liste de groupes dans le cadre
de la redéfinition de sumstats
En SNP pas de groupes, renvoie juste le mot clef "SNP"
"""
return "SNP"
def redefineSumStatsAnalysis(self,setupEst):
""" methode ping pong pour sélectionner la bonne methode
de redefinition d'un groupe de sumstats
"""
setupEst.redefineSumStatsSnp()
def getNextWidget(self,hist_model):
""" méthode ping pong pour connaitre l'objet qui suit un
historical model fixed ou drawn
"""
return hist_model.getNextWidgetSnp()
def checkAll(self):
""" vérification du modèle historique et mutationnel
cette fonction est appelée au chargement du projet pour restituer l'etat du projet
"""
log(2,"Checking validity of Historical Model and Sum Stats")
# historical model :
self.hist_model_win.definePriors(silent=True)
if self.hist_model_win.checkAll(silent=True):
self.setHistValid(True)
self.hist_model_win.majProjectGui()
# mutation model : plus facile d'utiliser directement la validation
self.sum_stat_wins.validate(silent=True)
self.ascert_frame.validate(silent=True)
def returnToMe(self):
self.ui.refTableStack.removeWidget(self.ui.refTableStack.currentWidget())
self.ui.refTableStack.setCurrentIndex(0)
def loadSumStatsConf(self):
""" charge les summary statistics depuis le fichier gen_conf_name
"""
if os.path.exists(str(self.dir).encode(self.fsCoding)):
if os.path.exists((u"%s/%s"%(self.dir,self.parent.gen_conf_name)).encode(self.fsCoding)):
f = codecs.open((u"%s/%s"%(self.dir,self.parent.gen_conf_name)).encode(self.fsCoding),"rU","utf-8")
lines = f.readlines()
f.close()
nl = 1
diconb = {}
dicoFrom = {}
dicoGrTy = {}
dicoStatLines = {}
tyUsed= []
while (lines[nl].strip() != ""):
numGr = int(lines[nl].split('G')[-1][0])
fro = lines[nl].split('from')[-1].split()[0]
for couple in lines[nl].split('>')[:-1]:
if '<' in couple :
ty = couple[-1]
numTy = couple.split('<')[0].split()
if len(numTy) != 1 :
raise Exception("Read SNP loci : Parsing error on : %s" % lines[nl])
numTy = numTy[0]
exec("self.sum_stat_wins.ui.taken%sEdit.setText(numTy)"%ty)
tyUsed += ty
diconb[ty] = numTy
dicoFrom[ty] = fro
dicoGrTy[numGr] = ty
self.sum_stat_wins.ui.fromEdit.setText(fro)
for tyOrdered in self.typesOrdered:
if tyOrdered not in tyUsed:
exec("self.sum_stat_wins.ui.taken%sEdit.setText('0')"%tyOrdered)
nl += 1
nl += 2
while nl < len(lines) and lines[nl].strip() != "":
numGroup = int(lines[nl].strip().split()[1][1:])
ty = dicoGrTy[numGroup]
statlines = []
nl += 1
while nl < len(lines) and "group" not in lines[nl]:
statlines.append( lines[nl] )
nl += 1
dicoStatLines[ty] = statlines
for ty in dicoStatLines.keys():
self.sum_stat_wins.setSumConf(dicoStatLines[ty])
self.updateNbStats()
def loadFromDir(self):
""" charge les infos à partir du répertoire self.dir
"""
log(2,"Launching load procedures")
# GUI
self.ui.dirEdit.setText(self.dir)
self.ui.browseDataFileButton.setDisabled(True)
self.ui.browseDataFileButton.hide()
self.ui.groupBox_6.show()
self.ui.groupBox_7.show()
self.ui.groupBox_8.show()
self.ui.setHistoricalButton.setDisabled(False)
self.ui.setGeneticButton.setDisabled(False)
try:
self.loadMyConf()
# lecture de conf.hist.tmp
self.hist_model_win.loadHistoricalConf()
self.ascert_frame.loadAscertConf()
self.loadSumStatsConf()
self.sum_stat_wins.lockLociSelection()
self.loadAnalysis()
except Exception as e:
log(1, traceback.format_exc())
raise Exception("Impossible to read the project configuration\n\n%s"%e)
