def loadMMS(self):
""" chargement de la partie mutation model sequences des préférences
"""
lines = []
cfg = self.config
if cfg.has_key("mutation_s_default_values"):
try:
for param in ["MEANMU", "GAMMU", "MEANK1", "GAMK1", "MEANK2", "GAMK2"]:
exec(
'lines.append("{0} %s[%s,%s,%s,%s]"%(cfg["mutation_s_default_values"]["{0}_law"],cfg["mutation_s_default_values"]["{0}_zero"],cfg["mutation_s_default_values"]["{0}_one"],cfg["mutation_s_default_values"]["{0}_two"],cfg["mutation_s_default_values"]["{0}_three"]))'.format(
param
)
)
lines.append(
"MODEL %s %s %s"
% (
cfg["mutation_s_default_values"]["MODEL_model"],
cfg["mutation_s_default_values"]["MODEL_inv_sites_pc"],
cfg["mutation_s_default_values"]["MODEL_gamma_shape"],
)
)
self.mutmodS.setMutationConf(lines)
except Exception as e:
log(3, "Malformed mutation_s_default_values in configuration")
else:
log(3, "No MMS conf found")
def putChoices(self):
""" met les choix de scenario en place
"""
bg = QButtonGroup(self)
left = True
for i in range(self.nb_sc):
num = i+1
if self.analysis.category == "modelChecking":
check = QRadioButton("Scenario %s"%num,self)
bg.addButton(check)
else:
check = QCheckBox("Scenario %s"%num,self)
if self.analysis.category == "compare":
check.setChecked(True)
self.checklist.append(check)
if left:
self.ui.verticalLayout.addWidget(check)
else:
self.ui.verticalLayout_2.addWidget(check)
left = not left
# les deux cas où on a pas le choix des scenarios parce qu'ils sont trop peu
if self.nb_sc == 1:
self.checklist[0].setChecked(True)
self.checklist[0].setDisabled(True)
self.next_widget.ui.redefButton.hide()
log(4,"type of next widget : %s"%type(self.next_widget))
if self.nb_sc == 2 and "Comparison" in str(type(self.next_widget)):
self.checklist[0].setChecked(True)
self.checklist[0].setDisabled(True)
self.checklist[1].setChecked(True)
self.checklist[1].setDisabled(True)
self.next_widget.ui.redefButton.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 drawAll(self):
""" dessine les graphes de tous les paramètres
"""
# nettoyage
for fr in self.findChildren(QFrame,"frameDraw"):
self.ui.horizontalLayout_2.removeWidget(fr)
fr.hide()
del fr
for fr in self.findChildren(QFrame,"frameValues"):
self.ui.horizontalLayout_3.removeWidget(fr)
fr.hide()
del fr
self.dicoPlot = {}
if os.path.exists((u"%s/analysis/%s/paramstatdens%s.txt"%(self.parent.dir,self.directory,self.file_subname)).encode(self.fsCoding)):
f = codecs.open((u"%s/analysis/%s/paramstatdens%s.txt"%(self.parent.dir,self.directory,self.file_subname)).encode(self.fsCoding),"rU","utf-8")
lines = f.readlines()
f.close()
dico_info_draw = {}
l = 0
orderedNames = []
while l < (len(lines) - 1):
name = lines[l].strip()
values = lines[l+1]
absv = lines[l+3]
ordpr = lines[l+4]
ordpo = lines[l+5]
dico_info_draw[name] = [values,absv,ordpr,ordpo]
orderedNames.append(name)
l += 6
for name in orderedNames:
self.addDraw(name,dico_info_draw[name][0],dico_info_draw[name][1],dico_info_draw[name][2],dico_info_draw[name][3])
else:
log(3, "paramstatdens%s.txt not found for analysis %s"%(self.file_subname,self.analysis.name))
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 addRow(self,name="locus",type="M"):
""" ajoute un locus à la liste principale (de locus)
"""
self.ui.tableWidget.insertRow(self.ui.tableWidget.rowCount())
#self.ui.tableWidget.setCellWidget(self.ui.tableWidget.rowCount()-1,i,QPushButton("View"))
self.ui.tableWidget.setItem(self.ui.tableWidget.rowCount()-1,0,QTableWidgetItem("%s"%(name)))
self.ui.tableWidget.setItem(self.ui.tableWidget.rowCount()-1,1,QTableWidgetItem("%s"%type))
self.ui.tableWidget.item(self.ui.tableWidget.rowCount()-1,0).setFlags(self.ui.tableWidget.item(self.ui.tableWidget.rowCount()-1,0).flags() & ~Qt.ItemIsEditable)
self.ui.tableWidget.item(self.ui.tableWidget.rowCount()-1,1).setFlags(self.ui.tableWidget.item(self.ui.tableWidget.rowCount()-1,1).flags() & ~Qt.ItemIsEditable)
if type == "M":
#self.ui.tableWidget.setItem(self.ui.tableWidget.rowCount()-1,2,QTableWidgetItem("2"))
#self.ui.tableWidget.setItem(self.ui.tableWidget.rowCount()-1,3,QTableWidgetItem("40"))
#self.ui.tableWidget.item(self.ui.tableWidget.rowCount()-1,2).setTextAlignment(Qt.AlignRight)
#self.ui.tableWidget.item(self.ui.tableWidget.rowCount()-1,3).setTextAlignment(Qt.AlignRight)
dos = QTableWidgetItem("2")
tres = QTableWidgetItem("40")
dos.setTextAlignment(Qt.AlignRight|Qt.AlignTop)
tres.setTextAlignment(Qt.AlignRight|Qt.AlignTop)
self.ui.tableWidget.setItem(self.ui.tableWidget.rowCount()-1,2,dos)
self.ui.tableWidget.setItem(self.ui.tableWidget.rowCount()-1,3,tres)
log(3,"Adding a locus (%s)"%tres.textAlignment())
else:
self.ui.tableWidget.setItem(self.ui.tableWidget.rowCount()-1,2,QTableWidgetItem(" "))
self.ui.tableWidget.setItem(self.ui.tableWidget.rowCount()-1,3,QTableWidgetItem(" "))
self.ui.tableWidget.item(self.ui.tableWidget.rowCount()-1,2).setFlags(self.ui.tableWidget.item(self.ui.tableWidget.rowCount()-1,2).flags() & ~Qt.ItemIsEditable)
self.ui.tableWidget.item(self.ui.tableWidget.rowCount()-1,3).setFlags(self.ui.tableWidget.item(self.ui.tableWidget.rowCount()-1,3).flags() & ~Qt.ItemIsEditable)
def setGenetic(self):
""" passe sur l'onglet correspondant
"""
log(1, "Entering in Genetic Data Setting")
self.ui.refTableStack.addWidget(self.gen_data_win)
self.ui.refTableStack.setCurrentWidget(self.gen_data_win)
self.setGenValid(False)
def hideFixedParams(self):
fixed_params_list = self.parents.hist_model_win.getFixedParamList()
for box in self.paramList:
name = str(box.findChild(QLabel,"paramNameLabel").text())
if name in fixed_params_list:
box.hide()
log(3,"Hiding parameter %s because its value is fixed"%name)
def setScenarios(self,scList):
""" écrit la liste des scenarios à estimer
"""
sumRec = 0
plur= ""
if len(scList)>1:
plur = "s"
lstxt=""
self.scNumList = []
for i in scList:
lstxt+="%s, "%i
sumRec+=self.parent.parent.readNbRecordsOfScenario(int(i))
log(3,"Sum of scenarios records : %s"%sumRec)
self.scNumList.append(i)
lstxt = lstxt[:-2]
txt = "Chosen scenario%s : %s"%(plur,lstxt)
self.ui.scenariosLabel.setText(txt)
self.ui.totNumSimLabel.setText(str(sumRec))
# on le fait seulement si on n'est pas en édition
if self.analysis.computationParameters == "":
self.ui.cnosdEdit.setText(str(sumRec))
nosdDefault = sumRec/100
if nosdDefault < 1000:
nosdDefault = 1000
self.ui.nosdEdit.setText(str(nosdDefault))
def clearHistoricalModel(self):
""" détruit le modèle historique et en instancie un nouveau
"""
log(1,"Clearing historical model")
self.ui.refTableStack.removeWidget(self.hist_model_win)
self.hist_model_win = SetHistoricalModel(self)
self.ui.refTableStack.insertWidget(0,self.hist_model_win)
self.ui.refTableStack.setCurrentWidget(self.hist_model_win)
def setHistorical(self):
""" passe sur l'onglet correspondant
"""
log(1,"Entering in Historical Model Setting")
## nécéssaire seulement sous windows
## on dirait que sous linux, le simple setCurrentWidget rend l'onglet enabled
self.ui.refTableStack.addWidget(self.hist_model_win)
self.ui.refTableStack.setCurrentWidget(self.hist_model_win)
self.setHistValid(False)
def loadRecent(self):
recent_list = []
if self.config.has_key("recent") and self.config["recent"].has_key("projectPathList"):
log(3, "Loading recent list")
for rec in self.config["recent"]["projectPathList"].split("\n"):
if len(rec) > 0 and rec.strip() != "":
recent_list.append(rec.strip())
log(4, "Loading recent : %s" % rec.strip())
self.parent.setRecent(recent_list)
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 run(self):
self.ui.runReftableButton.setText("Pre-processing of the observed dataset : please wait")
check = self.__check()
if check == True :
if "pre-processing" in str(self.ui.runReftableButton.text()).lower() :
self.ui.runReftableButton.setText("Running ...")