output.notify(self,"Load error","Impossible to read the project configuration\n\n%s"%e)
def loadMyConf(self):
""" lit le fichier conf.tmp pour charger le fichier de données
"""
log(2,"Reading '%s' to load datafile"%self.parent.main_conf_name)
if os.path.exists((u"%s/%s"%(self.ui.dirEdit.text(), self.parent.main_conf_name)).encode(self.fsCoding)):
f = open((u"%s/%s"%(self.dir,self.parent.main_conf_name)).encode(self.fsCoding),"rU")
lines = f.readlines()
self.dataFileName = lines[0].strip()
self.ui.dataFileEdit.setText(self.dataFileName)
# lecture du dataFile pour les infos de Gui Projet
if os.path.exists((u"%s/%s"%(self.dir,self.dataFileName)).encode(self.fsCoding)):
if self.loadDataFile((u"%s/%s"%(self.dir,self.dataFileName)).encode(self.fsCoding)):
## comme on a lu le datafile, on peut remplir le tableau de locus dans setGeneticData
pass
else:
log(1, traceback.format_exc())
raise Exception("Impossible to load the datafile (%s) because it is possibly malformed"%self.dataFileName)
else:
log(1, traceback.format_exc())
raise Exception("Datafile doesn't exist (%s)"%self.dataFileName)
else:
log(1, traceback.format_exc())
raise Exception("Main conf file not found (%s)"%self.parent.main_conf_name)
def loadDataFile(self,name):
""" Charge le fichier de données passé en paramètre. Cette fonction est appelée lors
de l'ouverture d'un projet existant et lors du choix du fichier de données pour un nouveau projet
"""
log(2,"Loading datafile '%s'"%name)
## conversion de dos à unix
#if not isUnixText(name):
# dos2unix(name)
buttonPreviousText = self.runReftableButton.text()
self.runReftableButton.setText("Checking data file format : please wait")
try:
self.data = DataSnp(name)
typestr = ""
for ty in self.typesOrdered :
if ty in self.data.ntypeloc.keys():
typestr += " %s : %s,"%(ty,self.data.ntypeloc[ty])
typestr = typestr[:-1]
if str(self.data.commentValuesDict['maf']).lower() == "hudson" :
if self.data.nloctot != self.data.nloc :
output.notify(self,"Monomorphic Loci warning","Your dataset includes a fraction of monomorphic loci :\n\nONLY POLYMORPHIC LOCI WILL BE CONSIDERED AFTERWARDS.")
self.ui.dataFileInfoLabel.setText("MAF = hudson : %s polymorphic loci + %s monomorphic loci\n%s individuals in %s samples\n%s" % \
(self.data.nloc,(self.data.nloctot-self.data.nloc),self.data.nindtot,self.data.nsample,typestr))
else :
self.ui.dataFileInfoLabel.setText("MAF = %s : %s loci fitting the MAF (over %s)\n%s individuals in %s samples\n%s" % \
(self.data.commentValuesDict['maf'], self.data.nloc,self.data.nloctot,self.data.nindtot,self.data.nsample,typestr))
self.ui.dataFileEdit.setText(name)
self.dataFileSource = name
except Exception as e:
log(1, traceback.format_exc())
keep = ""
if self.ui.dataFileEdit.text() != "":
keep = "\n\nThe file was not loaded, nothing was changed"
output.notify(self,"Data file error","%s%s"%(e,keep))
self.runReftableButton.setText(buttonPreviousText)
return False
# on declare les sumstats apres avoir chargé le datafile car c'est nécessaire
# feinte pour que le parent.parent renvoie au projet
self.dummy = QFrame()
self.dummy.parent = self
self.clearSummaryStats()
# selection du type de snp pour sumstats kkpz a retirer
#self.typeCombo = QComboBox(self)
#for ty in self.typesOrdered:
# if ty in self.data.ntypeloc.keys():
# self.typeCombo.addItem(ty)
#self.ui.horizontalLayout_6.addWidget(QLabel("for locus type :"))
#self.ui.horizontalLayout_6.addWidget(self.typeCombo)