else :
log(1, "checkFileExistThread could not find %s" % self.file)
self.terminate()
del self
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 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 Genetic Data")
# 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.gen_data_win.validate(silent=True)
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 saveRecent(self):
log(3, "Saving recent list")
if not self.config.has_key("recent"):
self.config["recent"] = {}
recList = self.parent.getRecent()
cfgRecentIndex = 0
rec_cfg = ""
for rec in recList:
log(4, "Saving into recent list : %s" % rec)
rec_cfg += "{0}\n".format(rec)
# delete last '\n'
rec_cfg = rec_cfg[:-1]
self.config["recent"]["projectPathList"] = rec_cfg
def saveFile(self):
fname = str(QFileDialog.getSaveFileName(self,"Save log file","","(logfile) *.log"))
if fname != "":
if not fname.endswith(".log"):
fname = "%s.log"%fname
sf=open(fname.encode(self.fsCoding),'w')
lf=open(self.parent.logfile.encode(self.fsCoding),'r')
text=lf.read()
lf.close()
sf.write(text)
sf.close()
log(1,"Saving logfile into %s"%fname)
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
self.gen_data_win.fillLocusTableFromData()
else:
log(1, traceback.format_exc())
raise Exception(
"Impossible to load the datafile (%s) which 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 loadHM(self):
""" chargement de la partie historical model des préférences
"""
cfg = self.config
if cfg.has_key("hist_model_default_values"):
dico_val = {}
pairs = cfg["hist_model_default_values"].items()
for p in pairs:
dico_val[p[0]] = p[1]
try:
for key in [
"nmin",
"nmax",
"nmean",
"nstdev",
"tmin",
"tmax",
"tmean",
"tstdev",
"amin",
"amax",
"amean",
"astdev",
]:
editname = key[0].upper() + key[1:]
exec('self.hist_model.%sEdit.setText(str(dico_val["%s"]))' % (editname, key))
for pair in [
("nlaw", "UN"),
("nlaw", "LN"),
("nlaw", "NO"),
("nlaw", "LU"),
("alaw", "UN"),
("alaw", "LN"),
("alaw", "NO"),
("alaw", "LU"),
("tlaw", "UN"),
("tlaw", "LN"),
("tlaw", "NO"),
("tlaw", "LU"),
]:
exec(
'if dico_val["%s"] == "%s": self.hist_model.%sRadio.setChecked(True)'
% (pair[0], pair[1], pair[0][0].upper() + pair[1])
)
except Exception as e:
log(3, "Malformed hist_model_default_values section in configuration\n\n%s" % e)
else:
log(3, "No hist conf found")
def viewMmmq(self):
""" clic sur le bouton view numerical
"""
if os.path.exists((u"%s/analysis/%s/mmmq%s.txt"%(self.parent.dir,self.directory,self.file_subname)).encode(self.fsCoding)):
f = open((u"%s/analysis/%s/mmmq%s.txt"%(self.parent.dir,self.directory,self.file_subname)).encode(self.fsCoding),'r')
data = f.read()
f.close()
self.parent.drawAnalysisFrame = ViewTextFile(data,self.returnToMe,self.parent)
self.parent.drawAnalysisFrame.choiceFrame.hide()
self.parent.ui.analysisStack.addWidget(self.parent.drawAnalysisFrame)
self.parent.ui.analysisStack.setCurrentWidget(self.parent.drawAnalysisFrame)
else:
log(3, "mmmq%s.txt not found for analysis %s"%(self.file_subname,self.analysis.name))
def drawAll(self):
""" dessine les graphes de tous les paramètres
"""
if os.path.exists((u"%s/analysis/%s/compdirect.txt"%(self.parent.dir,self.directory)).encode(self.fsCoding)):
(first_line_tab,dico_coord) = self.getCoord("%s/analysis/%s/compdirect.txt"%(self.parent.dir,self.directory))
self.addDraw(first_line_tab,dico_coord,True)
else:
log(3, "compdirect.txt not found")
if self.analysis.logreg==True :
if os.path.exists((u"%s/analysis/%s/complogreg.txt"%(self.parent.dir,self.directory)).encode(self.fsCoding)):
(first_line_tab,dico_coord) = self.getCoord("%s/analysis/%s/complogreg.txt"%(self.parent.dir,self.directory))
self.addDraw(first_line_tab,dico_coord,False)
else:
log(3, "complogreg.txt not found")
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 initialize(self):
app = QApplication(sys.argv)
dd = datetime.now()
logfile = os.path.expanduser("~/.diyabc/logs/test_%02d_%02d_%s-%02dh_%02dm-%s.log"%(dd.day,dd.month,dd.year,dd.hour,dd.minute,os.getpid()))
diyabc = Diyabc(app,logfile=logfile)
diyabc.show()
# pour le dragNdrop des dossier projet
diyabc.setAcceptDrops(True)
# pour les logs dans un fichier et sur le terminal
# chaque TeeLogger remplace une sortie et écrit dans
# le fichier qu'on lui donne
myOut = TeeLogger(logfile,True,diyabc.showLog)
myErr = TeeLogger(logfile,False,diyabc.showLog)
sys.stdout = myOut
sys.stderr = myErr
log(1,"\033[5;36m DIYABC launched \033[00m")
return diyabc
def validate(self):
""" clic sur le bouton validate
verifie la validité de tous les groupes (mutmodel valide && nbsumstats > 0 && nblocus > 0)
si valide : sort , maj de l'icone de validité et sauve
si non valide : informe et sauve
"""
log(3,"Validation of Genetic Data of analysis")
#print self.group_info_dico
#print self.dico_num_and_numgroup_locus
mutconf_list = []
problem = u""
for i,box in enumerate(self.groupList):
title = str(box.title())
if "Microsatellites" in title:
mutconf_list.append(self.setMutation_dico[box].getMutationConf())
if box not in self.setMutationValid_dico.keys() or not self.setMutationValid_dico[box]:
problem += u"Mutation model of group %s is not considered as valid\n"%(i+1)
elif "Sequences" in title:
mutconf_list.append(self.setMutationSeq_dico[box].getMutationConf())
if box not in self.setMutationSeqValid_dico.keys() or not self.setMutationSeqValid_dico[box]:
problem += u"Mutation model of group %s is not considered as valid\n"%(i+1)
else:
problem += u"Group %s is empty\n"%(i+1)
if problem != u"":
QMessageBox.information(self,"Impossible to validate the genetic data",problem)
self.parents.setGenValid(False)
else:
# c'est valide, on passe à la dernière phase de paramètrage
if self.analysis.drawn:
self.analysis.mutationModelDrawn = mutconf_list
else:
self.analysis.mutationModelFixed = mutconf_list
if self.analysis.category == "bias":
#next_title = "bias and precision"
last_parametrisation = SetupEstimationBias(self.analysis,self)
else:
#next_title = "evaluate confidence"
last_parametrisation = SetupComparisonConfidence(self.analysis,self)
#self.parent.addTab(last_parametrisation,next_title)
#self.parent.removeTab(self.parent.indexOf(self))
#self.parent.setCurrentWidget(last_parametrisation)
self.ui.parents.analysisStack.addWidget(last_parametrisation)
self.ui.parents.analysisStack.removeWidget(self)
self.ui.parents.analysisStack.setCurrentWidget(last_parametrisation)
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")
def loadMMM(self):
""" chargement de la partie mutation model microsats des préférences
"""
lines = []
dico = {}
cfg = self.config
if cfg.has_key("mutation_m_default_values"):
try:
for param in ["MEANMU", "GAMMU", "MEANP", "GAMP", "MEANSNI", "GAMSNI"]:
exec(
'lines.append("{0} %s[%s,%s,%s,%s]"%(cfg["mutation_m_default_values"]["{0}_law"],cfg["mutation_m_default_values"]["{0}_zero"],cfg["mutation_m_default_values"]["{0}_one"],cfg["mutation_m_default_values"]["{0}_two"],cfg["mutation_m_default_values"]["{0}_three"]))'.format(
param
)
)
self.mutmodM.setMutationConf(lines)
except Exception as e:
log(3, "Malformed mutation_m_default_values in configuration")
else:
log(3, "No MMM conf found")
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 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()