self.runReftableButton.setText(buttonPreviousText)
return True
def clearSummaryStats(self):
self.sum_stat_wins = SetSummaryStatisticsSnp(parent=self.dummy,numGroup='A')
self.sum_stat_wins.hide()
def save(self):
""" sauvegarde du projet -> mainconf, histconf, genconf, theadconf
Si le gen et hist sont valides, on génère le header
"""
log(2,"Saving project '%s'"%self.dir)
self.parent.showStatus("Saving project %s"%self.name)
if self.dir != None and self.dataFileName != "":
# save meta project
if os.path.exists((u"%s/%s"%(self.dir,self.parent.main_conf_name)).encode(self.fsCoding)):
os.remove((u"%s/%s"%(self.dir,self.parent.main_conf_name)).encode(self.fsCoding))
f = codecs.open((u"%s/%s"%(self.dir,self.parent.main_conf_name)).encode(self.fsCoding),'w',"utf-8")
f.write("%s\n"%self.dataFileName)
# recup du nombre de params (depuis historical model et les mutational qui varient)
nb_param = self.hist_model_win.getNbParam()
f.write("%s parameters and %s summary statistics\n\n"%(nb_param,self.getNbSumStats()))
f.close()
# save hist conf
self.hist_model_win.writeHistoricalConfFromGui()
# save gen conf
self.writeGeneticConfFromGui()
# save th conf et production du reftable header
if self.gen_state_valid and self.hist_state_valid:
self.writeThConf()
self.writeAscertConf()
self.writeRefTableHeader()
self.saveAnalysis()
self.parent.clearStatus()
self.parent.showStatus("Project %s successfully saved"%self.name,2000)
else:
output.notify(self,"Saving is impossible","Project %s is not yet completly created"%self.name)
self.parent.clearStatus()
def writeAscertConf(self):
log(2,"Writing ascertainment in %s"%self.parent.ascertainment_conf_name)
ascert_string = u""
if self.ascert_frame.ascYesRadio.isChecked():
ascert_string += "%s\n"%str(self.ascert_frame.asc1ValEdit.text()).strip()
ascert_string += "%s\n"%str(self.ascert_frame.asc2ValEdit.text()).strip()
ascert_string += "%s\n"%str(self.ascert_frame.asc3ValEdit.text()).strip()
else:
ascert_string = u"\n"
if os.path.exists((u"%s/%s"%(self.dir,self.parent.ascertainment_conf_name)).encode(self.fsCoding)):
os.remove((u"%s/%s"%(self.dir,self.parent.ascertainment_conf_name)).encode(self.fsCoding))
f = codecs.open((u"%s/%s"%(self.dir,self.parent.ascertainment_conf_name)).encode(self.fsCoding),'w',"utf-8")
f.write("%s"%(ascert_string))
f.close()
def writeRefTableHeader(self):
""" écriture du header.txt à partir des conf
"""
super(ProjectSnp,self).writeRefTableHeader()
if os.path.exists((u"%s/%s"%(self.dir,self.parent.ascertainment_conf_name)).encode(self.fsCoding)):
f = codecs.open((u"%s/%s"%(self.dir,self.parent.ascertainment_conf_name)).encode(self.fsCoding),"rU","utf-8")
ascert_string = f.read()
f.close()
else:
output.notify(self,"Header generation problem","Impossible to add ascertainment part to header : ascertainment file doesn't exist")
return
if os.path.exists((u"%s/%s"%(self.dir,self.parent.reftableheader_name)).encode(self.fsCoding)):
log(2,"Adding ascertainment part to header")
fdest = codecs.open((u"%s/%s"%(self.dir,self.parent.reftableheader_name)).encode(self.fsCoding),"a","utf-8")
fdest.write("\n\n%s"%ascert_string)
fdest.close()
else:
output.notify(self,"Header generation problem","Impossible to add ascertainment part to header : header doesn't exist")
def writeThConf(self):
""" ecrit le header du tableau de resultat qui sera produit par les calculs
il contient, les paramètres historicaux, les summary stats
"""
log(2,"Writing last part of the header (the parameter table header) in %s"%self.parent.table_header_conf_name)
hist_params_txt = self.hist_model_win.getParamTableHeader()
sum_stats_txt = self.getSumStatsTableHeader()
if os.path.exists((u"%s/%s"%(self.dir,self.parent.table_header_conf_name)).encode(self.fsCoding)):
os.remove((u"%s/%s"%(self.dir,self.parent.table_header_conf_name)).encode(self.fsCoding))
f = codecs.open((u"%s/%s"%(self.dir,self.parent.table_header_conf_name)).encode(self.fsCoding),'w',"utf-8")
f.write("scenario%s%s"%(hist_params_txt,sum_stats_txt))
f.close()
def getSumStatsTableHeader(self):
""" retourne la partie sumstats du table header
"""
result = u""
numGroup = 1
sums_txt = self.sum_stat_wins.getSumStatsTableHeader(numGroup)
result += sums_txt
if self.ascert_frame.ascYesRadio.isChecked():
result += output.centerHeader("PPL",14)
return result
def writeGeneticConfFromGui(self):
""" Sauvegarde des summary statistics dans le fichier gen_conf_name
"""
locidesc = ""
statsdesc = ""
res = ""
numGr = 1
totNbStat = 0
if self.ascert_frame.ascYesRadio.isChecked():
totNbStat += 1
(nstat,statstr) = self.sum_stat_wins.getSumConf()
totNbStat += nstat
if nstat > 0:
for ty in self.data.ntypeloc.keys():
exec("taken = self.sum_stat_wins.ui.taken%sEdit.text()"%ty)
if int(taken) > 0 :
locidesc += "%s <%s> "%(taken,ty)
statsdesc += "group G%s (%s)\n%s"%(numGr,nstat,statstr)
locidesc += "G%s from %s\n"%(numGr,self.sum_stat_wins.ui.fromEdit.text())
res += "loci description (%s)\n"%(numGr)
res += locidesc
res += "\ngroup summary statistics (%s)\n"%(totNbStat)
if self.ascert_frame.ascYesRadio.isChecked():
nb = int(statsdesc.split('group G')[-1].split(')')[0].split('(')[1])
num = int(statsdesc.split('group G')[-1].split()[0])
statsdesc = statsdesc.replace('group G%s (%s)'%(num,nb),'group G%s (%s)'%(num,nb+1))
statsdesc += "PPL\n"
res += statsdesc
res += "\n"
if os.path.exists((u"%s/%s"%(self.dir,self.parent.gen_conf_name)).encode(self.fsCoding)):
os.remove((u"%s/%s" % (self.dir,self.parent.gen_conf_name)).encode(self.fsCoding))
f = codecs.open((u"%s/%s"%(self.dir,self.parent.gen_conf_name)).encode(self.fsCoding),'w',"utf-8")
f.write(res)
f.close()
def freezeHistModel(self,yesno=True):
super(ProjectSnp,self).freezeHistModel(yesno)
self.ascert_frame.ui.scrollArea.setDisabled(yesno)
if yesno:
if "Set " in str(self.ui.ascertButton.text()):
self.ui.ascertButton.setText(str(self.ui.ascertButton.text()).replace("Set ","View "))
elif "View " not in str(self.ui.ascertButton.text()):
self.ui.ascertButton.setText("View "+str(self.ui.ascertButton.text()))
else:
if "View " in str(self.ui.ascertButton.text()):
self.ui.ascertButton.setText(str(self.ui.ascertButton.text()).replace("View ","Set "))
elif "Set " not in str(self.ui.ascertButton.text()):
self.ui.ascertButton.setText("Set "+str(self.ui.ascertButton.text()))
def freezeGenData(self,yesno=True):
try:
g = self.sum_stat_wins
for e in g.findChildren(QLineEdit):
e.setDisabled(yesno)
for e in g.findChildren(QPushButton):
e.setDisabled(yesno)
for e in g.findChildren(QCheckBox):
e.setDisabled(yesno)
g.ui.clearButton.setDisabled(yesno)
g.ui.exitButton.setDisabled(yesno)
g.ui.okButton.setDisabled(False)
g.ui.addAdmixButton.setDisabled(yesno)
if yesno:
self.ui.setGeneticButton.setText(" View")
else:
self.ui.setGeneticButton.setText(" Set")
except AttributeError as e:
log(4,"Fail to freeze gen data")